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Sample records for microbial culture collections

  1. The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

    Science.gov (United States)

    Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A.; Inderbitzin, Patrik; Sitepu, Irnayuli R.; Torok, Tamas; Brown, Daniel R.; Cho, Juliana; Wertz, John E.; Mukherjee, Supratim; Cady, Sherry L.

    2015-01-01

    The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. PMID:26092453

  2. Microbial culture collection for enhancement of microbial biotechnology

    International Nuclear Information System (INIS)

    Jong Bor Chyan; Pauline Liew Woan Ying; Goh Chee Meng; Mat Rasol Awang

    2007-01-01

    A bacterial culture collection was established in Agrotechnology and Biosciences Division since 2004. The culture collection was named MINT Bacterial Culture Collection (MBCC). The main objective is to preserve the indigenous bacterial cultures isolated from various environments. Later, the collection was extended to commercially available plasmids, recombinant clones and selected PCR products. This paper describes the importance of culture collection, the experience and the difficulties encountered. (Author)

  3. Microbial culture collections as pillars for promoting fungal diversity, conservation and exploitation.

    Science.gov (United States)

    Sette, Lara Durães; Pagnocca, Fernando Carlos; Rodrigues, André

    2013-11-01

    Fungi are a diverse group of organisms with an overall global number of 1.5M up to 3.3M species on Earth. Besides their ecological roles as decomposers, fungi are important in several aspects of applied research. Here, we review how culture collections may promote the knowledge on diversity, conservation and biotechnological exploitation of fungi. The impact of fungi diversity on biotechnological studies is discussed. We point out the major roles of microbial repositories, including fungal preservation, prospecting, identification, authentication and supply. A survey on the World Data Center for Microorganisms (WDCM) powered by the World Federation for Culture Collections and on the Genetic Heritage Management Council (CGEN) database revealed that 46 Brazilian culture collections registered in these databases are dedicate to preserving fungi. Most of these culture collections are located in the Southeast of Brazil. This scenario also demonstrates that Brazil has many collections focused on fungal strains, but the lack of up-to-date information in WDCM as well as of a solid national platform for culture collections registration do not allow accurate assessment of fungal preservation. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Culture collections.

    Science.gov (United States)

    Smith, David

    2012-01-01

    Culture collections no matter their size, form, or institutional objectives play a role in underpinning microbiology, supplying the resources for study, innovation, and discovery. Their basic roles include providing a mechanism for ex situ conservation of organisms; they are repositories for strains subject to publication, taking in safe, confidential, and patent deposits from researchers. They supply strains for use; therefore, the microorganisms provided must be authentic and preserved well, and any associated information must be valid and sufficient to facilitate the confirmation of their identity and to facilitate their use. The organisms must be collected in compliance with international conventions, international and national legislation and distributed to users indicating clearly the terms and conditions under which they are received and can be used. Collections are harmonizing approaches and characterizing strains to meet user needs. No one single collection can carry out this task alone, and therefore, it is important that output and strategy are coordinated to ensure culture collections deliver the basic resources and services microbiological innovation requires. This chapter describes the types of collection and how they can implement quality management systems and operate to deliver their basic functions. The links to information sources given not only provide support for the practitioners within collections but also provide guidance to users on accessing the huge resource available and how they can help ensure microbiology has the resources and a solid platform for future development. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Leveraging culture collections for the discovery and development of microbial biological control agents

    Science.gov (United States)

    The incorporation of living microbial biological control agents into integrated pest management programs is highly desirable because it reduces the use of chemical insecticides harmful to livestock, humans and the environment. In addition, it provides an alternative means to combat resistance to che...

  6. Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres.

    Science.gov (United States)

    Smith, David; McCluskey, Kevin; Stackebrandt, Erko

    2014-01-01

    Through their long history of public service, diverse microbial Biological Resource Centres (mBRCs) have made myriad contributions to society and science. They have enabled the maintenance of specimens isolated before antibiotics, made available strains showing the development and change of pathogenicity toward animals, humans and plants, and have maintained and provided reference strains to ensure quality and reproducibility of science. However, this has not been achieved without considerable financial commitment. Different collections have unique histories and their support is often tied to their origins. However many collections have grown to serve large constituencies and need to develop novel funding mechanisms. Moreover, several international initiatives have described mBRCs as a factor in economic development and have led to the increased professionalism among mBRCs.

  7. Microalgal Culture Collection Transfers

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Milford Microalgal culture Collection holds over 200 live cultures representing 13 classes of of algae. The cultures are maintained in three different growing...

  8. Cyanobacterial diversity held in microbial biological resource centers as a biotechnological asset: the case study of the newly established LEGE culture collection.

    Science.gov (United States)

    Ramos, Vitor; Morais, João; Castelo-Branco, Raquel; Pinheiro, Ângela; Martins, Joana; Regueiras, Ana; Pereira, Ana L; Lopes, Viviana R; Frazão, Bárbara; Gomes, Dina; Moreira, Cristiana; Costa, Maria Sofia; Brûle, Sébastien; Faustino, Silvia; Martins, Rosário; Saker, Martin; Osswald, Joana; Leão, Pedro N; Vasconcelos, Vitor M

    2018-01-01

    Cyanobacteria are a well-known source of bioproducts which renders culturable strains a valuable resource for biotechnology purposes. We describe here the establishment of a cyanobacterial culture collection (CC) and present the first version of the strain catalog and its online database (http://lege.ciimar.up.pt/). The LEGE CC holds 386 strains, mainly collected in coastal (48%), estuarine (11%), and fresh (34%) water bodies, for the most part from Portugal (84%). By following the most recent taxonomic classification, LEGE CC strains were classified into at least 46 genera from six orders (41% belong to the Synechococcales), several of them are unique among the phylogenetic diversity of the cyanobacteria. For all strains, primary data were obtained and secondary data were surveyed and reviewed, which can be reached through the strain sheets either in the catalog or in the online database. An overview on the notable biodiversity of LEGE CC strains is showcased, including a searchable phylogenetic tree and images for all strains. With this work, 80% of the LEGE CC strains have now their 16S rRNA gene sequences deposited in GenBank. Also, based in primary data, it is demonstrated that several LEGE CC strains are a promising source of extracellular polymeric substances (EPS). Through a review of previously published data, it is exposed that LEGE CC strains have the potential or actual capacity to produce a variety of biotechnologically interesting compounds, including common cyanotoxins or unprecedented bioactive molecules. Phylogenetic diversity of LEGE CC strains does not entirely reflect chemodiversity. Further bioprospecting should, therefore, account for strain specificity of the valuable cyanobacterial holdings of LEGE CC.

  9. Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

    Directory of Open Access Journals (Sweden)

    Reis Maria AM

    2008-07-01

    Full Text Available Abstract Background This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients. Results The model was validated with experimental data collected in a sequencing batch reactor (SBR operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments, and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i either with acetate or (ii with propionate as carbon source material. Metabolic flux analysis (MFA was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h. The results were compared with published pure culture metabolic studies. Conclusion Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of

  10. Electrospinning of microbial polyester for cell culture

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Oh Hyeong [Department of Polymer Science and Engineering, Kumoh National Institute of Technology, 1 Yangho-dong, Gumi, Gyeongbuk 730-701 (Korea, Republic of); Lee, Ik Sang [Department of Polymer Science and Engineering, Kumoh National Institute of Technology, 1 Yangho-dong, Gumi, Gyeongbuk 730-701 (Korea, Republic of); Ko, Young-Gwang [Department of Polymer Science and Engineering, Kumoh National Institute of Technology, 1 Yangho-dong, Gumi, Gyeongbuk 730-701 (Korea, Republic of); Meng, Wan [Department of Polymer Science, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701 (Korea, Republic of); Jung, Kyung-Hye [Department of Polymer Science, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701 (Korea, Republic of); Kang, Inn-Kyu [Department of Polymer Science, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701 (Korea, Republic of); Ito, Yoshihiro [Kanagawa Academy of Science and Technology, KSP East 309, Sakado 3-2-1, Takatsu-ku, Kawasaki 213-0012 (Japan)

    2007-03-01

    Biodegradable and biocompatible poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), a copolymer of microbial polyester, was fabricated as a nanofibrous mat by electrospinning. The specific surface area and the porosity of electrospun PHBV nanofibrous mat were determined. When the mechanical properties of flat film and electrospun PHBV nanofibrous mats were investigated, both the tensile modulus and strength of electrospun PHBV were less than those of cast PHBV film. However, the elongation ratio of nanofiber mat was higher than that of the cast film. The structure of electrospun nanofibers using PHBV-trifluoroethanol solutions depended on the solution concentrations. When x-ray diffraction patterns of bulk PHBV before and after electrospinning were compared, the crystallinity of PHBV was not significantly affected by the electrospinning process. Chondrocytes adhered and grew on the electrospun PHBV nanofibrous mat better than on the cast PHBV film. Therefore, the electrospun PHBV was considered to be suitable for cell culture.

  11. Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell

    Science.gov (United States)

    Miceli, Joseph F.; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I.; Krajmalnik-Brown, Rosa

    2014-01-01

    Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (~11 A/m2) and Coulombic efficiency (~70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ~80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed micro bial cultures containing complementing biochemical pathways. PMID:25048958

  12. Dynamics of culturable soil microbial communities during ...

    African Journals Online (AJOL)

    Ecological zones impacted significantly (P < 0.05) on bacterial proliferation, but not on fungal growth. Sampling period significantly (P < 0.05) affected microbial density and the semi-arid agroecozone was more supportive of microbial proliferation than the arid zone. A total of nine predominant fungal species belonging to ...

  13. Microbial cultures in open globe injuries in southern India.

    Science.gov (United States)

    Gupta, Arvind; Srinivasan, Renuka; Kaliaperumal, Subashini; Setia, Sajita

    2007-07-01

    To determine the risk factors leading to positive intraocular culture in patients with open globe injury. A prospective interventional study involving 110 eyes of 110 patients of more than 15 years of age, presenting with open globe injury, was undertaken. Emergency repair of the injured globe was done. Prolapsed intraocular tissue or aqueous humour was sent for microbial work up before repair. In endophthalmitis cases intravitreal antibiotics were given according to the antimicrobial sensitivity. Chi-square and logistic regression analysis were used to determine the risk factors. Fifty-six patients showed microbial contamination. Bacteria were cultured in 42 patients and fungi in 14 patients. Nineteen patients developed endophthalmitis, of which 18 patients showed microbial growth initially. In univariate analysis, initial visual acuity (8 mm, P 72 h, P 8 mm, P = 0.013) were associated with increased risk of positive microbial culture. Six patients had intraocular foreign body but were culture negative. Age, gender, site of injury and presence of cataract did not significantly affect the culture positivity. Microbial contamination is a risk factor for the development for endophthalmitis. Despite the high frequency of microbial contamination, it develops only in few cases. Systemic antibiotics, virulence of the organism and host factors play a role in the manifestation of endophthalmitis. Prophylaxis with intraocular antibiotics should be strongly considered in cases with poor vision at presentation, larger corneoscleral laceration, delayed surgical intervention and uveal tissue or vitreous prolapse.

  14. Microalgae Culture Collection: 1984-1985

    Energy Technology Data Exchange (ETDEWEB)

    1984-09-01

    The Microalgae Culture Collection at the Solar Energy Research Institute has been established for the maintenance and distribution of strains that have been characterized for biomass fuel applications.

  15. Growth-arresting Activity of Acmella Essential Oil and its Isolated Component D-Limonene (1, 8 P-Mentha Diene) against Trichophyton rubrum (Microbial Type Culture Collection 296).

    Science.gov (United States)

    Padhan, Diptikanta; Pattnaik, Smaranika; Behera, Ajaya Kumar

    2017-10-01

    Spilanthes acmella is used as a remedy in toothache complaints by the tribal people of Western part of Odisha, India. The objective of this study was to study the growth-arresting activity of an indigenous Acmella essential oil (EO) ( S. acmella Murr, Asteraceae ) and its isolated component, d-limonene against Trichophyton rubrum (microbial type culture collection 296). The EO was extracted from flowers of indigenous S. acmella using Clevenger's apparatus and analyzed by gas chromatography-mass spectrometry (GC-MS). High pressure liquid chromatography (HPLC) was carried out to isolate the major constituent. The isolated fraction was subjected to fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (NMR). The antidermatophytic activity was screened for using "disc diffusion" and "slant dilution" method followed by optical, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) studies. The molecular dockings were made between d-limonene with cell wall synthesis-related key enzymes (14 methyl deaminase and monooxygenase). The GC-MS analysis EO had inferred the presence of 7 number of major (≥2%) components. The component with highest peak area (%) was found to be 41.02. The HPLC-isolated fraction was identified as d-limonene (1,8 p-Mentha-diene) by FTIR and NMR. Qualitative and quantitative assays had suggested the growth inhibitory activity of Acmella EO and its component. Shrinkage, evacuation, cell wall puncture, and leakage of cellular constituents by the activity of Acmella oil and d-limonene were evidenced from optical, SEM, and TEM studies. The computer simulation had predicted the binding strengths of d-limonene and fluconazole with dermatophyte cell wall enzymes. There could have been synergistic action of all or some of compounds present in indigenous Acmella EO. There was presence of seven number of (d-limonene, ocimene, β-myrcene, cyclohexene, 3-(1, 5-dimethyl-4-hexenyl)-6-methylene,

  16. Microalgae culture collection, 1986-1987

    Energy Technology Data Exchange (ETDEWEB)

    Barclay, W.; Johansen, J.; Chelf, P.; Nagle, N.; Roessler, P.; Lemke, P.

    1986-12-01

    The SERI Microalgae Culture Collection provides a repository for strains identified or developed for mass culture biomass production and makes these strains readily available to the research community. The strains in the collection have been selected for their potential in biomass fuel applications, and many produce significant quantities of cellular storage lipids. All of the newly added strains have been recently isolated by SERI and its subcontractors in organized screening programs. Many have been tested in outdoor mass culture systems, and several have demonstrated excellent performance as biomass producers. The strains added to the collection this year have been isolated from inland saline waters and marine waters. We believe that the strains in this collection can provide a source of extremely useful organisms, both for laboratory experimentation and for mass culture research. Most of the strains are currently nonaxenic. Again this year, cultures will be shipped free of charge to interested researchers. An important function of the culture collection catalog, in addition to listing the available strains, is to provide culture and performance data for each of the organisms. By collecting a summary of the requirements and characteristics of these organisms, we hope to allow requestors of cultures to begin productive research with a minimum of preliminary work on culture techniques.

  17. Applications Research of Microbial Ecological Preparation in Sea Cucumber Culture

    Science.gov (United States)

    Jiang, Jiahui; Wang, Guangyu

    2017-12-01

    At present, micro ecological preparation is widely applied in aquaculture with good effect. The application of micro ecological preparation in sea cucumber culture can effectively improve the economic benefits. The micro ecological preparation can play the role of inhibiting harmful bacteria, purifying water quality and saving culture cost in the process of sea cucumber culture. We should select appropriate bacteria, guarantee stable environment and use with long-term in the applications of microbial ecological preparation in sea cucumber culture to obtain good effects.

  18. Microbial contaminants of cultured Hibiscus cannabinus and Telfaria ...

    African Journals Online (AJOL)

    Nine microbial contaminants comprising of five bacteria and four fungi species were isolated from Hibiscus cannabinus and Telfaria occidentalis cultured tissues. The rate of occurrence of bacteria isolates was higher than that of fungi. The bacterial isolates includes Pseudomonas syringae pv phaseolicoli, Bacillus ...

  19. Microalgae Culture Collection, 1985-1986

    Energy Technology Data Exchange (ETDEWEB)

    1986-01-01

    The SERI Microalgae Culture Collection was established in support of the US Department of Energy's Biofuels Program to provide a repository for strains identified or developed for mass culture biomass production and to make these strains readily available to the research community. The strains in the collection have been selected for their potential in biomass fuel applications, and many produce significant quantities of cellular storage lipids. The Culture Collection Catalog lists 20 strains of ten species. Many have been tested in outdoor mass culture systems, and several have demonstrated excellent performance as biomass producers, with yields of up to 40 grams of organic matter per square meter per day. The majority of strains added to the collection this year have been isolated from inland saline waters, although marine species are included as well. We believe that the strains in this collection can provide a source of extremely useful organisms, both for laboratory experimentation and for mass culture research. 98 refs., 31 figs., 52 tabs.

  20. Microbial Biosynthesis of Silver Nanoparticles in Different Culture Media.

    Science.gov (United States)

    Luo, Ke; Jung, Samuel; Park, Kyu-Hwan; Kim, Young-Rok

    2018-01-31

    Microbial biosynthesis of metal nanoparticles has been extensively studied for the applications in biomedical sciences and engineering. However, the mechanism for their synthesis through microorganism is not completely understood. In this study, several culture media were investigated for their roles in the microbial biosynthesis of silver nanoparticles (AgNPs). The size and morphology of the synthesized AgNPs were analyzed by UV-vis spectroscopy, Fourier-transform-infrared (FT-IR), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The results demonstrated that nutrient broth (NB) and Mueller-Hinton broth (MHB) among tested media effectively reduced silver ions to form AgNPs with different particle size and shape. Although the involved microorganism enhanced the reduction of silver ions, the size and shape of the particles were shown to mainly depend on the culture media. Our findings suggest that the growth media of bacterial culture play an important role in the synthesis of metallic nanoparticles with regard to their size and shape. We believe our findings would provide useful information for further exploration of microbial biosynthesis of AgNPs and their biomedical applications.

  1. An Information System for European culture collections: the way forward.

    Science.gov (United States)

    Casaregola, Serge; Vasilenko, Alexander; Romano, Paolo; Robert, Vincent; Ozerskaya, Svetlana; Kopf, Anna; Glöckner, Frank O; Smith, David

    2016-01-01

    Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible

  2. Growth of microbial mixed cultures under anaerobic, alkaline conditions

    International Nuclear Information System (INIS)

    Wenk, M.

    1993-09-01

    Cement and concrete are the most important engineered barrier materials in a repository for low- and intermediate-level waste and thus represent the most significant component of the total disposal inventory. Based on the chemical composition of the concrete used in the repository and the groundwater fluxes in the modelled host rock, it is to be expected that the pH in the near vicinity of the repository could exceed a value of 10.5 for more than a million years. The groundwater in the repository environment also has a limited carbon concentration. Since microorganisms will be present in a repository and can even find suitable living conditions within the waste itself, investigations were carried out in order to establish the extent to which microbial activity is possible under the extreme conditions of the repository near-field. For the investigations, alkalophilic cultures were enriched from samples from alkaline habitats and from Valanginian Marl. Anaerobic bacteria with fermentative, sulfate-reducing and methanogenic metabolism were selected. The growth and activity of the mixed cultures were studied under alkaline conditions and the dependence on pH and carbon concentration determined. All the mixed cultures investigated are alkalophilic. The optimum growth range for the cultures is between pH 9.0 and pH 10.0. The activity limit for the fermentative mixed culture is at pH 12, for the sulfate-reducers at pH 11 and for the methanogens at pH 10.5. Given the limited supply of carbon, the mixed cultures can only grow under slightly alkaline conditions. Only the fermentative cultures are capable of surviving with limited carbon supply at pH 13. (author) 24 figs., 18 tabs., 101 refs

  3. Microbial community dynamics in thermophilic undefined milk starter cultures.

    Science.gov (United States)

    Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

    2016-01-18

    Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

  4. International Marine Biotechnology Culture Collection (IMBCC)

    Energy Technology Data Exchange (ETDEWEB)

    Zaborsky, O.R.; Baker, K. [Univ. of Hawaii at Manoa, Honolulu, HI (United States)

    1996-10-01

    The objective of this project is to establish a premier culture collection of tropical marine microorganisms able to generate hydrogen from water or organic substances. Both eukaryotic and prokaryotic microorganisms will serve as the biological reservoir or {open_quotes}library{close_quotes} for other DOE Hydrogen Program contractors, the biohydrogen research community and industry. This project consists of several tasks: (a) transfer of the Mitsui-Miami strains to Hawaii`s International Marine Biotechnology Culture Collection (IMBCC) housed at the Hawaii Natural Energy Institute (HNEI); (b) maintain and distribute Mitsui-Miami strains; (c) characterize key strains by traditional and advanced biotechnological techniques; (d) expand Hawaii`s IMBCC; and (e) establish and operate an information resource (database). The project was initiated only late in the summer of 1995 but progress has been made on all tasks. Of the 161 cyanobacterial strains imported, 147 survived storage and importation and 145 are viable. with most exhibiting growth. Of the 406 strains of other photosynthetic bacteria imported, 392 survived storage and importation and 353 are viable, with many exhibiting growth. This project is linked to cooperative efforts being supported by the Japanese Ministry of International Trade and Industry (MITI) through its Marine Biotechnology Institute (MBI) and Research Institute of Innovative Technology for the Earth (RITE).

  5. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy.

    Science.gov (United States)

    Mlynáriková, Katarína; Samek, Ota; Bernatová, Silvie; Růžička, Filip; Ježek, Jan; Hároniková, Andrea; Šiler, Martin; Zemánek, Pavel; Holá, Veronika

    2015-11-24

    Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organism depending on the nutritional requirements and clinical usage directly on a Petri dish. Some of the media have a significant influence on the microbial fingerprint (Roosvelt-Park Institute Medium, CHROMagar) and should not be used for the acquisition of Raman spectra. It was found that the most suitable medium for microbiological experiments regarding these organisms was Mueller-Hinton agar.

  6. Microbial ecology and starter culture technology in coffee processing.

    Science.gov (United States)

    Vinícius de Melo Pereira, Gilberto; Soccol, Vanete Thomaz; Brar, Satinder Kaur; Neto, Ensei; Soccol, Carlos Ricardo

    2017-09-02

    Coffee has been for decades the most commercialized food product and most widely consumed beverage in the world, with over 600 billion cups served per year. Before coffee cherries can be traded and processed into a final industrial product, they have to undergo postharvest processing on farms, which have a direct impact on the cost and quality of a coffee. Three different methods can be used for transforming the coffee cherries into beans, known as wet, dry, and semi-dry methods. In all these processing methods, a spontaneous fermentation is carried out in order to eliminate any mucilage still stuck to the beans and helps improve beverage flavor by microbial metabolites. The microorganisms responsible for the fermentation (e.g., yeasts and lactic acid bacteria) can play a number of roles, such as degradation of mucilage (pectinolytic activity), inhibition of mycotoxin-producing fungi growth, and production of flavor-active components. The use of starter cultures (mainly yeast strains) has emerged in recent years as a promising alternative to control the fermentation process and to promote quality development of coffee product. However, scarce information is still available about the effects of controlled starter cultures in coffee fermentation performance and bean quality, making it impossible to use this technology in actual field conditions. A broader knowledge about the ecology, biochemistry, and molecular biology could facilitate the understanding and application of starter cultures for coffee fermentation process. This review provides a comprehensive coverage of these issues, while pointing out new directions for exploiting starter cultures in coffee processing.

  7. Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

    Science.gov (United States)

    Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

    2014-12-01

    Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

  8. A Moderately Thermophilic Mixed Microbial Culture for Bioleaching of Chalcopyrite Concentrate at High Pulp Density

    Science.gov (United States)

    Wang, Yuguang; Zeng, Weimin; Qiu, Guanzhou; Chen, Xinhua

    2014-01-01

    Three kinds of samples (acid mine drainage, coal mine wastewater, and thermal spring) derived from different sites were collected in China. Thereafter, these samples were combined and then inoculated into a basal salts solution in which different substrates (ferrous sulfate, elemental sulfur, and chalcopyrite) served as energy sources. After that, the mixed cultures growing on different substrates were pooled equally, resulting in a final mixed culture. After being adapted to gradually increasing pulp densities of chalcopyrite concentrate by serial subculturing for more than 2 years, the final culture was able to efficiently leach the chalcopyrite at a pulp density of 20% (wt/vol). At that pulp density, the culture extracted 60.4% of copper from the chalcopyrite in 25 days. The bacterial and archaeal diversities during adaptation were analyzed by denaturing gradient gel electrophoresis and constructing clone libraries of the 16S rRNA gene. The results show that the culture consisted mainly of four species, including Leptospirillum ferriphilum, Acidithiobacillus caldus, Sulfobacillus acidophilus, and Ferroplasma thermophilum, before adapting to a pulp density of 4%. However, L. ferriphilum could not be detected when the pulp density was greater than 4%. Real-time quantitative PCR was employed to monitor the microbial dynamics during bioleaching at a pulp density of 20%. The results show that A. caldus was the predominant species in the initial stage, while S. acidophilus rather than A. caldus became the predominant species in the middle stage. F. thermophilum accounted for the greatest proportion in the final stage. PMID:24242252

  9. Application of MALDI-TOF MS for requalification of a Candida clinical isolates culture collection

    Directory of Open Access Journals (Sweden)

    Reginaldo Lima-Neto

    2014-06-01

    Full Text Available Microbial culture collections underpin biotechnology applications and are important resources for clinical microbiology by supplying reference strains and/or performing microbial identifications as a service. Proteomic profiles by MALDI-TOF MS have been used for Candida spp. identification in clinical laboratories and demonstrated to be a fast and reliable technique for the routine identification of pathogenic yeasts. The main aim of this study was to apply MALDI-TOF MS combined with classical phenotypic and molecular approaches to identify Candida clinical isolates preserved from 1 up to 52 years in a Brazilian culture collection and assess its value for the identification of yeasts preserved in this type of collections. Forty Candida spp. clinical isolates were identified by morphological and biochemical analyses. Identifications were also performed by the new proteomic approach based on MALDI-TOF MS. Results demonstrated 15% discordance when compared with morphological and biochemical analyses. Discordant isolates were analysed by ITS sequencing, which confirmed the MALDI-TOF MS identifications and these strains were renamed in the culture collection catalogue. In conclusion, proteomic profiles by MALDI-TOF MS represents a rapid and reliable method for identifying clinical Candida species preserved in culture collections and may present clear benefits when compared with the performance of existing daily routine methods applied at health centres and hospitals.

  10. Lipid recovery from a vegetable oil emulsion using microbial enrichment cultures

    NARCIS (Netherlands)

    Tamis, J.; Sorokin, D.Y.; Jiang, Y.; Van Loosdrecht, M.C.M.; Kleerebezem, R.

    2015-01-01

    Background Many waste streams have a relatively high vegetable oil content, which is a potential resource that should be recovered. Microbial storage compound production for the recovery of lipids from lipid-water emulsions with open (unsterilized) microbial cultures was investigated in a sequencing

  11. Biodeterioration of epoxy resin: a microbial survey through culture-independent and culture-dependent approaches.

    Science.gov (United States)

    Pangallo, Domenico; Bučková, Maria; Kraková, Lucia; Puškárová, Andrea; Šaková, Nikoleta; Grivalský, Tomaš; Chovanová, Katarina; Zemánková, Milina

    2015-02-01

    During the 20th century, synthetic polymers were greatly used in the field of art. In particular, the epoxy resins were used for both conservation and for creating sculptures. The biodeterioration of these polymers has not been adequately studied. The aim of this investigation was to examine the microflora responsible for the deterioration of an epoxy statue exposed to outdoor conditions. Fungal and bacterial microflora were isolated from the art object, clustered by fluorescence-ITS (internal transcribed spacer), identified by ITS and 16S rRNA sequencing and tested for their lipolytic abilities by three agar assays. Different algal, bacterial, cyanobacterial and fungal clone libraries were constructed. The surrounding airborne microflora was analyzed using culture-dependent and culture-independent approaches. The results indicated the presence, on the statue surface, of an interesting and differentiate microbial community composed of rock-inhabiting members, algal photobionts (Trebouxia spp., Chloroidium ellipsoideum and Chlorella angustoellipsoidea), Cyanobacteria (Leptolyngbya sp., Phormidium sp., Cylindrospermum stagnale, Hassallia byssoidea and Geitlerinema sp.), black yeasts related to the species Friedmanniomyces endolithicus, Pseudotaeniolina globosa, Phaeococcomyces catenatus and Catenulostroma germanicum and several plant-associated fungi. This investigation provides new information on the potential microfloral inhabitants of epoxy resin discovering a new ecological niche, occupied mainly by several members of rock-colonizing microbial species. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  12. Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

    International Nuclear Information System (INIS)

    Son, Ahjeong; Schmidt, Carl J.; Shin, Hyejin; Cha, Daniel K.

    2011-01-01

    Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

  13. Microbial community analysis of perchlorate-reducing cultures growing on zero-valent iron

    Energy Technology Data Exchange (ETDEWEB)

    Son, Ahjeong, E-mail: ason@auburn.edu [Department of Civil Engineering, Auburn University, Auburn, AL 36849 (United States); Schmidt, Carl J. [Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 (United States); Shin, Hyejin [Department of Mathematics and Statistics, Auburn University, Auburn, AL 36849 (United States); Cha, Daniel K. [Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716 (United States)

    2011-01-30

    Anaerobic microbial mixed cultures demonstrated its ability to completely remove perchlorate in the presence of zero-valent iron. In order to understand the major microbial reaction in the iron-supported culture, community analysis comprising of microbial fatty acids and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) techniques was performed for perchlorate reducing cultures. Analysis of fatty acid methyl esters (FAMEs) and subsequent principal component analysis (PCA) showed clear distinctions not only between iron-supported perchlorate reducing culture and seed bacteria, but also among perchlorate-reducing cultures receiving different electron donors. The DGGE pattern targeting the chlorite dismutase (cld) gene showed that iron-supported perchlorate reducing culture is similar to hydrogen-fed cultures as compared to acetate-fed culture. The phylogenetic tree suggested that the dominant microbial reaction may be a combination of the autotrophic and heterotrophic reduction of perchlorate. Both molecular and chemotaxonomic experimental results support further understanding in the function of zero-valent iron as an adequate electron source for enhancing the microbial perchlorate reduction in natural and engineered systems.

  14. Classical Pop: Documenting Popular Musical Culture in Library Audio Collections.

    Science.gov (United States)

    Tarakan, Sheldon Lewis

    1983-01-01

    Discusses the library's role in developing a classical pop collection (defined as that music which is best representative of an era, event, or recognizable cultural trend). Popular culture, establishing the collection, funding, and archives are highlighted. A 230-item discography, addresses of five record companies, and 14 references are appended.…

  15. 75 FR 42818 - Agency Information Collection; Activity Under OMB Review; Collection of Safety Culture Data for...

    Science.gov (United States)

    2010-07-22

    ... Collection; Activity Under OMB Review; Collection of Safety Culture Data for Program Evaluation AGENCY... . SUPPLEMENTARY INFORMATION: Title: Collection of Safety Culture Data for Program Evaluation. Type of Request... data on the nation's transportation system is an important component of BTS' responsibility to the...

  16. Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

    International Nuclear Information System (INIS)

    Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

    2009-01-01

    Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)

  17. Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

    Energy Technology Data Exchange (ETDEWEB)

    Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

    2009-07-01

    Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)

  18. Functional implications of the microbial community structure of undefined mesophilic starter cultures

    NARCIS (Netherlands)

    Smid, E.J.; Erkus, O.; Spus, M.; Wolkers-Rooijackers, J.C.M.; Alexeeva, S.V.; Kleerebezem, M.

    2014-01-01

    This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the

  19. Data management and database structure at the ARS Culture Collection

    Science.gov (United States)

    The organization and management of collection data for the 96,000 strains held in the ARS Culture Collection has been an ongoing process. Originally, the records for the four separate collections were maintained by individual curators in notebooks and/or card files and subsequently on the National C...

  20. Selection of culturable environmental microbial strains for cellular ...

    African Journals Online (AJOL)

    Environmental pollution by organic compounds is a global problem. Biological treatment methods are used to restore polluted environments. Microbial immobilization on abiotic surfaces is a recent strategy to improve the efficiency of these processes. In this technique, cell adhesion is a fundamental step for subsequent ...

  1. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils

    OpenAIRE

    Stefani, Franck O. P.; Bell, Terrence H.; Marchand, Charlotte; de la Providencia, Ivan E.; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

    2015-01-01

    Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequenci...

  2. Harnessing the landscape of microbial culture media to predict new organism–media pairings

    Science.gov (United States)

    Oberhardt, Matthew A.; Zarecki, Raphy; Gronow, Sabine; Lang, Elke; Klenk, Hans-Peter; Gophna, Uri; Ruppin, Eytan

    2015-01-01

    Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language media recipes into a Known Media Database (KOMODO), which includes >18,000 strain–media combinations, >3300 media variants and compound concentrations (the entire collection of the Leibniz Institute DSMZ repository). Using KOMODO, we show that although media are usually tuned for individual strains using biologically common salts, trace metals and vitamins/cofactors are the most differentiating components between defined media of strains within a genus. We leverage KOMODO to predict new organism–media pairings using a transitivity property (74% growth in new in vitro experiments) and a phylogeny-based collaborative filtering tool (83% growth in new in vitro experiments and stronger growth on predicted well-scored versus poorly scored media). These resources are integrated into a web-based platform that predicts media given an organism's 16S rDNA sequence, facilitating future cultivation efforts. PMID:26460590

  3. Microchemostat - microbial continuous culture in a polymer-based, instrumented microbioreactor

    DEFF Research Database (Denmark)

    Zhang, Z.; Bocazzi, P.; Choi, H. G.

    2006-01-01

    -based microbioreactor system integrated with optical density (OD), pH, and dissolved oxygen (DO) real-time measurements for continuous cultivation of microbial cells. Escherichia coli (E. coli) cells are continuously cultured in a 150 mL, membrane-aerated, well-mixed microbioreactor fed by a pressure-driven flow......In a chemostat, microbial cells reach a steady state condition at which cell biomass production, substrates and the product concentrations remain constant. These features make continuous culture a unique and powerful tool for biological and physiological research. We present a polymer...

  4. Visualising Cultures: The "European Picture Book Collection" Moves "Down Under"

    Science.gov (United States)

    Cotton, Penni; Daly, Nicola

    2015-01-01

    The potential for picture books in national collections to act as mirrors reflecting the reader's cultural identity, is widely accepted. This paper shows that the books in a New Zealand Picture Book Collection can also become windows into unfamiliar worlds for non-New Zealand readers, giving them the opportunity to learn more about a context in…

  5. A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

    Directory of Open Access Journals (Sweden)

    Jaderson Silveira Leite Armanhi

    2018-01-01

    Full Text Available The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent with the sugarcane microbiome profile (culture-independent, we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.

  6. Production of microbial biomass protein by sequential culture fermentation of Arachniotus sp., and Candida utilis

    International Nuclear Information System (INIS)

    Ahmed, S.; Ahmad, F.; Hashmi, A.S.

    2010-01-01

    Sequential culture fermentation by Arachniotus sp. at 35 deg. C for 72 h and followed by Candida utilis fermentation at 35 deg. C for 72 h more resulted in higher production of microbial biomass protein. 6% (w/v) corn stover, 0.0075% CaCl/sub 2/.2H/sub 2/O, 0.005% MgSO/sub 4/.7H/sub 2/O, 0.01% KH/sub 2/PO/sub 4/, C:N ratio of 30:1 and 1% molasses gave higher microbial biomass protein production by the sequential culture fermentation of Arachniotus sp., and C. utilis. The mixed microbial biomass protein produced in the 75-L fermentor contained 16.41%, 23.51%, 10.9%, 12.11% and 0.12% true protein, crude protein, crude fiber, ash and RNA content, respectively. The amino acid profile of final mixed microbial biomass protein showed that it was enriched with essential amino acids. Thus, the potential utilization of corn stover can minimize the cost for growth of these microorganisms and enhance microbial biomass protein production by sequential culture fermentation. (author)

  7. Functional implications of the microbial community structure of undefined mesophilic starter cultures.

    Science.gov (United States)

    Smid, Eddy J; Erkus, Oylum; Spus, Maciej; Wolkers-Rooijackers, Judith C M; Alexeeva, Svetlana; Kleerebezem, Michiel

    2014-08-29

    This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the population dynamics during cheese making and during starter culture propagation. Furthermore, the link between starter composition and starter functionality will be discussed. Finally, recent advances in predictive metabolic modelling of the multi-strain cultures will be discussed in the context of microbe-microbe interactions.

  8. Effect of starter cultures on microbial and physicochemical ...

    African Journals Online (AJOL)

    sunny

    2014-10-22

    Oct 22, 2014 ... 1Research Unity, Food and Science Technologies–UR 04 AGR02, High Food Industries School of Tunisia, 58 Avenue .... The mixture of each batch was stuffed into artificial ..... Effects of starter cultures and additives on.

  9. Assessment of microbial diversity under arid plants by culture ...

    African Journals Online (AJOL)

    Capparis deciduas) and pearl millet (Pennisetum glaucum) was assessed and defined by culture-dependent and cultureindependent approaches on the basis of 16S rRNA and random amplified polymorphic DNA (RAPD) analysis. The average ...

  10. Effects of 2-hydroxy-4-(methylthio) butanoic acid (HMB) on microbial growth in continuous culture.

    Science.gov (United States)

    Noftsger, S M; St-Pierre, N R; Karnati, S K R; Firkins, J L

    2003-08-01

    2-Hydroxy-4-(methylthio) butanoic acid (HMB) positively affects milk composition and yield, potentially through ruminal actions. Four continuous culture fermenters were used to determine the optimal concentration of HMB for digestibility of organic matter (OM), neutral detergent fiber (NDF), acid detergent fiber (ADF), and hemicellulose and synthesis of microbial N. A highly degradable mix of hay and grain was used as a basal diet to simulate a typical lactation diet. Three concentrations of HMB (0, 0.055, and 0.110%) and one concentration of dl-Met (0.097%) were infused into the fermenters according to a 4 x 4 Latin square design. Digesta samples were collected during the last 3 d of each of the four 10-d experimental periods. Digestibility of OM, hemicellulose, and NDF was largely insensitive to treatment. Digestibility of ADF showed a quadratic effect to supplementation of HMB, with 0.055% having lower digestibility than 0 or 0.110%. Total production of VFA was not influenced by HMB supplementation, but differences in concentration and production of individual VFA were seen. Isobutyrate increased linearly with increasing HMB supplementation. Propionate concentration decreased linearly with increased HMB supplementation, but propionate production showed a quadratic trend (P = 0.13). A higher concentration of acetate was detected for dl-Met compared with the highest HMB concentration. There were trends (P HMB. Microbial efficiency was not different among treatments. The proportion of bacterial N produced from NH3-N decreased linearly with increasing HMB, and bacteria receiving dl-Met synthesized more N from NH3-N than those receiving HMB. These data suggest that supplementation of HMB may have a sparing effect on branched chain volatile fatty acids because the fatty acids are not needed to provide carbon for synthesis of valine, isoleucine and leucine with ammonia. Comparisons of bacterial community structure in the fermenter effluent samples using PCR amplicons

  11. Molecular characterization of some lignicolous species from fungal culture collection

    Directory of Open Access Journals (Sweden)

    Stević Nevena

    2014-01-01

    Full Text Available Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, which can be explained by its great inter-species variability. This paper presents results from analysing ITS1 region sequences (17 obtained from fungal DNA of culture collection of autochthonous, lignicolous genera Piptoporus, Pleurotus, Ganoderma and Schizophyllum cultured on malt agar plates for 14 days at 25°C. BLAST (Basic Local Alignment Search Tool was used for comparison with online databases, while alignment of sequences was made with MEGA 5.10 software. Morphological determination of species or genus was confirmed for 13 cultures, while the others were disproved. The resulting alignment indicated small intra-species variability of ITS1 region and pointed to it as an ideal marker for verification of fungal culture collections' authenticity. [Projekat Ministarstva nauke Republike Srbije, br. III43002 and by the Provincial Secretariat for Science and Technological Development, Vojvodina, Serbia APV 114-4513592/2013-03: Molecular and phenotypic diversity of taxa of economical and epidemiological importance, and endangered and endemic species in Europe

  12. Formation of industrial mixed culture biofilm in chlorophenol cultivated medium of microbial fuel cell

    Science.gov (United States)

    Hassan, Huzairy; Jin, Bo; Dai, Sheng; Ngau, Cornelius

    2016-11-01

    The formation of microbial biofilm while maintaining the electricity output is a challenging topic in microbial fuel cell (MFC) studies. This MFC critical factor becomes more significant when handling with industrial wastewater which normally contains refractory and toxic compounds. This study explores the formation of industrial mixed culture biofilm in chlorophenol cultivated medium through observing and characterizing microscopically its establishment on MFC anode surface. The mixed culture was found to develop its biofilm on the anode surface in the chlorophenol environment and established its maturity and dispersal stages with concurrent electricity generation and phenolic degradation. The mixed culture biofilm engaged the electron transfer roles in MFC by generating current density of 1.4 mA/m2 and removing 53 % of 2,4-dichlorophenol. The results support further research especially on hazardous wastewater treatment using a benign and sustainable method.

  13. Culture-dependent and -independent investigations of microbial diversity on urinary catheters

    DEFF Research Database (Denmark)

    Xu, Yijuan; Moser, Claus Ernst; Abu Al-Soud, Waleed

    2012-01-01

    Catheter-associated urinary tract infection is caused by bacteria, which ascend the catheter along its external or internal surface to the bladder and subsequently develop into biofilms on the catheter and uroepithelium. Antibiotic-treated bacteria and bacteria residing in biofilm can be difficult...... to culture. In this study we used culture-based and 16S rRNA gene-based culture-independent methods (fingerprinting, cloning, and pyrosequencing) to determine the microbial diversity of biofilms on 24 urinary catheters. Most of the patients were catheterized for...

  14. Microbial dynamics in anaerobic enrichment cultures degrading di-n-butyl phthalic acid ester

    DEFF Research Database (Denmark)

    Trably, Eric; Batstone, Damien J.; Christensen, Nina

    2008-01-01

    losses were observed in the sterile controls (20-22%), substantial DBP biodegradation was found in the enrichment cultures (90-99%). In addition, significant population changes were observed. The dominant bacterial species in the DBP-degrading cultures was affiliated to Soehngenia saccharolytica...... in enrichment cultures degrading phthalic acid esters under methanogenic conditions. A selection pressure was applied by adding DBP at 10 and 200 mg L(-1) in semi-continuous anaerobic reactors. The microbial dynamics were monitored using single strand conformation polymorphism (SSCP). While only limited abiotic...

  15. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy

    Czech Academy of Sciences Publication Activity Database

    Mlynariková, K.; Samek, Ota; Bernatová, Silvie; Růžička, F.; Ježek, Jan; Hároniková, A.; Šiler, Martin; Zemánek, Pavel; Holá, V.

    2015-01-01

    Roč. 15, č. 11 (2015), s. 29635-29647 ISSN 1424-8220 R&D Projects: GA MŠk ED0017/01/01; GA ČR(CZ) GA15-20645S; GA MŠk(CZ) LO1212 Institutional support: RVO:68081731 Keywords : Raman spectroscopy * bacteria * yeasts * culture media Subject RIV: BH - Optics, Masers, Lasers Impact factor: 2.033, year: 2015

  16. Influence of Culture Media on Microbial Fingerprints Using Raman Spectroscopy

    OpenAIRE

    Mlyn?rikov?, Katar?na; Samek, Ota; Bernatov?, Silvie; R??i?ka, Filip; Je?ek, Jan; H?ronikov?, Andrea; ?iler, Martin; Zem?nek, Pavel; Hol?, Veronika

    2015-01-01

    Raman spectroscopy has a broad range of applications across numerous scientific fields, including microbiology. Our work here monitors the influence of culture media on the Raman spectra of clinically important microorganisms (Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans). Choosing an adequate medium may enhance the reproducibility of the method as well as simplifying the data processing and the evaluation. We tested four different media per organis...

  17. Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

    Energy Technology Data Exchange (ETDEWEB)

    Vinas, M.; Sabate, J.; Solanas, A.M. [Barcelona Univ., Barcelona (Spain). Dept. of Microbiology; Guasp, C.; Lalucat, J. [Illes Balears Univ., Palma de Mallorca (Spain). Dept. of Biology

    2005-11-15

    Microbial consortia are used in the decontamination of polluted environmental sites. A microbial consortium obtained by batch enrichment culture is a closed system with controlled conditions in which micro-organisms with a potentially high growth rate are selected and become dominant. The aim of this study was to identify the members of consortium AM, in which earlier batch enrichment work had shown high biodegradation rates of the aromatic fraction of polycyclic aromatic hydrocarbon (PAH). The AM consortium was obtained by sequential enrichment in liquid culture with a PAH mixture of 3- and 4- ringed PAHs as the sole source of carbon and energy. The consortium was examined using a triple approach method based on various cultivation strategies, denaturing gradient electrophoresis (DGGE) and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and 7 by both DGGE and clone libraries were obtained, yielding 19 different microbial components. Proteobacteria were the dominant group, representing 83 per cent of the total, while the Cytophaga-Flexibactor-Bacteroides group (CFB) was 11 per cent, and Ascomycota fungi were 6 per cent. It was determined that {beta}-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences was achieved by the cultivation method that showed members of the {alpha},{beta}, and {gamma}-Proteobacteria, CFB bacterial group, and Ascomycota fungi. Only 6 of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1) achieved the greatest PAH depletion. Results indicated that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium. It was concluded that microbial consortia are more complex than previously realized. 54 refs., 3 tabs., 3 figs.

  18. The ARS Culture Collection and Developments in Biotechnology

    Science.gov (United States)

    The ARS Culture Collection (NRRL) has played a prominent role in the development of biotechnology since its founding in 1940 when the Northern Regional Research Laboratory opened. Early discoveries included selection of production strains for penicillin, dextran blood extender, xanthan gum and the v...

  19. Digital Collections, Digital Libraries & the Digitization of Cultural Heritage Information.

    Science.gov (United States)

    Lynch, Clifford

    2002-01-01

    Discusses digital collections and digital libraries. Topics include broadband availability; digital rights protection; content, both non-profit and commercial; digitization of cultural content; sustainability; metadata harvesting protocol; infrastructure; authorship; linking multiple resources; data mining; digitization of reference works;…

  20. Unraveling microbial ecology of industrial-scale Kombucha fermentations by metabarcoding and culture-based methods.

    Science.gov (United States)

    Coton, Monika; Pawtowski, Audrey; Taminiau, Bernard; Burgaud, Gaëtan; Deniel, Franck; Coulloumme-Labarthe, Laurent; Fall, Abdoulaye; Daube, Georges; Coton, Emmanuel

    2017-05-01

    Kombucha, historically an Asian tea-based fermented drink, has recently become trendy in Western countries. Producers claim it bears health-enhancing properties that may come from the tea or metabolites produced by its microbiome. Despite its long history of production, microbial richness and dynamics have not been fully unraveled, especially at an industrial scale. Moreover, the impact of tea type (green or black) on microbial ecology was not studied. Here, we compared microbial communities from industrial-scale black and green tea fermentations, still traditionally carried out by a microbial biofilm, using culture-dependent and metabarcoding approaches. Dominant bacterial species belonged to Acetobacteraceae and to a lesser extent Lactobacteriaceae, while the main identified yeasts corresponded to Dekkera, Hanseniaspora and Zygosaccharomyces during all fermentations. Species richness decreased over the 8-day fermentation. Among acetic acid bacteria, Gluconacetobacter europaeus, Gluconobacter oxydans, G. saccharivorans and Acetobacter peroxydans emerged as dominant species. The main lactic acid bacteria, Oenococcus oeni, was strongly associated with green tea fermentations. Tea type did not influence yeast community, with Dekkera bruxellensis, D. anomala, Zygosaccharomyces bailii and Hanseniaspora valbyensis as most dominant. This study unraveled a distinctive core microbial community which is essential for fermentation control and could lead to Kombucha quality standardization. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Benzoate-driven dehalogenation of chlorinated ethenes in microbial cultures from a contaminated aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Bunge, M.; Kleikemper, J.; Miniaci, C.; Duc, L.; Muusse, M.G.; Zeyer, J. [Swiss Federal Institute of Technology (ETH), Zurich (Switzerland). Inst. of Biogeochemistry and Pollutant Dynamics, Soil Biology; Hause, G. [Halle-Wittenberg Univ., Halle (Germany). Biocenter

    2007-10-15

    Microbial dehalogenation of tetrachloroethene (PCE) and cis-dichloroethene (cis-DCE) was studied in cultures from a continuous stirred tank reactor initially inoculated with aquifer material from a PCE-contaminated site. Cultures amended with hydrogen and acetate readily dechlorinated PCE and cis-DCE; however, this transformation was incomplete and resulted in the accumulation of chlorinated intermediates and only small amounts of ethene within 60 days of incubation. Conversely, microbial PCE and cis-DCE dechlorination in cultures with benzoate and acetate resulted in the complete transformation to ethene within 30 days. Community fingerprinting by denaturing gradient gel electrophoresis (DGGE) revealed the predominance of phylotypes closely affiliated with Desulfitobacterium, Dehalococcoides, and Syntrophus species. The Dehalococcoides culture VZ, obtained from small whitish colonies in cis-DCE dechlorinating agarose cultures, revealed an irregular cell diameter between 200 and 500 nm, and a spherical or biconcave disk-shaped morphology. These organisms were identified as responsible for the dechlorination of cis-DCE to ethene in the PCE-dechlorinating consortia, operating together with the Desulfitobacterium as PCE-to-cis-DCE dehalogenating bacterium and with a Syntrophus species as potential hydrogen-producing partner in cultures with benzoate. (orig.)

  2. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

    Directory of Open Access Journals (Sweden)

    Franck O P Stefani

    Full Text Available Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA with culture-dependent (isolation using seven different growth media techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

  3. Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.

    Science.gov (United States)

    Stefani, Franck O P; Bell, Terrence H; Marchand, Charlotte; de la Providencia, Ivan E; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed

    2015-01-01

    Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.

  4. Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures.

    Science.gov (United States)

    Liang, Shaobo; Gliniewicz, Karol; Mendes-Soares, Helena; Settles, Matthew L; Forney, Larry J; Coats, Erik R; McDonald, Armando G

    2015-03-01

    Three undefined mixed cultures (activated sludge) from different municipal wastewater treatment plants were used as seeds in a novel lactic acid fermentation process fed with potato peel waste (PPW). Anaerobic sequencing batch fermenters were run under identical conditions to produce predominantly lactic acid. Illumina sequencing was used to examine the 16S rRNA genes of bacteria in the three seeds and fermenters. Results showed that the structure of microbial communities of three seeds were different. All three fermentation products had unique community structures that were dominated (>96%) by species of the genus Lactobacillus, while members of this genus constituted undefined mixed cultures were robust and resilient, which provided engineering prospects for the microbial utilization of carbohydrate wastes to produce lactic acid. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Role of collective self-esteem on youth violence in a collective culture.

    Science.gov (United States)

    Lim, Lena L; Chang, Weining C

    2009-02-01

    Youth violence involvement has always been the focus of significant research attention. However, as most of the studies on youth violence have been conducted in Western cultures, little is known about the antecedents of violence in the Asian context. Researchers have suggested that collectivism might be the reason for the lower violent crime rates in Asia. Nevertheless, the present study proposes an alternative approach to the collectivistic orientation and violence relationship: The possibility that allocentrism (collectivist tendency at the individual difference level) might shape the meaning of and the attitudes towards violence; thus not all aspects of a collectivist culture serve as deterrents for violence. Instead of viewing it as a random individual act, violence in a collective cultural context could be seen, under certain circumstances, as a social obligation to one's in-group (especially when one's in-group is supportive of violence) and as an internalization of the norms and values of the culture. Thus, the present study investigates the relationship between allocentrism and its relation to violence in a highly collectivist Asian culture, Singapore. We further hypothesized that collective self-esteem might serve as the mediator between allocentrism and the values of violence. Using a sample of 149 incarcerated Singaporean male adolescents, results support the proposed theoretical model whereby collective self-esteem was found to mediate between allocentrism and the culture's norms and attitudes of violence, which eventually lead to physical violence behaviours.

  6. Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

    CERN Document Server

    Laurinavichius, K S

    1998-01-01

    Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

  7. Community proteomics provides functional insight into polyhydroxyalkanoate production by a mixed microbial culture cultivated on fermented dairy manure.

    Science.gov (United States)

    Hanson, Andrea J; Guho, Nicholas M; Paszczynski, Andrzej J; Coats, Erik R

    2016-09-01

    Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures (MMCs). To maximize PHA production, MMCs are enriched for bacteria with a high polymer storage capacity through the application of aerobic dynamic feeding (ADF) in a sequencing batch reactor (SBR), which consequently induces a feast-famine metabolic response. Though the feast-famine response is generally understood empirically at a macro-level, the molecular level is less refined. The objective of this study was to investigate the microbial community composition and proteome profile of an enriched MMC cultivated on fermented dairy manure. The enriched MMC exhibited a feast-famine response and was capable of producing up to 40 % (wt. basis) PHA in a fed-batch reactor. High-throughput 16S rRNA gene sequencing revealed a microbial community dominated by Meganema, a known PHA-producing genus not often observed in high abundance in enrichment SBRs. The application of the proteomic methods two-dimensional electrophoresis and LC-MS/MS revealed PHA synthesis, energy generation, and protein synthesis prominently occurring during the feast phase, corroborating bulk solution variable observations and theoretical expectations. During the famine phase, nutrient transport, acyl-CoA metabolism, additional energy generation, and housekeeping functions were more pronounced, informing previously under-determined MMC functionality under famine conditions. During fed-batch PHA production, acetyl-CoA acetyltransferase and PHA granule-bound phasin proteins were in increased abundance relative to the SBR, supporting the higher PHA content observed. Collectively, the results provide unique microbial community structural and functional insight into feast-famine PHA production from waste feedstocks using MMCs.

  8. Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps

    Science.gov (United States)

    De Prisco, Annachiara; Di Prisco, Gennaro; La Storia, Antonietta; Caprio, Emilio

    2017-01-01

    Flower pollen is collected by honeybee foragers, adhered on their rear legs and transported into the hives in the form of pellets. Once in the hives, bee pollen is moisturised with nectar and bee mouth secretions and due to enzymatically modifications it becomes the so-called bee-bread, the protein reservoir of young bees. Bee pollen can be artificially removed from bee legs and collected by using specific systems, the bee pollen traps. Bee pollen is commercialized for human consumption as fresh product and after freezing or drying. Although bee pollen is nowadays largely consumed in developed countries, as food or food supplement according to local legislation, little is known on its safety related to microbiological hazards. In this work, we aimed to characterize for the first time the microbiological profile of Italian bee pollen in fresh, frozen and dried form collected along an entire harvesting season. Moreover, monthly microbiological analyses were performed on frozen (storage at -18°C) and dried (storage at room temperature) bee pollen over a 4 months period. Further aim of this work was the evaluation of the possible impact on production level of three different traps used for pollen collection. Our results on microbial contamination of fresh and frozen bee pollen show that a more comprehensive microbiological risk assessment of bee pollen is required. On the other side, dried pollen showed very low microbial contamination and no pathogen survived after the drying process and during storage. PMID:28934240

  9. Microbial reduction of uranium(VI) in sediments of different lithologies collected from Sellafield

    International Nuclear Information System (INIS)

    Newsome, Laura; Morris, Katherine; Trivedi, Divyesh; Atherton, Nick; Lloyd, Jonathan R.

    2014-01-01

    Highlights: • U(VI) (aq) mobility can be controlled by stimulating biogeochemical interactions. • Indigenous microbes in varied sediments reduced U(VI) to insoluble U(IV). • Sediment cell numbers and amount of bioavailable Fe(III) could limit this process. - Abstract: The presence of uranium in groundwater at nuclear sites can be controlled by microbial processes. Here we describe the results from stimulating microbial reduction of U(VI) in sediment samples obtained from a nuclear-licensed site in the UK. A variety of different lithology sediments were selected to represent the heterogeneity of the subsurface at a site underlain by glacial outwash deposits and sandstone. The natural sediment microbial communities were stimulated via the addition of an acetate/lactate electron donor mix and were monitored for changes in geochemistry and molecular ecology. Most sediments facilitated the removal of 12 ppm U(VI) during the onset of Fe(III)-reducing conditions; this was reflected by an increase in the proportion of known Fe(III)- and U(VI)-reducing species. However U(VI) remained in solution in two sediments and Fe(III)-reducing conditions did not develop. Sequential extractions, addition of an Fe(III)-enrichment culture and most probable number enumerations revealed that a lack of bioavailable iron or low cell numbers of Fe(III)-reducing bacteria may be responsible. These results highlight the potential for stimulation of microbial U(VI)-reduction to be used as a bioremediation strategy at UK nuclear sites, and they emphasise the importance of both site-specific and borehole-specific investigations to be completed prior to implementation

  10. Microbial pollution indicators and culturable heterotrophic bacteria in a Mediterranean area (Southern Adriatic Sea Italian coasts)

    Science.gov (United States)

    Stabili, L.; Cavallo, R. A.

    2011-05-01

    In the present study we evaluated the degree of microbial water pollution along the coast line between Brindisi and Santa Maria di Leuca (Southern Adriatic Sea) as well as the culturable heterotrophic bacteria abundances and biodiversity in relation to the microbiological quality of the water. A total of 3773 colonies were isolated, subcultured and identified by several morphological, cultural and biochemical methods including the standardized API 20 E and API 20 NE tests. Along the examined coastal tract the microbial pollution indicators were always below the tolerance limits for bathing waters defined by the CEE directive, suggesting a good sanitary quality. Concerning culturable heterotrophic bacteria, different temporal density trends were observed in the four sites in relation to their geographical position. A positive relationship between the bacterial abundances and the temperature was observed in S. Cataldo and Otranto. The culturable bacterial community was mainly composed of the genera Aeromonas, Pseudomonas, Photobacterium and Flavobacterium. The Enterobacteriaceae family represented a conspicuous component of the bacterial community too. Bacilli were predominant among the Gram-positive bacteria. Of interest is the isolation of yeasts (2% at the surface and 1% at the bottom) taking into account their capability of biodegradation of various materials. Because of the low level of microbial pollution recorded, our results are indicative of the natural variation and diversity of the culturable bacterial community in such an oligotrophic ecosystem and could represent a good point of comparison with other ecosystems as well as a baseline for long term studies aimed to evaluate the effects of environmental fluctuations and human impacts on this aspect of biodiversity in coastal areas.

  11. From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

    Science.gov (United States)

    Garza, Daniel R; Dutilh, Bas E

    2015-11-01

    Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

  12. Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

    Science.gov (United States)

    Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

    2016-02-01

    The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future.

  13. Effects of dietary changes and yeast culture (Saccharomyces cerevisiae) on rumen microbial fermentation of Holstein heifers.

    Science.gov (United States)

    Moya, D; Calsamiglia, S; Ferret, A; Blanch, M; Fandiño, J I; Castillejos, L; Yoon, I

    2009-09-01

    The effects of a dietary challenge to induce digestive upsets and supplementation with yeast culture on rumen microbial fermentation were studied using 12 Holstein heifers (277 +/- 28 kg of BW) fitted with a ruminal cannula, in a crossover design with 2 periods of 5 wk. In each period, after 3 wk of adaptation to a 100% forage diet, the dietary challenge consisted of increasing the amount of grain at a rate of 2.5 kg/d (as-fed basis) over a period of 4 d, until a 10:90 forage:concentrate diet was reached, and then it was maintained for 10 d. Between periods, animals were fed again the 100% forage diet without any treatment for 1 wk as a wash-out period. Treatments started the first day of each period, and they were a control diet (CL) or the same diet with addition of yeast culture (YC, Diamond V XPCLS). Digestive upsets were determined by visual observation of bloat or by a reduction in feed intake (as-fed basis) of 50% or more compared with intake on the previous day. Feed intake was determined daily at 24-h intervals during the adaptation period and daily at 2, 6, and 12 h postfeeding during the dietary challenge. Ruminal liquid samples were collected daily during the dietary challenge to determine ruminal pH at 0, 3, 6, and 12 h postfeeding, and total and individual VFA, lactic acid, ammonia-N, and rumen fluid viscosity at 0 and 6 h postfeeding. The 16s rRNA gene copies of Streptococcus bovis and Megasphaera elsdenii were determined by quantitative PCR. Foam height and strength of the rumen fluid were also determined the day after the digestive upset to evaluate potential foam production. A total of 20 cases (83.3%) of digestive upsets were recorded in both periods during the dietary challenge, all diagnosed due to a reduction in feed intake. Rumen fermentation profile at 0 h on the digestive upset day was characterized by low ruminal pH, which remained under 6.0 for 18 h, accompanied by elevated total VFA concentration and, in some cases, by elevated lactate

  14. Bifurcations of a periodically forced microbial continuous culture model with restrained growth rate

    Science.gov (United States)

    Ren, Jingli; Yuan, Qigang

    2017-08-01

    A three dimensional microbial continuous culture model with a restrained microbial growth rate is studied in this paper. Two types of dilution rates are considered to investigate the dynamic behaviors of the model. For the unforced system, fold bifurcation and Hopf bifurcation are detected, and numerical simulations reveal that the system undergoes degenerate Hopf bifurcation. When the system is periodically forced, bifurcation diagrams for periodic solutions of period-one and period-two are given by researching the Poincaré map, corresponding to different bifurcation cases in the unforced system. Stable and unstable quasiperiodic solutions are obtained by Neimark-Sacker bifurcation with different parameter values. Periodic solutions of various periods can occur or disappear and even change their stability, when the Poincaré map of the forced system undergoes Neimark-Sacker bifurcation, flip bifurcation, and fold bifurcation. Chaotic attractors generated by a cascade of period doublings and some phase portraits are given at last.

  15. Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation

    Science.gov (United States)

    Wu, Qun; Ling, Jie

    2014-01-01

    Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified: Saccharomyces cerevisiae, Pichia membranaefaciens, Issatchenkia orientalis, Bacillus licheniformis, and Bacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found that S. cerevisiae was positively correlated to nonanal, and B. licheniformis was positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, while I. orientalis was positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. Although P. membranaefaciens and B. amyloliquefaciens were not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor. PMID:24814798

  16. Microbial Diversity in Sulfate-Reducing Marine Sediment Enrichment Cultures Associated with Anaerobic Biotransformation of Coastal Stockpiled Phosphogypsum (Sfax, Tunisia

    Directory of Open Access Journals (Sweden)

    Hana Zouch

    2017-08-01

    Full Text Available Anaerobic biotechnology using sulfate-reducing bacteria (SRB is a promising alternative for reducing long-term stockpiling of phosphogypsum (PG, an acidic (pH ~3 by-product of the phosphate fertilizer industries containing high amounts of sulfate. The main objective of this study was to evaluate, for the first time, the diversity and ability of anaerobic marine microorganisms to convert sulfate from PG into sulfide, in order to look for marine SRB of biotechnological interest. A series of sulfate-reducing enrichment cultures were performed using different electron donors (i.e., acetate, formate, or lactate and sulfate sources (i.e., sodium sulfate or PG as electron acceptors. Significant sulfide production was observed from enrichment cultures inoculated with marine sediments, collected near the effluent discharge point of a Tunisian fertilizer industry (Sfax, Tunisia. Sulfate sources impacted sulfide production rates from marine sediments as well as the diversity of SRB species belonging to Deltaproteobacteria. When PG was used as sulfate source, Desulfovibrio species dominated microbial communities of marine sediments, while Desulfobacter species were mainly detected using sodium sulfate. Sulfide production was also affected depending on the electron donor used, with the highest production obtained using formate. In contrast, low sulfide production (acetate-containing cultures was associated with an increase in the population of Firmicutes. These results suggested that marine Desulfovibrio species, to be further isolated, are potential candidates for bioremediation of PG by immobilizing metals and metalloids thanks to sulfide production by these SRB.

  17. Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Nymul; Maezato, Yukari; McClure, Ryan S.; Brislawn, Colin J.; Mobberley, Jennifer M.; Isern, Nancy; Chrisler, William B.; Markillie, Lye Meng; Barney, Brett M.; Song, Hyun-Seob; Nelson, William C.; Bernstein, Hans C.

    2018-01-10

    The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in a competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

  18. Topological defects control collective dynamics in neural progenitor cell cultures

    Science.gov (United States)

    Kawaguchi, Kyogo; Kageyama, Ryoichiro; Sano, Masaki

    2017-04-01

    Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.

  19. Application of the Lyapunov exponent to detect noise-induced chaos in oscillating microbial cultures

    International Nuclear Information System (INIS)

    Patnaik, P.R.

    2005-01-01

    Oscillating microbial processes can, under certain conditions, gravitate into chaotic behavior induced by external noise. Detection and control of chaos are important for the survival of the microorganisms and to operate a process usefully. In this study the largest Lyapunov exponent is recommended as a convenient and reliable index of chaos in continuous oscillating cultures. For the growth of Saccharomyces cerevisiae as a model system, the exponents increase with the oxygen mass transfer coefficient and decrease as the dilution rate increases. By comparing with the corresponding time-domain oscillations determined earlier, it is inferred that weakly oscillating cultures are less likely to be driven to chaotic behavior. The main carbon source, glucose, is quite robust to chaotic destabilization, thus enhancing its suitability as a manipulated variable for bioreactor control

  20. Dark fermentative hydrogen production by defined mixed microbial cultures immobilized on ligno-cellulosic waste materials

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Sanjay K.S. [Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi 110007 (India); Department of Biotechnology, University of Pune, Pune 411007 (India); Purohit, Hemant J. [Environmental Genomics Unit, National Environmental Engineering Research Institute (NEERI), CSIR, Nehru Marg, Nagpur 440020 (India); Kalia, Vipin C. [Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi 110007 (India)

    2010-10-15

    Mixed microbial cultures (MMCs) based on 11 isolates belonging to Bacillus spp. (Firmicutes), Bordetella avium, Enterobacter aerogenes and Proteus mirabilis (Proteobacteria) were employed to produce hydrogen (H{sub 2}) under dark fermentative conditions. Under daily fed culture conditions (hydraulic retention time of 2 days), MMC6 and MMC4, immobilized on ligno-cellulosic wastes - banana leaves and coconut coir evolved 300-330 mL H{sub 2}/day. Here, H{sub 2} constituted 58-62% of the total biogas evolved. It amounted to a H{sub 2} yield of 1.54-1.65 mol/mol glucose utilized over a period of 60 days of fermentation. The involvement of various Bacillus spp. -Bacillus sp., Bacillus cereus, Bacillus megaterium, Bacillus pumilus and Bacillus thuringiensis as components of the defined MMCs for H{sub 2} production has been reported here for the first time. (author)

  1. Microbial Diversity of a Camembert-Type Cheese Using Freeze-Dried Tibetan Kefir Coculture as Starter Culture by Culture-Dependent and Culture-Independent Methods

    Science.gov (United States)

    Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

    2014-01-01

    The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese. PMID:25360757

  2. Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods.

    Directory of Open Access Journals (Sweden)

    Jun Mei

    Full Text Available The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR-denaturing gradient gel electrophoresis (DGGE analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates. Meanwhile, Kazachstania servazzii (51 isolates represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates. However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.

  3. Microbial diversity of a Camembert-type cheese using freeze-dried Tibetan kefir coculture as starter culture by culture-dependent and culture-independent methods.

    Science.gov (United States)

    Mei, Jun; Guo, Qizhen; Wu, Yan; Li, Yunfei

    2014-01-01

    The biochemical changes occurring during cheese ripening are directly and indirectly dependent on the microbial associations of starter cultures. Freeze-dried Tibetan kefir coculture was used as a starter culture in the Camembert-type cheese production for the first time. Therefore, it's necessary to elucidate the stability, organization and identification of the dominant microbiota presented in the cheese. Bacteria and yeasts were subjected to culture-dependent on selective media and culture-independent polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis and sequencing of dominant bands to assess the microbial structure and dynamics through ripening. In further studies, kefir grains were observed using scanning electron microscopy (SEM) methods. A total of 147 bacteria and 129 yeasts were obtained from the cheese during ripening. Lactobacillus paracasei represents the most commonly identified lactic acid bacteria isolates, with 59 of a total of 147 isolates, followed by Lactococcus lactis (29 isolates). Meanwhile, Kazachstania servazzii (51 isolates) represented the mainly identified yeast isolate, followed by Saccharomyces cerevisiae (40 isolates). However, some lactic acid bacteria detected by sequence analysis of DGGE bands were not recovered by plating. The yeast S. cerevisiae and K. servazzii are described for the first time with kefir starter culture. SEM showed that the microbiota were dominated by a variety of lactobacilli (long and curved) cells growing in close association with a few yeasts in the inner portion of the grain and the short lactobacilli were observed along with yeast cells on the exterior portion. Results indicated that conventional culture method and PCR-DGGE should be combined to describe in maximal detail the microbiological composition in the cheese during ripening. The data could help in the selection of appropriate commercial starters for Camembert-type cheese.

  4. The binning of metagenomic contigs for microbial physiology of mixed cultures.

    Science.gov (United States)

    Strous, Marc; Kraft, Beate; Bisdorf, Regina; Tegetmeyer, Halina E

    2012-01-01

    So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population. In the present study eight metagenomic samples from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to existing algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a 100 times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt).

  5. The binning of metagenomic contigs for microbial physiology of mixed cultures

    Directory of Open Access Journals (Sweden)

    Marc eStrous

    2012-12-01

    Full Text Available So far, microbial physiology has dedicated itself mainly to pure cultures. In nature, cross feeding and competition are important aspects of microbial physiology and these can only be addressed by studying complete communities such as enrichment cultures. Metagenomic sequencing is a powerful tool to characterize such mixed cultures. In the analysis of metagenomic data, well established algorithms exist for the assembly of short reads into contigs and for the annotation of predicted genes. However, the binning of the assembled contigs or unassembled reads is still a major bottleneck and required to understand how the overall metabolism is partitioned over different community members. Binning consists of the clustering of contigs or reads that apparently originate from the same source population.In the present study eight metagenomic samples originating from the same habitat, a laboratory enrichment culture, were sequenced. Each sample contained 13-23 Mb of assembled contigs and up to eight abundant populations. Binning was attempted with existing methods but they were found to produce poor results, were slow, dependent on non-standard platforms or produced errors. A new binning procedure was developed based on multivariate statistics of tetranucleotide frequencies combined with the use of interpolated Markov models. Its performance was evaluated by comparison of the results between samples with BLAST and in comparison to exisiting algorithms for four publicly available metagenomes and one previously published artificial metagenome. The accuracy of the new approach was comparable or higher than existing methods. Further, it was up to a hunderd times faster. It was implemented in Java Swing as a complete open source graphical binning application available for download and further development (http://sourceforge.net/projects/metawatt.

  6. Culturable microbial groups and thallium-tolerant fungi in soils with high thallium contamination.

    Science.gov (United States)

    Sun, Jialong; Zou, Xiao; Ning, Zengping; Sun, Min; Peng, Jingquan; Xiao, Tangfu

    2012-12-15

    Thallium (Tl) contamination in soil exerts a significant threat to the ecosystem health due to its high toxicity. However, little is known about the effect of Tl on the microbial community in soil. The present study aimed at characterizing the culturable microbial groups in soils which experience for a long time high Tl contamination and elevated Hg and As. The contamination originates from As, Hg and Tl sulfide mineralization and the associated mining activities in the Guizhou Province, Southwest China. Our investigation showed the existence of culturable bacteria, filamentous fungi and actinomyces in long-term Tl-contaminated soils. Some fungal groups grow in the presence of high Tl level up to 1000 mg kg⁻¹. We have isolated and identified nine Tl-tolerant fungal strains based on the morphological traits and ITS analysis. The dominant genera identified were Trichoderma, Penicillium and Paecilomyces. Preliminary data obtained in this study suggested that certain microbes were able to face high Tl pollution in soil and maintain their metabolic activities and resistances. The highly Tl-tolerant fungi that we have isolated are potentially useful in the remediation of Tl-contaminated sites. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Electrochemically Driven Fermentation of Organic Substrates with Undefined Mixed Microbial Cultures.

    Science.gov (United States)

    Villano, Marianna; Paiano, Paola; Palma, Enza; Miccheli, Alfredo; Majone, Mauro

    2017-08-10

    Growing scientific interest in mixed microbial culture-based anaerobic biotechnologies for the production of value-added chemicals and fuels from organic waste residues requires a parallel focus on the development and implementation of strategies to control the distribution of products. This study examined the feasibility of an electrofermentation approach, based on the introduction of a polarized (-700 mV vs. the standard hydrogen electrode) graphite electrode in the fermentation medium, to steer the product distribution during the conversion of organic substrates (glucose, ethanol, and acetate supplied as single compounds or in mixtures) by undefined mixed microbial cultures. In batch experiments, the polarized electrode triggered a nearly 20-fold increase (relative to open circuit controls) in the yield of isobutyrate production (0.43±0.01 vs. 0.02±0.02 mol mol -1 glucose) during the anaerobic fermentation of the ternary mixture of substrates, without adversely affecting the rate of substrate bioconversion. The observed change in the fermentative metabolism was most likely triggered by the (potentiostatic) regulation of the oxidation-reduction potential of the reaction medium rather than by the electrode serving as an electron donor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A common basis for facilitated legitimate exchange of biological materials proposed by the European Culture Collections' Organisation

    Directory of Open Access Journals (Sweden)

    Dagmar Fritze

    2009-12-01

    Full Text Available Being charged with the task of accessioning and supplying of living microbiological material, microbial culture collections are institutions that play a central role between the interests of a variety of user communities. On the one side are the providers of living microbiological material, such as individual scientists, institutions and countries of origin and on the other side are the various kinds of recipients/users of cultures of microorganisms from academia and industry. Thus, providing access to high quality biological material and scientific services while at the same time observing donor countries' rights, intellectual property rights, biosafety and biosecurity aspects poses demanding challenges. E.g. donor countries rights relate to Article 15 of the Convention on Biological Diversity: "Contracting parties …. recognize the sovereign rights of states over their natural resources …. shall facilitate access to resources … and not impose restrictions that run counter to the aims of the Convention. Access to natural resources shall be by mutually agreed terms and subject to prior informed consent ..." The use of a proposed standard contract by culture collections is discussed as a way of contractually safeguarding the existing research commons, while observing the new rights established in the Convention on Biological Diversity as well as other existing and new legislation impacting on the accessibility of living microbial material.

  9. Dose-effect curves for electron-beam irradiation of some collection microbial strains

    International Nuclear Information System (INIS)

    Ferdes, O.; Dumitru, E.; Catargiu, L.; Ferdes, M.; Minea, R.; Oproiu, C.; Niculescu, A.

    1994-01-01

    There were electron-beam irradiated some microbial strains of B.subtilis ICA I-60 both in germination and in sporulated forms. The irradiation were performed at the IPTRD's electron accelerator at 6 MeV, and in the dose range between 0.1-5.0 kGy, at different dose-rate varying from 50 Gy/minute to 100 Gy/minute. The dosimetry was carried out by a PTW medical dosemeter. There were established the dose-effect relationships and curves, the inactivation dose (factor) and the optimum domain for electron-beam mutagenesis. There were obtained some mutant strains with 2-3.5 higher biosynthesis potential, which are in the IFC's collection. (Author)

  10. Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions.

    Directory of Open Access Journals (Sweden)

    Thomas J Moutinho

    Full Text Available Interactions between microbes are central to the dynamics of microbial communities. Understanding these interactions is essential for the characterization of communities, yet challenging to accomplish in practice. There are limited available tools for characterizing diffusion-mediated, contact-independent microbial interactions. A practical and widely implemented technique in such characterization involves the simultaneous co-culture of distinct bacterial species and subsequent analysis of relative abundance in the total population. However, distinguishing between species can be logistically challenging. In this paper, we present a low-cost, vertical membrane, co-culture plate to quantify contact-independent interactions between distinct bacterial populations in co-culture via real-time optical density measurements. These measurements can be used to facilitate the analysis of the interaction between microbes that are physically separated by a semipermeable membrane yet able to exchange diffusible molecules. We show that diffusion across the membrane occurs at a sufficient rate to enable effective interaction between physically separate cultures. Two bacterial species commonly found in the cystic fibrotic lung, Pseudomonas aeruginosa and Burkholderia cenocepacia, were co-cultured to demonstrate how this plate may be implemented to study microbial interactions. We have demonstrated that this novel co-culture device is able to reliably generate real-time measurements of optical density data that can be used to characterize interactions between microbial species.

  11. 75 FR 11988 - Notice of Request for Approval To Collect New Information: Collection of Safety Culture Data

    Science.gov (United States)

    2010-03-12

    ..., information about changes to the safety culture of the affected workplaces will be used as one of several data...: RITA-2008-0002] Notice of Request for Approval To Collect New Information: Collection of Safety Culture.... mail to Federal offices in Washington, DC, we recommend that persons consider an alternative method...

  12. Feasibility of biohydrogen production from industrial wastes using defined microbial co-culture

    Directory of Open Access Journals (Sweden)

    Peng Chen

    2015-01-01

    Full Text Available BACKGROUND: The development of clean or novel alternative energy has become a global trend that will shape the future of energy. In the present study, 3 microbial strains with different oxygen requirements, including Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, were used to construct a hydrogen production system that was composed of a mixed aerobic-facultative anaerobic-anaerobic consortium. The effects of metal ions, organic acids and carbohydrate substrates on this system were analyzed and compared using electrochemical and kinetic assays. It was then tested using small-scale experiments to evaluate its ability to convert starch in 5 L of organic wastewater into hydrogen. For the one-step biohydrogen production experiment, H1 medium (nutrient broth and potato dextrose broth was mixed directly with GAM broth to generate H2 medium (H1 medium and GAM broth. Finally, Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D of three species microbial co-culture to produce hydrogen under anaerobic conditions. For the two-step biohydrogen production experiment, the H1 medium, after cultured the microbial strains Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, was centrifuged to remove the microbial cells and then mixed with GAM broth (H2 medium. Afterward, the bacterial strain Clostridium acetobutylicum ATCC 824 was inoculated into the H2 medium to produce hydrogen by anaerobic fermentation. RESULTS: The experimental results demonstrated that the optimum conditions for the small-scale fermentative hydrogen production system were at pH 7.0, 35°C, a mixed medium, including H1 medium and H2 medium with 0.50 mol/L ferrous chloride, 0.50 mol/L magnesium sulfate, 0.50 mol/L potassium chloride, 1% w/v citric acid, 5% w/v fructose and 5% w/v glucose. The overall hydrogen production efficiency in the shake flask fermentation group was 33.7 m

  13. Effects of cinnamaldehyde and garlic oil on rumen microbial fermentation in a dual flow continuous culture.

    Science.gov (United States)

    Busquet, M; Calsamiglia, S; Ferret, A; Cardozo, P W; Kamel, C

    2005-07-01

    Eight continuous culture fermentors inoculated with ruminal liquor from heifers fed a 50:50 alfalfa hay:concentrate diet (17.6% crude protein, 28.0% neutral detergent fiber) were used in 3 replicated periods to study the effects of cinnamaldehyde (CIN) and garlic oil (GAR) on rumen microbial fermentation. Treatments were no additive (negative control); 1.25 mg/L (MON) and 12.5 mg/L (MON10) of the ionophore antibiotic monensin (positive control); 31.2 mg/L CIN (CIN) and 312 mg/L (CIN10) of CIN; and 31.2 mg/L GAR (GAR) and 312 mg/L (GAR10) of GAR (Allium sativa). The MON10 caused expected changes in microbial fermentation patterns (a decrease in fiber digestion, ammonia N concentration, and proportions of acetate and butyrate; an increase in the proportion of propionate; and a trend to increase small peptide plus AA N concentration). The CIN decreased the proportion of acetate and branch-chained volatile fatty acids (VFA) and increased the proportion of propionate; CIN10 decreased the proportion of acetate and increased the proportion of butyrate compared with the control. The GAR10 increased the proportion of propionate and butyrate and decreased the proportion of acetate and branch-chained VFA compared with the control. The GAR10 also increased the small peptide plus amino acid N concentration, although no effects were observed on large peptides or ammonia N concentrations. The CIN and GAR10 resulted in similar effects as monensin, with the exception of the effects on the molar proportion of butyrate, which suggests that they might have a different mode of action in affecting in vitro microbial fermentation.

  14. Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures

    Energy Technology Data Exchange (ETDEWEB)

    Penner, Tara J.; Foght, Julia M. [Department of Biological Sciences, University of Alberta, Edmonton, Alberta (Canada); Budwill, Karen [Carbon and Energy Management, Alberta Innovates-Technology Futures, 250 Karl Clark Road, Edmonton, Alberta (Canada)

    2010-05-01

    Coalbed methane is an unconventional fuel source associated with certain coal seams. Biogenic methane can comprise a significant portion of the gas found in coal seams, yet the role of microbes in methanogenesis in situ is uncertain. The purpose of this study was to detect and identify major bacterial and archaeal species associated with coal sampled from sub-bituminous methane-producing coal beds in western Canada, and to examine the potential for methane biogenesis from coal. Enrichment cultures of coal samples were established to determine how nutrient amendment influenced the microbial community and methane production in the laboratory. 16S rRNA gene clone libraries were constructed using DNA extracted and amplified from uncultured coal samples and from methanogenic coal enrichment cultures. Libraries were screened using restriction fragment length polymorphism, and representative clones were sequenced. Most (> 50%) of the bacterial sequences amplified from uncultured coal samples were affiliated with Proteobacteria that exhibit nitrate reduction, nitrogen fixation and/or hydrogen utilization activities, including Pseudomonas, Thauera and Acidovorax spp., whereas enrichment cultures were dominated by Bacteroidetes, Clostridia and/or Lactobacillales. Archaeal 16S rRNA genes could not be amplified from uncultured coal, suggesting that methanogens are present in coal below the detection levels of our methods. However, enrichment cultures established with coal inocula produced significant volumes of methane and the archaeal clone libraries were dominated by sequences closely affiliated with Methanosarcina spp. Enrichment cultures incubated with coal plus organic nutrients produced more methane than either nutrient or coal supplements alone, implying that competent methanogenic consortia exist in coal beds but that nutrient limitations restrict their activity in situ. This report adds to the scant literature on coal bed microbiology and suggests how microbes may be

  15. Retention and transport of an anaerobic trichloroethene dechlorinating microbial culture in anaerobic porous media.

    Science.gov (United States)

    Zhang, Huixin; Ulrich, Ania C; Liu, Yang

    2015-06-01

    The influence of solution chemistry on microbial transport was examined using the strictly anaerobic trichloroethene (TCE) bioaugmentation culture KB-1(®). A column was employed to determine transport behaviors and deposition kinetics of three distinct functional species in KB-1(®), Dehalococcoides, Geobacter, and Methanomethylovorans, over a range of ionic strengths under a well-controlled anaerobic condition. A quantitative polymerase chain reaction (qPCR) was utilized to enumerate cell concentration and complementary techniques were implemented to evaluate cell surface electrokinetic potentials. Solution chemistry was found to positively affect the deposition rates, which was consistent with calculated Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energies. Retained microbial profiles showed spatially constant colloid deposition rate coefficients, in agreement with classical colloid filtration theory (CFT). It was interesting to note that the three KB-1(®) species displayed similar transport and retention behaviors under the defined experimental conditions despite their different cell electrokinetic properties. A deeper analysis of cell characteristics showed that factors, such as cell size and shape, concentration, and motility were involved in determining adhesion behavior. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Microbial Fuel Cells using Mixed Cultures of Wastewater for Electricity Generation

    International Nuclear Information System (INIS)

    Zain, S.M; Roslani, N.S.; Hashim, R.; Anuar, N.; Suja, F.; Basi, N.E.A.; Anuar, N.; Daud, W.R.W.

    2011-01-01

    Fossil fuels (petroleum, natural gas and coal) are the main resources for generating electricity. However, they have been major contributors to environmental problems. One potential alternative to explore is the use of microbial fuel cells (MFCs), which generate electricity using microorganisms. MFCs uses catalytic reactions activated by microorganisms to convert energy preserved in the chemical bonds between organic molecules into electrical energy. MFC has the ability to generate electricity during the wastewater treatment process while simultaneously treating the pollutants. This study investigated the potential of using different types of mixed cultures (raw sewage, mixed liquor from the aeration tank and return waste activated sludge) from an activated sludge treatment plant in MFCs for electricity generation and pollutant removals (COD and total kjeldahl nitrogen, TKN). The MFC in this study was designed as a dual-chambered system, in which the chambers were separated by a Nafion TM membrane using a mixed culture of wastewater as a bio catalyst. The maximum power density generated using activated sludge was 9.053 mW/ cm 2 , with 26.8 % COD removal and 40 % TKN removal. It is demonstrated that MFC offers great potential to optimize power generation using mixed cultures of wastewater. (author)

  17. A defined co-culture of Geobacter sulfurreducens and Escherichia coli in a membrane-less microbial fuel cell.

    Science.gov (United States)

    Bourdakos, Nicholas; Marsili, Enrico; Mahadevan, Radhakrishnan

    2014-04-01

    Wastewater-fed microbial fuel cells (MFCs) are a promising technology to treat low-organic carbon wastewater and recover part of the chemical energy in wastewater as electrical power. However, the interactions between electrochemically active and fermentative microorganisms cannot be easily studied in wastewater-fed MFCs because of their complex microbial communities. Defined co-culture MFCs provide a detailed understanding of such interactions. In this study, we characterize the extracellular metabolites in laboratory-scale membrane-less MFCs inoculated with Geobacter sulfurreducens and Escherichia coli co-culture and compare them with pure culture MFCs. G. sulfurreducens MFCs are sparged to maintain anaerobic conditions, while co-culture MFCs rely on E. coli for oxygen removal. G. sulfurreducens MFCs have a power output of 128 mW m(-2) , compared to 63 mW m(-2) from the co-culture MFCs. Analysis of metabolites shows that succinate production in co-culture MFCs decreases current production by G. sulfurreducens and that the removal of succinate is responsible for the increased current density in the late co-culture MFCs. Interestingly, pH adjustment is not required for co-culture MFCs but a base addition is necessary for E. coli MFCs and cultures in vials. Our results show that defined co-culture MFCs provide clear insights into metabolic interactions among bacteria while maintaining a low operational complexity. © 2013 Wiley Periodicals, Inc.

  18. The Legal Status of Microbial Food Cultures in the European Union

    DEFF Research Database (Denmark)

    Herody, Caroline; Soyeux, Y; Hansen, Egon Bech

    2010-01-01

    The production of fermented foods is one of the oldest food processing technologies known to man. Since the dawn of civilisation, methods for the fermentation of milks, meats, fish and vegetables have been used to produce safe foods with distinctive organoleptic properties. Microbial food cultures...... (MFC) with a technological impact on food are called “starter cultures”. They may be present as natural microflora in the food, or as a result of the intentional addition of the microorganisms in an industrial food fermentation process. MFC that are used for their beneficial effect on consumers’ health...... are called probiotics. Probiotics are always intentionally added to the food as they have been carefully selected and studied to guarantee that they provide a proven beneficial effect to consumers. They may be used in both fermented and non-fermented foods such as food supplements. This paper aims to provide...

  19. Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.

    Science.gov (United States)

    Hanson, Andrea J; Paszczynski, Andrzej J; Coats, Erik R

    2016-03-01

    The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. An Autonomous System for Experimental Evolution of Microbial Cultures: Test Results Using Ultraviolet-C Radiation and Escherichia Coli.

    Science.gov (United States)

    Ouandji, Cynthia; Wang, Jonathan; Arismendi, Dillon; Lee, Alonzo; Blaich, Justin; Gentry, Diana

    2017-01-01

    At its core, the field of microbial experimental evolution seeks to elucidate the natural laws governing the history of microbial life by understanding its underlying driving mechanisms. However, observing evolution in nature is complex, as environmental conditions are difficult to control. Laboratory-based experiments for observing population evolution provide more control, but manually culturing and studying multiple generations of microorganisms can be time consuming, labor intensive, and prone to inconsistency. We have constructed a prototype, closed system device that automates the process of directed evolution experiments in microorganisms. It is compatible with any liquid microbial culture, including polycultures and field samples, provides flow control and adjustable agitation, continuously monitors optical density (OD), and can dynamically control environmental pressures such as ultraviolet-C (UV-C) radiation and temperature. Here, the results of the prototype are compared to iterative exposure and survival assays conducted using a traditional hood, UV-C lamp, and shutter system.

  1. Digital Extension of Music Memory Music as a Collective Cultural Memory

    Directory of Open Access Journals (Sweden)

    Dimitrije Buzarovski

    2014-11-01

    Full Text Available Artistic works represent a very important part of collective cultural memory. Every artistic work, by definition, can confirm its existence only through the presence in collective cultural memory. The migration from author’s individual memory to common collective cultural memory forms the cultural heritage. This equally applies to tangible and intangible cultural artifacts. Being part of collective cultural memory, music reflects the spatial (geographic and temporal (historic dimensions of this memory. Until the appearance of written signs (scores music was preserved only through collective cultural memory. Scores have facilitated further distribution of music artifacts. The appearance of different means for audio, and later audio/video recordings have greatly improved the distribution of music. The transition from analog to digital recording and carriers has been a revolutionary step which substantially extended the chances for the survival of music artifacts in collective memory.

  2. 76 FR 33395 - 30-Day Notice of Proposed Information Collections: ECA Sports & Culture Evaluation Surveys

    Science.gov (United States)

    2011-06-08

    ... Information Collection: Sports & Culture Evaluation, Sports Envoys Survey. OMB Control Number: None. Type of... Evaluation, Sports Surveys. OMB Control Number: None. Type of Request: New Collection. Originating Office...: Sports & Culture Evaluation, Kennedy Center (KC) Cultural Visitors Survey. OMB Control Number: None. Type...

  3. 76 FR 16030 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

    Science.gov (United States)

    2011-03-22

    ... and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture... collection clearance will allow ECA/P/V as part of their larger Sports and Culture Evaluation to conduct a... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports...

  4. 76 FR 16032 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

    Science.gov (United States)

    2011-03-22

    ... Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture Evaluation IWP... collection clearance will allow ECA/P/V as part of their larger Sports and Culture Evaluation to conduct a... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports...

  5. Survival of microbial cultures on mineral while passing dense layers of the atmosphere

    Science.gov (United States)

    Viacheslav, Ilyin; Novikova, Nataliya; Deshevaya, Elena; Polikarpov, Nikolay; Slobodkin, Alexander; Gavrilov, Sergey; Ionov, Viktor; Morozova, Julia

    The purpose of the experiment is to study the possibility of extremophilic microorganisms survival in meteorite-like mineral while passing through the dense layers of the atmosphere. For this purpose cultures of bacteria were placed into the holes made in basalt pieces fixed to the outer wall of the spacecraft Bion M1. Control: similar materials placed in the outer container, prevented from overheating in the dense layers of the atmosphere by lid. In the flight experiment five strains of thermophilic bacteria and 2 strains of hyperthermophilic archaea from the collection of the Institute of Microbiology, RAS were used. In addition, microorganisms were selected from the collection of the Institute of Biomedical Problems, isolated from the environment objects of ISS: 10 fungal cultures and a culture of bacteria Bacillus pumilus. For thermophiles and hyperthermophiles the ability to redox interactions with minerals is considered as a priority physiological property. Ability of thermophiles to anaerobic growth also meets the conditions of the experiment - testing cell survival of microorganisms in the conditions of extraterrestrial space and ancient anaerobic atmosphere of the Earth. After 30-days flight in orbit control all spore-forming microorganisms have been successfully survived. Hyperthermophilic archaea growth in all control was significantly less intensive. Meanwhile, in one experimental samples there was obtained signs of survival of spore forming bacteria culture Carboxydocella ferrireducens. However, the maximum concentration of cells was 2 orders of magnitude below the values characteristic of an actively growing culture of the microorganism. Due to damage of holes in the stone, this result was obtained only in one replicate and for final prove of survival of C. ferrireducens when returning through the dense layers of the atmosphere it is necessary to repeat the experiment It should be noted that an important indicator of the possibility of survival of C

  6. Degradation of paracetamol by pure bacterial cultures and their microbial consortium.

    Science.gov (United States)

    Zhang, Lili; Hu, Jun; Zhu, Runye; Zhou, Qingwei; Chen, Jianmeng

    2013-04-01

    Three bacterial strains utilizing paracetamol as the sole carbon, nitrogen, and energy source were isolated from a paracetamol-degrading aerobic aggregate, and assigned to species of the genera Stenotrophomonas and Pseudomonas. The Stenotrophomonas species have not included any known paracetamol degraders until now. In batch cultures, the organisms f1, f2, and fg-2 could perform complete degradation of paracetamol at concentrations of 400, 2,500, and 2,000 mg/L or below, respectively. A combination of three microbial strains resulted in significantly improved degradation and mineralization of paracetamol. The co-culture was able to use paracetamol up to concentrations of 4,000 mg/L, and mineralized 87.1 % of the added paracetamol at the initial of 2,000 mg/L. Two key metabolites of the biodegradation pathway of paracetamol, 4-aminophenol, and hydroquinone were detected. Paracetamol was degraded predominantly via 4-aminophenol to hydroquinone with subsequent ring fission, suggesting new pathways for paracetamol-degrading bacteria. The degradation of paracetamol could thus be performed by the single isolates, but is stimulated by a synergistic interaction of the three-member consortium, suggesting a possible complementary interaction among the various isolates. The exact roles of each of the strains in the consortium need to be further elucidated.

  7. Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor

    Directory of Open Access Journals (Sweden)

    Igor Magalhães da Veiga Moreira

    2017-05-01

    Full Text Available Chocolate production suffered a vast impact with the emergence of the “witches’ broom” disease in cocoa plants. To recover cocoa production, many disease-resistant hybrid plants have been developed. However, some different cocoa hybrids produce cocoa beans that generate chocolate with variable quality. Fermentation of cocoa beans is a microbiological process that can be applied for the production of chocolate flavor precursors, leading to overcoming the problem of variable chocolate quality. The aim of this work was to use a cocktail of microorganisms as a starter culture on the fermentation of the ripe cocoa pods from PH15 cocoa hybrid, and evaluate its influence on the microbial communities present on the fermentative process on the compounds involved during the fermentation, and to perform the chocolate sensorial characterization. According to the results obtained, different volatile compounds were identified in fermented beans and in the chocolate produced. Bitterness was the dominant taste found in non-inoculated chocolate, while chocolate made with inoculated beans showed bitter, sweet, and cocoa tastes. 2,3-Butanediol and 2,3-dimethylpyrazine were considered as volatile compounds making the difference on the flavor of both chocolates. Saccharomyces cerevisiae UFLA CCMA 0200, Lactobacillus plantarum CCMA 0238, and Acetobacter pasteurianus CCMA 0241 are proposed as starter cultures for cocoa fermentation.

  8. Microbial diversity in an Armenian geothermal spring assessed by molecular and culture-based methods.

    Science.gov (United States)

    Panosyan, Hovik; Birkeland, Nils-Kåre

    2014-11-01

    The phylogenetic diversity of the prokaryotic community thriving in the Arzakan hot spring in Armenia was studied using molecular and culture-based methods. A sequence analysis of 16S rRNA gene clone libraries demonstrated the presence of a diversity of microorganisms belonging to the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Epsilonproteobacteria, Firmicutes, Bacteroidetes phyla, and Cyanobacteria. Proteobacteria was the dominant group, representing 52% of the bacterial clones. Denaturing gradient gel electrophoresis profiles of the bacterial 16S rRNA gene fragments also indicated the abundance of Proteobacteria, Bacteroidetes, and Cyanobacteria populations. Most of the sequences were most closely related to uncultivated microorganisms and shared less than 96% similarity with their closest matches in GenBank, indicating that this spring harbors a unique community of novel microbial species or genera. The majority of the sequences of an archaeal 16S rRNA gene library, generated from a methanogenic enrichment, were close relatives of members of the genus Methanoculleus. Aerobic endospore-forming bacteria mainly belonging to Bacillus and Geobacillus were detected only by culture-dependent methods. Three isolates were successfully obtained having 99, 96, and 96% 16S rRNA gene sequence similarities to Arcobacter sp., Methylocaldum sp., and Methanoculleus sp., respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Impact of a Microbial Cocktail Used as a Starter Culture on Cocoa Fermentation and Chocolate Flavor.

    Science.gov (United States)

    Magalhães da Veiga Moreira, Igor; de Figueiredo Vilela, Leonardo; da Cruz Pedroso Miguel, Maria Gabriela; Santos, Cledir; Lima, Nelson; Freitas Schwan, Rosane

    2017-05-09

    Chocolate production suffered a vast impact with the emergence of the "witches' broom" disease in cocoa plants. To recover cocoa production, many disease-resistant hybrid plants have been developed. However, some different cocoa hybrids produce cocoa beans that generate chocolate with variable quality. Fermentation of cocoa beans is a microbiological process that can be applied for the production of chocolate flavor precursors, leading to overcoming the problem of variable chocolate quality. The aim of this work was to use a cocktail of microorganisms as a starter culture on the fermentation of the ripe cocoa pods from PH15 cocoa hybrid, and evaluate its influence on the microbial communities present on the fermentative process on the compounds involved during the fermentation, and to perform the chocolate sensorial characterization. According to the results obtained, different volatile compounds were identified in fermented beans and in the chocolate produced. Bitterness was the dominant taste found in non-inoculated chocolate, while chocolate made with inoculated beans showed bitter, sweet, and cocoa tastes. 2,3-Butanediol and 2,3-dimethylpyrazine were considered as volatile compounds making the difference on the flavor of both chocolates. Saccharomyces cerevisiae UFLA CCMA 0200, Lactobacillus plantarum CCMA 0238, and Acetobacter pasteurianus CCMA 0241 are proposed as starter cultures for cocoa fermentation.

  10. Cultural dimensions, collective values and their importance for institutions

    NARCIS (Netherlands)

    Klasing, Mariko J.

    2013-01-01

    This paper critically assesses the role of culture in determining the quality of institutions. Employing various measures of cultural differences, I find that only differences related to the degree of individualism in society and the extent to which inequality in the distribution of power is

  11. Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture.

    Science.gov (United States)

    Zhao, Siyan; Rogers, Matthew J; He, Jianzhong

    2017-07-01

    Trihalomethanes such as chloroform and bromoform, although well-known as a prominent class of disinfection by-products, are ubiquitously distributed in the environment due to widespread industrial usage in the past decades. Chloroform and bromoform are particularly concerning, of high concentrations detected and with long half-lives up to several hundred days in soils and groundwater. In this study, we report a Dehalobacter- and Desulfovibrio-containing co-culture that exhibits dehalogenation of chloroform (~0.61 mM) to dichloromethane and bromoform (~0.67 mM) to dibromomethane within 10-15 days. This co-culture was further found to dechlorinate 1,1,1-trichloroethane (1,1,1-TCA) (~0.65 mM) to 1,1-dichloroethane within 12 days. The Dehalobacter species present in this co-culture, designated Dehalobacter sp. THM1, was found to couple growth with dehalogenation of chloroform, bromoform, and 1,1,1-TCA. Strain THM1 harbors a newly identified reductive dehalogenase (RDase), ThmA, which catalyzes chloroform, bromoform, and 1,1,1-TCA dehalogenation. Additionally, based on the sequences of thmA and other identified chloroform RDase genes, ctrA, cfrA, and tmrA, a pair of chloroform RDase gene-specific primers were designed and successfully applied to investigate the chloroform dechlorinating potential of microbial communities. The comparative analysis of chloroform RDases with tetrachloroethene RDases suggests a possible approach in predicting the substrate specificity of uncharacterized RDases in the future.

  12. The influence of fish culture in floating net cages on microbial indicators of water quality

    Directory of Open Access Journals (Sweden)

    K. Gorlach-Lira

    Full Text Available This work was carried out to analyse the microbiological parameters of the water quality of a reservoir used for the irrigation and culture of tilapia (Oreochromis niloticus in floating net cages. The physico-chemical parameters, counts of mesophilic total aerobic bacteria, total and thermotolerant coliforms and fecal streptococci, and the presence of Escherichia coli in samples of water collected in three sites of the reservoir (pre-culture site, culture site, post-culture site were analysed. The levels of ammonia (0.047-0.059 mg/L, nitrite (0.001-0.021 mg/L and total phosphorus (0.050-0.355 mg/L in the water did not show significant differences (p > 0.05 between sampling sites. The levels of total bacteria in the water varied between 1.3 x 104 and 67.3 x 104 CFU/100 mL. The MPN values of thermotolerant coliforms (< 930 MPN/100 mL were within values recommended for water used for fish culture and/or irrigation. The presence of E. coli and fecal streptococci were verified in 48% and 56% of analysed samples, respectively. The site with floating net cages showed more samples contaminated with E. coli and fecal streptococci than other sampling points.

  13. Selection and screening of microbial consortia for efficient and ecofriendly degradation of plastic garbage collected from urban and rural areas of Bangalore, India.

    Science.gov (United States)

    Skariyachan, Sinosh; Megha, M; Kini, Meghna Niranjan; Mukund, Kamath Manali; Rizvi, Alya; Vasist, Kiran

    2015-01-01

    Industrialization and urbanization have led to massive accumulation of plastic garbage all over India. The persistence of plastic in soil and aquatic environment has become ecological threat to the metropolitan city such as Bangalore, India. Present study investigates an ecofriendly, efficient and cost-effective approach for plastic waste management by the screening of novel microbial consortia which are capable of degrading plastic polymers. Plastic-contaminated soil and water samples were collected from six hot spots of urban and rural areas of Bangalore. The plastic-degrading bacteria were enriched, and degradation ability was determined by zone of clearance method. The percentage of polymer degradation was initially monitored by weight loss method, and the main isolates were characterized by standard microbiology protocols. These isolates were used to form microbial consortia, and the degradation efficiency of the consortia was compared with individual isolate and known strains obtained from the Microbial Type Culture Collection (MTCC) and Gene Bank, India. One of the main enzymes responsible for polymer degradation was identified, and the biodegradation mechanism was hypothesized by bioinformatics studies. From this study, it is evident that the bacteria utilized the plastic polymer as a sole source of carbon and showed 20-50% weight reduction over a period of 120 days. The two main bacteria responsible for the degradation were microbiologically characterized to be Pseudomonas spp. These bacteria could grow optimally at 37 °C in pH 9.0 and showed 35-40% of plastic weight reduction over 120 days. These isolates were showed better degradation ability than known strains from MTCC. The current study further revealed that the microbial consortia formulated by combining Psuedomonas spp. showed 40 plastic weight reduction over a period of 90 days. Further, extracellular lipase, one of the main enzymes responsible for polymer degradation, was identified. The

  14. Cultural Characteristics of Shimizuomyces paradoxus Collected from Korea

    OpenAIRE

    Sung, Gi-Ho; Shrestha, Bhushan; Park, Ki-Byung; Sung, Jae-Mo

    2010-01-01

    This study investigated the cultural characteristics of Shimizuomyces paradoxus in different nutritional and environmental conditions. The highest mycelial growth was observed in Schizophyllum (mushroom) genetics complete medium plus yeast extract agar medium, and the optimal temperature and pH were 25? and pH 8.0, respectively. The optimal carbon and nitrogen sources were 1% dextrose and 1% peptone in agar. However, in liquid culture the highest dry mycelium weight was found for the potato d...

  15. 77 FR 74048 - Culturally Significant Object Imported for Exhibition Determinations: “Connecting Collections...

    Science.gov (United States)

    2012-12-12

    ... determine that the object to be included in the exhibition ``Connecting Collections: Collecting Connections... DEPARTMENT OF STATE [Public Notice 8112] Culturally Significant Object Imported for Exhibition Determinations: ``Connecting Collections: Collecting Connections. 50 Years of Pre-Columbian Art at Dumbarton Oaks...

  16. Comparative analysis and culturing of the microbial community of Aiptasia pallida, A Sea Anemone Model for Coral Biology

    KAUST Repository

    Binsarhan, Mohammad

    2016-01-01

    Recent works has highlighted the contribution of microbes to animal function. In this regard, the microbial community associated with corals has become a growing field of research in order to understand how microbes contribute to the host organisms’ response to environmental changes. It has been shown that microbes associated with corals have important functions in the coral holobiont such as immunity and nutrient assimilation. However, corals are notoriously difficult to work with. To this end, the sea anemone Aiptasia is becoming a model organism for coral symbiosis. Given the importance of host-­microbiome interactions, the topic of this thesis is to assess microbial structure of Aiptasia, culture prominent bacterial members, and compare bacterial community structure to corals. Different molecular methods have been applied using 16S rRNA bacterial gene fragments to characterize the microbial composition of Aiptasia. 16S rRNA gene sequence derived from cultured bacteria was compared to 16S rRNA gene sequences retrieved from native Red Sea Aiptasia. Inter-­individual as well as methodological differences were found to account for variance in microbiome composition. However, all approaches showed a highly abundant microbial taxon belonging to the genus Alteromonas in all samples. The Alteromonas species was successfully isolated for further research targeting microbiome selection mechanisms in Aiptasia. Future investigations by using different molecular tools will help to define the functions and relationship between the Aiptasia and its complex microbiome.

  17. Microbial Stereoselective One-Step Conversion of Diols to Chiral Lactones in Yeast Cultures

    Directory of Open Access Journals (Sweden)

    Filip Boratyński

    2015-12-01

    Full Text Available It has been shown that whole cells of different strains of yeast catalyze stereoselective oxidation of meso diols to the corresponding chiral lactones. Among screening-scale experiments, Candida pelliculosa ZP22 was selected as the most effective biocatalyst for the oxidation of monocyclic diols 3a–b with respect to the ratio of high conversion to stereoselectivity. This strain was used in the preparative oxidation, affording enantiomerically-enriched isomers of lactones: (+-(3aR,7aS-cis-hexahydro-1(3H -isobenzofuranone (2a and (+-(3aS,4,7,7aR-cis-tetrahydro-1(3H-isobenzofuranone (2b. Scaling up the culture growth, as well as biotransformation conditions has been successfully accomplished. Among more bulky substrates, bicyclic diol 3d was totally converted into enantiomerically-pure exo-bridged (+-(3aR,4S,7R,7aS-cis-tetrahydro-4,7-methanoisobenzofuran -1(3H-one (2d by Yarrovia lipolytica AR71. Microbial oxidation of diol 3f by Candida sake AM908 and Rhodotorula rubra AM4 afforded optically-pure cis-3-butylhexahydro-1(3H -isobenzofuranone (2f, however with low conversion.

  18. Characterization of mixed-culture biofilms established in microbial fuel cells

    International Nuclear Information System (INIS)

    Yang, Suling; Du, Fangzhou; Liu, Hong

    2012-01-01

    For the successful operation of a microbial fuel cell, it is important to characterize the biofilm on the anode. The behavior of MFCs during initial biofilm growth and characterization of anodic biofilm were studied using two-chamber MFCs with activated sludge as inoculum. After three times' replacement of the anodic growth medium, the biofilms were well developed, and a maximum closed circuit potential of 0.41 V and 0.37 V (1000 Ω resistor) was achieved using acetate and glucose, respectively. Electron microscopy revealed that there were rod-shaped cells 0.2–0.3 μm wide by 1.5–2.5 μm long in the anode biofilm in the acetate-fed MFC, and these cells were mainly arranged by monolayer. The biofilm in the glucose-fed MFC was made of cocci-shaped cells in chains and a thick matrix. Both using acetate and glucose, the anodic bacterial communities were different than those of the activated sludge. Cyclic voltammograms suggested that extracellular electron transfer in these MFCs was accomplished mainly by the biofilms on the anode and not by bacteria-produced mediators. -- Highlights: ► The mixed-culture biofilms established in MFCs were characterized. ► The possible electron transfer mechanism was presented. ► In these MFCs the anodic area should be much larger.

  19. Analysis of microbial community variation during the mixed culture fermentation of agricultural peel wastes to produce lactic acid.

    Science.gov (United States)

    Liang, Shaobo; Gliniewicz, Karol; Gerritsen, Alida T; McDonald, Armando G

    2016-05-01

    Mixed cultures fermentation can be used to convert organic wastes into various chemicals and fuels. This study examined the fermentation performance of four batch reactors fed with different agricultural (orange, banana, and potato (mechanical and steam)) peel wastes using mixed cultures, and monitored the interval variation of reactor microbial communities with 16S rRNA genes using Illumina sequencing. All four reactors produced similar chemical profile with lactic acid (LA) as dominant compound. Acetic acid and ethanol were also observed with small fractions. The Illumina sequencing results revealed the diversity of microbial community decreased during fermentation and a community of largely lactic acid producing bacteria dominated by species of Lactobacillus developed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Governance, collective bargaining and peace culture in labour ...

    African Journals Online (AJOL)

    This struggle by the labour unions to improve on the unfair policies and working conditions has generated severe threat in maintaining peace culture in labour relations. It has adversely been affecting the growth of national economy in relation to global economic change. This situation has created almost total failure on the ...

  1. Impact of nitrogen feeding regulation on polyhydroxyalkanoates production by mixed microbial cultures.

    Science.gov (United States)

    Silva, Fernando; Campanari, Sabrina; Matteo, Stefania; Valentino, Francesco; Majone, Mauro; Villano, Marianna

    2017-07-25

    A sequencing batch reactor (SBR) is typically used for selecting mixed microbial cultures (MMC) for polyhydroxyalkanoate (PHA) production. Since many waste streams suitable as process feedstock for PHA production are nitrogen-deficient, a nutrient supply in the SBR is typically required to allow for efficient microbial growth. The scope of this study was to devise a nitrogen feeding strategy which allows controlling the nitrogen levels during the feast and famine regime of a lab-scale SBR, thereby selecting for PHA-storing microorganisms. At the beginning of the cycle the reactor was fed with a synthetic mixture of acetic and propionic acids at an overall organic load rate of 8.5gCODL -1 d -1 (i.e. 260CmmolL -1 d -1 ), whereas nitrogen (in the form of ammonium sulphate) was added either simultaneously to the carbon feed (coupled feeding strategy) or after the end of the feast phase (uncoupled feeding strategy). As a main result, PHA production was more than doubled (up to about 1300±64mgCODL -1 ) when carbon and nitrogen were separately fed and the higher PHA production also corresponded to an 82% increase in the polymer HV content (up to 20±1%, wtwt -1 ). Three SBR runs were performed with the uncoupled carbon and nitrogen feeding at different carbon to nitrogen (C/N) ratios (of 14.3, 17.9, and 22.3CmolNmol -1 , respectively) which were varied by progressively reducing the concentration of the nitrogen feeding. In spite of a comparable PHA storage yield at 14.3 and 17.9CmolNmol -1 (0.41±0.05 gCOD PHA gCOD VFA -1 and 0.38±0.05 gCOD PHA gCOD VFA -1 , respectively), the storage response of the selected MMC significantly decreased when the C/N ratio was set at the highest investigated value. Notably, an increase in this parameter also resulted in a change in the HV content in the polymer regardless the composition of the organic acids solution. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media

    International Nuclear Information System (INIS)

    Wu, Manli; Chen, Liming; Tian, Yongqiang; Ding, Yi; Dick, Warren A.

    2013-01-01

    A consortium composed of many different bacterial species is required to efficiently degrade polycyclic aromatic hydrocarbons (PAH) in oil-contaminated soil. We obtained six PAH-degrading microbial consortia from three oil-contaminated soils using two different isolation culture media. Denaturing gradient gel electrophoresis (DGGE) and sequence analyses of amplified 16s rRNA genes confirmed the bacterial community was greatly affected by both the culture medium and the soil from which the consortia were enriched. Three bacterial consortia enriched using malt yeast extract (MYE) medium showed higher degradation rates of PAHs than consortia enriched using Luria broth (LB) medium. Consortia obtained from a soil and then added back to that same soil was more effective in degrading PAHs than adding, to the same soil, consortia isolated from other, unrelated soils. This suggests that inoculum used for bioremediation should be from the same, or very similar nearby soils, as the soil that is actually being bioremediated. -- Highlights: •Six PAH-degrading microbial consortia were isolated from three oil-contaminated soils. •The bacterial community by 16s rRNA genes was affected by culture media and source soil. •Inoculum should be from the same or similar soil as the soil being bioremediated. -- Bioremediation of oil-contaminated soils was most effective when using inoculum of microbial consortia from the same or similar soil as the soil being bioremediated

  3. Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques.

    Science.gov (United States)

    Bjerrum, L; Engberg, R M; Leser, T D; Jensen, B B; Finster, K; Pedersen, K

    2006-07-01

    The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were <97% related to known cultured species. The chicken ileum was dominated by lactobacilli, whereas the cecum harbored a more diverse microbial community. The cecum was dominated by a large group of bacteria with hitherto no close cultured relatives but most closely related to Faecalibacterium prausnitzii. Approximately 49 and 20% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study of 2 different rearing systems; however, several differences were observed. For instance, Clostridium perfringens was found in significantly higher numbers in the birds from the organic farm compared with the conventional broilers, probably due to the addition of salinomycin to the conventional feed. In the ileum, the abundance of the different Lactobacillus species differed between the 2 broiler types. The culture-based and culture-independent techniques complemented each other well. Strengths and limitations of the different methods are discussed.

  4. Corporate culture and the culture of the labor collective: the methodology of distinguishing

    Directory of Open Access Journals (Sweden)

    M. Y. Dmytrenko

    2014-07-01

    The author points out the content and characteristics of corporate culture and the culture of the staff. The culture of the staff in the Late Modern constellations as well as corporate culture has both similarities and differences. Their common features are due to the influence of mass culture, subculture of the information society, organizational culture. Their differences are primarily of historical and anthropological nature. Corporate culture is defined as the essence of material, spiritual and social values created by the employees of the companies in the course of their activities and which reflect the uniqueness and individuality of this company. The author grounds the statement about the importance of working out methodological criteria for their differentiation.

  5. Microbial ecology: new insights into the great wide-open culture independent sea

    Science.gov (United States)

    Microbial communities are the basis for most, if not all, biochemical or biogeochemical functions in the environment. These environments are vastly different with respect to matrix, function, and biodiversity, and as such, present minute to stark differences in their respective microbial communities...

  6. Microbial lipid production by oleaginous yeast Cryptococcus sp. in the batch cultures using corncob hydrolysate as carbon source

    International Nuclear Information System (INIS)

    Chang, Yi-Huang; Chang, Ku-Shang; Lee, Ching-Fu; Hsu, Chuan-Liang; Huang, Cheng-Wei; Jang, Hung-Der

    2015-01-01

    To realize the feasibility of biodiesel production from high-lipid cell culture, microbial lipid production by the oleaginous yeasts was studied using glucose and sucrose as carbon source. Among the tested strains, Cryptococcus sp. SM5S05 accumulated the highest levels of intracellular lipids. The crude lipid contents of Cryptococcus sp. cultured in yeast malt agar reached 30% on a dry weight basis. The accumulation of lipids strongly depended on carbon/nitrogen ratio and nitrogen concentration. The highest content of lipids, measured at a carbon/nitrogen ratio of 60–90 and at a nitrogen concentration of 0.2%, was 60–57% lipids in the dry biomass. Batch cultures using corncob hydrolysate demonstrated that there was minimal inhibitory effect with a reducing sugar concentration of 60 g l −1 or higher. Batch cultures of Cryptococcus sp. SM5S05 in the corncob hydrolysate medium with 60 g l −1 glucose resulted in a dry biomass, lipid yields, and content of 12.6 g l −1 , 7.6 g l −1 , and 60.2%, respectively. The lipids contained mainly long-chain saturated and unsaturated fatty acids with 16 and 18 carbon atoms. The fatty acid profile of Cryptococcus oils was quite similar to that of conventional vegetable oil. The cost of lipid production could be further reduced with corncob hydrolysate being utilized as the raw material for the oleaginous yeast. The results showed that the microbial lipid from Cryptococcus sp. was a potential alternative resource for biodiesel production. - Highlights: • Microbial oil production from oleaginous yeast Cryptococcus sp. was studied. • Accumulation of lipid strongly depended on C/N ratio and nitrogen concentration. • Cultures in hydrolysate medium with 60 g/l glucose resulted in maximum lipid yields. • Maximal lipid content in the Cryptococcus sp. were 60.2% on dried weight basis

  7. Incubation of Aquilaria subintegra with Microbial Culture Supernatants Enhances Production of Volatile Compounds and Improves Quality of Agarwood Oil.

    Science.gov (United States)

    Monggoot, Sakon; Kulsing, Chadin; Wong, Yong Foo; Pripdeevech, Patcharee

    2018-06-01

    Incubation with microbial culture supernatants improved essential oil yield from Aquilaria subintegra woodchips. The harvested woodchips were incubated with de man, rogosa and sharpe (MRS) agar, yeast mold (YM) agar medium and six different microbial culture supernatants obtained from Lactobacillus bulgaricus , L. acidophilus , Streptococcus thermophilus , Lactococcus lactis , Saccharomyces carlsbergensis and S. cerevisiae prior to hydrodistillation. Incubation with lactic acid bacteria supernatants provided higher yield of agarwood oil (0.45% w/w) than that obtained from yeast (0.25% w/w), agar media (0.23% w/w) and water (0.22% w/w). The composition of agarwood oil from all media and microbial supernatant incubations was investigated by using gas chromatography-mass spectrometry. Overall, three major volatile profiles were obtained, which corresponded to water soaking (control), as well as, both YM and MRS media, lactic acid bacteria, and yeast supernatant incubations. Sesquiterpenes and their oxygenated derivatives were key components of agarwood oil. Fifty-two volatile components were tentatively identified in all samples. Beta-agarofuran, α-eudesmol, karanone, α-agarofuran and agarospirol were major components present in most of the incubated samples, while S. cerevisiae -incubated A. subintegra provided higher amount of phenyl acetaldehyde. Microbial culture supernatant incubation numerically provided the highest yield of agarwood oil compared to water soaking traditional method, possibly resulting from activity of extracellular enzymes produced by the microbes. Incubation of agarwood with lactic acid bacteria supernatant significantly enhanced oil yields without changing volatile profile/composition of agarwood essential oil, thus this is a promising method for future use.

  8. Nostalgia, irony and collectivity in late-modern culture

    DEFF Research Database (Denmark)

    Schiermer, Bjørn; Carlsen, Hjalmar Bang

    2017-01-01

    The paper seeks to promote a sociological understanding of the current wave of nostalgic expressions haunting late-modern Western culture and to re-evaluate the predominantly negative assessment of nostalgia. Filling two gaps in the existing research on nostalgia, the authors wish (1) to reintegr...... to ritual, we seek to erect a theoretical framework apt for articulating mediated forms of nostalgic ritual. Fourth, we use our theoretical framework to analyse a well-known instance of nostalgic ritual in Scandinavia: The Disney Christmas Show....

  9. Microbial profile of the vitreous aspirates in culture proven exogenous endophthalmitis: A 10-year retrospective study

    Directory of Open Access Journals (Sweden)

    H Bhattacharjee

    2016-01-01

    Full Text Available Purpose: To describe the microbiological profile and clinical outcome in the eyes with culture-proven exogenous endophthalmitis. Methods: A retrospective analysis of 495 eyes diagnosed as exogenous endophthalmitis was performed over a period of 10 years. In all, aseptically collected aqueous and vitreous aspirates were cultured for bacteria and fungus using standard microbiological techniques. Gram-stain and KOH preparation of the specimens were also performed. The antibiotic susceptibility testing for bacterial isolates was performed by Kirby-Bauer disk diffusion method. The treatment was modified according to the antibiotic sensitivity profile. The final clinical ocular condition was divided into improved, stable or deteriorated. Results: Of 148 culture-proven endophthalmitis eyes, 137 (92.57% were referred from elsewhere, and 11 (7.43% belonged to our institute. Aetiologically, 76 (51.35% eyes were post-cataract surgery, 61 (41.22% were post-traumatic, 5 (3.38% eyes post-intravitreal anti-vascular endothelial growth factor injection, 5 associated with corneal diseases and 1 bleb-related endophthalmitis. In 31 (20.95% eyes, primary intravitreal antibiotics were given outside. The cultures revealed monomicrobial growth in 92.57% (n = 137 and polymicrobial growth in 7.43% (n = 11. Among the bacteria (n = 121, 81.76%, Pseudomonas species dominated overall (n = 32, 27.11% and post-operative (n = 26, 38.23% endophthalmitis group. Staphylococcus epidermidis (n = 14, 28% was prominent in post-traumatic endophthalmitis group. Ninety-two percent (n = 108 isolates of bacteria were sensitive to vancomycin. In 78 (52.7% eyes, the clinical ocular condition improved or remained stable while deteriorated in 51 (34.46%. Conclusion: A bacterial predominance was observed among causative organisms of exogenous endophthalmitis with Pseudomonas species being the most common. The appropriate surgical intervention improved or stabilised the visual acuity in nearly

  10. Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.

    Science.gov (United States)

    Orphan, V J; Taylor, L T; Hafenbradl, D; Delong, E F

    2000-02-01

    Recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. In this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in California. Enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees C. Heterotrophic enrichments from all sites yielded sheathed rods (Thermotogales), pleomorphic rods resembling Thermoanaerobacter, and Thermococcus-like isolates. The predominant autotrophic microorganisms recovered from inorganic enrichments using H(2), acetate, and CO(2) as energy and carbon sources were methanogens, including isolates closely related to Methanobacterium, Methanococcus, and Methanoculleus species. Two 16S rRNA gene (rDNA) libraries were generated from total community DNA collected from production wellheads, using either archaeal or universal oligonucleotide primer sets. Sequence analysis of the universal library indicated that a large percentage of clones were highly similar to known bacterial and archaeal isolates recovered from similar habitats. Represented genera in rDNA clone libraries included Thermoanaerobacter, Thermococcus, Desulfothiovibrio, Aminobacterium, Acidaminococcus, Pseudomonas, Halomonas, Acinetobacter, Sphingomonas, Methylobacterium, and Desulfomicrobium. The archaeal library was dominated by methanogen-like rDNAs, with a lower percentage of clones belonging to the Thermococcales. Our results strongly support the hypothesis that sulfur-utilizing and methane-producing thermophilic microorganisms have a widespread distribution in oil reservoirs and the potential to actively participate in the biogeochemical transformation of carbon, hydrogen, and sulfur in situ.

  11. Effect of changing temperature on anaerobic hydrogen production and microbial community composition in an open-mixed culture bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Karadag, Dogan; Puhakka, Jaakko A. [Department of Chemistry and Bioengineering, Tampere University of Technology, Tampere (Finland)

    2010-10-15

    The temperature effect (37-65 C) on H{sub 2} production from glucose in an open-mixed culture bioreactor using an enrichment culture from a hot spring was studied. The dynamics of microbial communities was investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). At 45 and 60 C the H{sub 2} production was the highest i.e. 1.71 and 0.85 mol H{sub 2}/mol glucose, respectively. No H{sub 2} was produced at temperatures 50 and 55 C. At 37-45 C, H{sub 2} production was produced by butyrate type fermentation while fermentation mechanism changed to ethanol type at 60 C. Clostridium species were dominant at 37-45 C while at 50-55 C and 60 C the culture was dominated by Bacillus coagulans and Thermoanaerobacterium, respectively. In the presence of B. Coagulans the metabolism was directed to lactate production. The results show that the mixed culture had two optima for H{sub 2} production and that the microbial communities and metabolic patterns promptly changed according to changing temperatures. (author)

  12. Cultural Characteristics of Ophiocordyceps heteropoda Collected from Korea

    OpenAIRE

    Sung, Gi-Ho; Shrestha, Bhushan; Han, Sang-Kuk; Sung, Jae-Mo

    2011-01-01

    Isolates of Ophiocordyceps heteropoda (Kobayasi) collected from Mt. Halla on Jeju-do, Korea were tested for mycelial growth on different agar media and in the presence of different carbon and nitrogen sources. Similarly, isolates were also incubated at different temperatures as well as under continuous light and dark conditions. Growth was better on Hamada agar, basal medium, and malt-yeast agar, but poor on Czapek-Dox agar. Different carbon sources such as dextrin, saccharose, starch, lactos...

  13. Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection

    Science.gov (United States)

    Simões, Marta F.; Dias, Nicolina; Santos, Cledir; Lima, Nelson

    2016-01-01

    Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders. PMID:27681915

  14. Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection

    KAUST Repository

    Simoes, Marta

    2016-06-22

    Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders.

  15. Establishment of a Quality Management System Based on ISO 9001 Standard in a Public Service Fungal Culture Collection.

    Science.gov (United States)

    Simões, Marta F; Dias, Nicolina; Santos, Cledir; Lima, Nelson

    2016-06-22

    Collaborations between different Microbiological Resource Centres (mBRCs) and ethical sourcing practices are mandatory to guarantee biodiversity conservation, successful and sustainable preservation and fair share of benefits that arise from the use of genetic resources. Since microbial Culture Collections (CCs) are now engaged in meeting high quality operational standards, they are facing the challenge of establishing quality control criteria to certify their biological materials. The authentication/certification of strains is nowadays a demand from the bioeconomy sector for the global operation of mBRCs. The achievement of consistent quality assurance and trust within the mBRCs and microbial CCs context is a dynamic and never-ending process. A good option to facilitate that process is to implement a Quality Management System (QMS) based on the ISO 9001 standard. Here, we report a detailed description of all the steps taken for the QMS implementation at the Portuguese CC of filamentous fungi: Micoteca da Universidade do Minho (MUM). Our aim is to provide guidelines for the certification of other CCs, so that they can also enhance the search and choice of the most consistent, reliable, and effective operating methods, with assured procedures and validation of preservation; and guarantee trustworthy relations with all stakeholders.

  16. Applicability of Baumrind's Parent Typology to Collective Cultures: Analysis of Cultural Explanations of Parent Socialization Effects

    Science.gov (United States)

    Sorkhabi, Nadia

    2005-01-01

    This article reviews studies that have examined whether Baumrind's parenting styles are related to child outcomes similarly in cultures where independence is said to be emphasized versus cultures where interdependence is said to be emphasized. I present evidence showing that Baumrind's parenting styles have similar function in both collectivist…

  17. Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method.

    Science.gov (United States)

    Takahashi, M; Kita, Y; Kusaka, K; Mizuno, A; Goto-Yamamoto, N

    2015-02-01

    In the brewing industry, microbial management is very important for stabilizing the quality of the product. We investigated the detailed microbial community of beer during fermentation and maturation, to manage beer microbiology in more detail. We brewed a beer (all-malt) and two beerlike beverages (half- and low-malt) in pilot-scale fermentation and investigated the microbial community of them using a next-generation sequencer (454 GS FLX titanium), quantitative PCR, flow cytometry and a culture-dependent method. From 28 to 88 genera of bacteria and from 9 to 38 genera of eukaryotic micro-organisms were detected in each sample. Almost all micro-organisms died out during the boiling process. However, bacteria belonging to the genera Acidovorax, Bacillus, Brevundimonas, Caulobacter, Chryseobacterium, Methylobacterium, Paenibacillus, Polaromonas, Pseudomonas, Ralstonia, Sphingomonas, Stenotrophomonas, Tepidimonas and Tissierella were detected at the early and middle stage of fermentation, even though their cell densities were low (below approx. 10(3) cells ml(-1) ) and they were not almost detected at the end of fermentation. We revealed that the microbial community of beer during fermentation and maturation is very diverse and several bacteria possibly survive during fermentation. In this study, we revealed the detailed microbial communities of beer using next-generation sequencing. Some of the micro-organisms detected in this study were found in beer brewing process for the first time. Additionally, the possibility of growth of several bacteria at the early and middle stage of fermentation was suggested. © 2014 The Society for Applied Microbiology.

  18. Bottoms Up! Secrets to Overcoming Cultural Barriers for Data Collection in Vietnam

    DEFF Research Database (Denmark)

    Phi, Giang

    2018-01-01

    Qualitative data collection in remote areas of Asia can be rather challenging, especially when the researchers come from very different cultural backgrounds to the participants and the research topics centre on sensitive issues such as poverty....

  19. Equality bias impairs collective decision-making across cultures.

    Science.gov (United States)

    Mahmoodi, Ali; Bang, Dan; Olsen, Karsten; Zhao, Yuanyuan Aimee; Shi, Zhenhao; Broberg, Kristina; Safavi, Shervin; Han, Shihui; Nili Ahmadabadi, Majid; Frith, Chris D; Roepstorff, Andreas; Rees, Geraint; Bahrami, Bahador

    2015-03-24

    We tend to think that everyone deserves an equal say in a debate. This seemingly innocuous assumption can be damaging when we make decisions together as part of a group. To make optimal decisions, group members should weight their differing opinions according to how competent they are relative to one another; whenever they differ in competence, an equal weighting is suboptimal. Here, we asked how people deal with individual differences in competence in the context of a collective perceptual decision-making task. We developed a metric for estimating how participants weight their partner's opinion relative to their own and compared this weighting to an optimal benchmark. Replicated across three countries (Denmark, Iran, and China), we show that participants assigned nearly equal weights to each other's opinions regardless of true differences in their competence-even when informed by explicit feedback about their competence gap or under monetary incentives to maximize collective accuracy. This equality bias, whereby people behave as if they are as good or as bad as their partner, is particularly costly for a group when a competence gap separates its members.

  20. Examination of a Culturable Microbial Population from the Gastrointestinal Tract of the Wood-Eating Loricariid Catfish Panaque nigrolineatus

    Directory of Open Access Journals (Sweden)

    Harold J. Schreier

    2013-08-01

    Full Text Available Fish play a critical role in nutrient cycling and organic matter flow in aquatic environments. However, little is known about the microbial diversity within the gastrointestinal tracts that may be essential in these degradation activities. Panaque nigrolineatus is a loricariid catfish found in the Neotropics that have a rare dietary strategy of consuming large amounts of woody material in its natural environment. As a consequence, the gastrointestinal (GI tract of P. nigrolineatus is continually exposed to high levels of cellulose and other recalcitrant wood compounds and is, therefore, an attractive, uncharacterized system to study microbial community diversity. Our previous 16S rRNA gene surveys demonstrated that the GI tract microbial community includes phylotypes having the capacity to degrade cellulose and fix molecular nitrogen. In the present study we verify the presence of a resident microbial community by fluorescence microscopy and focus on the cellulose-degrading members by culture-based and 13C-labeled cellulose DNA stable-isotope probing (SIP approaches. Analysis of GI tract communities generated from anaerobic microcrystalline cellulose enrichment cultures by 16S rRNA gene analysis revealed phylotypes sharing high sequence similarity to known cellulolytic bacteria including Clostridium, Cellulomonas, Bacteroides, Eubacterium and Aeromonas spp. Related bacteria were identified in the SIP community, which also included nitrogen-fixing Azospirillum spp. Our ability to enrich for specialized cellulose-degrading communities suggests that the P. nigrolineatus GI tract provides a favorable environment for this activity and these communities may be involved in providing assimilable carbon under challenging dietary conditions.

  1. Digital Forensics and Born-Digital Content in Cultural Heritage Collections. CLIR Publication No. 149

    Science.gov (United States)

    Kirschenbaum, Matthew G.; Ovenden, Richard; Redwine, Gabriela

    2010-01-01

    The purpose of this report is twofold: first, to introduce the field of digital forensics to professionals in the cultural heritage sector; and second, to explore some particular points of convergence between the interests of those charged with collecting and maintaining born-digital cultural heritage materials and those charged with collecting…

  2. Collective Pedagogical Teacher Culture and Mathematics Achievement: Differences by Race, Ethnicity, and Socioeconomic Status

    Science.gov (United States)

    Moller, Stephanie; Mickelson, Roslyn Arlin; Stearns, Elizabeth; Banerjee, Neena; Bottia, Martha Cecilia

    2013-01-01

    Scholars have not adequately assessed how organizational cultures in schools differentially influence students' mathematics achievement by race and socioeconomic status (SES). We focus on what we term "collective pedagogical teacher culture", highlighting the role of professional communities and teacher collaboration in influencing…

  3. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia.

    Science.gov (United States)

    Entcheva, P; Liebl, W; Johann, A; Hartsch, T; Streit, W R

    2001-01-01

    Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Delta(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to bio operons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

  4. Acting and Collecting: Imagining Asia through material culture and musical theatre

    OpenAIRE

    Peter Thorley

    2015-01-01

    This paper explores the link between Asian-inspired material culture and musical theatre through the collections of Anglo-Australian performer Herbert Browne (1895-1975). Brown played lead roles in 1920s Australian musical theatre productions of The Mikado and Chu Chin Chow and re-lived his connection with oriental theatre by collecting and responding to objects performatively in the Chinoiserie room of his Melbourne home. Oriental musical theatre blended exotic cultures and locales in visual...

  5. Title: Effect of abiotic stress on reduction of microbial contamination ...

    African Journals Online (AJOL)

    TERI

    2016-03-23

    Mar 23, 2016 ... to 36% reduced microbial contamination in aseptic culture establishment ... collected from farmer's field of Assam, India. .... Average weight loss (%) ± SE. 0 .... Asian J. Plant Sci. 6:496-501. Holdgate DP, Zandvoort EA (1997).

  6. A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures.

    Science.gov (United States)

    Mazzoleni, Stefano; Landi, Carmine; Cartenì, Fabrizio; de Alteriis, Elisabetta; Giannino, Francesco; Paciello, Lucia; Parascandola, Palma

    2015-07-30

    Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new experiments of yeast growth in batch and fed-batch cultures. Model and experimental results showed that the growth decline observed in prolonged fed-batch cultures had to be ascribed to self-produced inhibitory compounds other than ethanol. The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.

  7. Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques

    DEFF Research Database (Denmark)

    Friis-Holm, Lotte Bjerrum; Engberg, R.M.; Leser, T.D.

    2006-01-01

    The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were ...% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study...

  8. Crosstalk Regulates the Capacity for Robust Collective Decision Making in Heterogeneous Microbial Communities

    Science.gov (United States)

    Yusufaly, Tahir; Boedicker, James

    Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating density-dependent gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where crosstalk between distinct QS systems leads to novel effects. Such knowledge is necessary both for understanding signaling in real microbial communities, and for the rational design of synthetic communities with designer properties. As a step towards this goal, we investigate the effects of crosstalk between Gram-negative bacteria communicating via LuxI/LuxR-type QS systems, with acyl-homoserine lactone (AHL) AI molecules. After mapping QS in a heterogeneous community onto an artificial neural network model, we systematically analyze how heterogeneity regulates the community's capability for stable yet flexible decision making. We find that there are preferred distributions of interactions which provide optimal tradeoffs between capacity, or the number of different decisions a population can make, and robustness, or the tolerance of the community to disturbances. We compare our results to inferences made from experimental data, and critically discuss implications for the biological significance of crosstalk.

  9. The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

    Science.gov (United States)

    Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

    2018-06-01

    Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture

  10. The Chinese-Indonesian collections in the National Museum of World Cultures, the Netherlands

    Directory of Open Access Journals (Sweden)

    Francine Brinkgreve

    2017-05-01

    Full Text Available Among the more than 130,000 objects from Indonesia in the Dutch National Museum of World Cultures, many once belonged to or were used by the Chinese population of Indonesia. In this article, the authors provide an overview of these collections by presenting their collecting histories from the earliest acquisitions to the most recent collections and by highlighting a number of objects, which in their materials, techniques, motifs, colours or function show a combination of elements from both Chinese and Indonesian cultures. The authors pay particular attention to objects which play a role in the Chinese-Indonesian wedding ceremony.

  11. Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures.

    Science.gov (United States)

    Hanly, Timothy J; Henson, Michael A

    2011-02-01

    Sequential uptake of pentose and hexose sugars that compose lignocellulosic biomass limits the ability of pure microbial cultures to efficiently produce value-added bioproducts. In this work, we used dynamic flux balance modeling to examine the capability of mixed cultures of substrate-selective microbes to improve the utilization of glucose/xylose mixtures and to convert these mixed substrates into products. Co-culture simulations of Escherichia coli strains ALS1008 and ZSC113, engineered for glucose and xylose only uptake respectively, indicated that improvements in batch substrate consumption observed in previous experimental studies resulted primarily from an increase in ZSC113 xylose uptake relative to wild-type E. coli. The E. coli strain ZSC113 engineered for the elimination of glucose uptake was computationally co-cultured with wild-type Saccharomyces cerevisiae, which can only metabolize glucose, to determine if the co-culture was capable of enhanced ethanol production compared to pure cultures of wild-type E. coli and the S. cerevisiae strain RWB218 engineered for combined glucose and xylose uptake. Under the simplifying assumption that both microbes grow optimally under common environmental conditions, optimization of the strain inoculum and the aerobic to anaerobic switching time produced an almost twofold increase in ethanol productivity over the pure cultures. To examine the effect of reduced strain growth rates at non-optimal pH and temperature values, a break even analysis was performed to determine possible reductions in individual strain substrate uptake rates that resulted in the same predicted ethanol productivity as the best pure culture. © 2010 Wiley Periodicals, Inc.

  12. LIIS: A web-based system for culture collections and sample annotation

    Directory of Open Access Journals (Sweden)

    Matthew S Forster

    2014-04-01

    Full Text Available The Lab Information Indexing System (LIIS is a web-driven database application for laboratories looking to store their sample or culture metadata on a central server. The design was driven by a need to replace traditional paper storage with an easier to search format, and extend current spreadsheet storage methods. The system supports the import and export of CSV spreadsheets, and stores general metadata designed to complement the environmental packages provided by the Genomic Standards Consortium. The goals of the LIIS are to simplify the storage and archival processes and to provide an easy to access library of laboratory annotations. The program will find utility in microbial ecology laboratories or any lab that needs to annotate samples/cultures.

  13. Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

    Science.gov (United States)

    Jahnke, Linda L.; Edger, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; DesMarais, David J.; Cady, Sherry; Hope, Janet M.; Summons, Roger E.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarkers and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber. "Thermocrinis sp. HI", Hydrogenobacter thermophilus TK-6, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyls. The fatty acids of all cultured organisms were dominated by a very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as CIS() monoethers with the expection of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known 'pink-streamers community' (PSC), siliceous filaments of a microbial consortia growing in the upper outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic Aquificales n-C-20:1 and cy-C-21, and in addition, a series of iso-branched fatty acids from i-C-15:0 to i-C-21:0, With i-C-17:0 dominant in the PSC and i-C-19:0 in the biofilm, suggesting the presence of two major bacterial groups. Bacteriohopanepolyols were absent and the minute quantities of archaeol detected showed that Archaea were only minor constituents. Carbon isotopic compositions of the PSC yielded information about community structure and likely physiology. Biomass was C-13-depleted (10.9%) relative to available

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

    NARCIS (Netherlands)

    Sutton, N.B.; Atashgahi, S.; Saccenti, E.; Grotenhuis, J.T.C.; Smidt, H.; Rijnaarts, H.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

  15. Utilizing a Robotic Sprayer for High Lateral and Mass Resolution MALDI FT-ICR MSI of Microbial Cultures

    Energy Technology Data Exchange (ETDEWEB)

    Anderton, Christopher R.; Chu, Rosalie K.; Tolic, Nikola; Creissen, Alain V.; Pasa-Tolic, Ljiljana

    2016-01-07

    The ability to visualize biochemical interactions between microbial communities using MALDI MSI has provided tremendous insights into a variety of biological fields. Matrix application using a sieve proved to be incredibly useful, but it had many limitations that include uneven matrix coverage and limitation in the types of matrices one could employ in their studies. Recently, there has been a concerted effort to improve matrix application for studying agar plated microbial cultures, many of which utilized automated matrix sprayers. Here, we describe the usefulness of using a robotic sprayer for matrix application. The robotic sprayer has two-dimensional control over where matrix is applied and a heated capillary that allows for rapid drying of the applied matrix. This method provided a significant increase in MALDI sensitivity over the sieve method, as demonstrated by FT-ICR MS analysis, facilitating the ability to gain higher lateral resolution MS images of Bacillus Subtilis than previously reported. This method also allowed for the use of different matrices to be applied to the culture surfaces.

  16. Effectiveness of a Novel Specimen Collection System in Reducing Blood Culture Contamination Rates.

    Science.gov (United States)

    Bell, Mary; Bogar, Catherine; Plante, Jessica; Rasmussen, Kristen; Winters, Sharon

    2018-04-20

    False-positive blood-culture results due to skin contamination of samples remain a persistent problem for health care providers. Our health system recognized that our rates of contamination across the 4 emergency department campuses were above the national average. A unique specimen collection system was implemented throughout the 4 emergency departments and became the mandatory way to collect adult blood cultures. The microbiology laboratory reported contamination rates weekly to manage potential problems; 7 months of data are presented here. There was an 82.8% reduction in false positives with the unique specimen collection system compared with the standard method (chi-squared test with Yates correction, 2-tailed, P = 0.0001). Based on the historical 3.52% rate of blood-culture contamination for our health facilities, 2.92 false positives were prevented for every 100 blood cultures drawn, resulting from adoption of the unique specimen collection system as the standard of care. This unique collection system can reduce the risk of blood culture contamination significantly and is designed to augment, rather than replace, the standard phlebotomy protocol already in use in most health care settings. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Microbial diversity in firework chemical exposed soil and water samples collected in Virudhunagar district, Tamil Nadu, India.

    Science.gov (United States)

    Dhasarathan, P; Theriappan, P; Ashokraja, C

    2010-03-01

    Microbial diversity of soil and water samples collected from pyrochemicals exposed areas of Virdhunagar district (Tamil Nadu, India) was studied. Soil and water samples from cultivable area, waste land and city area of the same region were also studied for a comparative acount. There is a remarkable reduction in total heterotrophic bacterial population (THB) in pyrochemicals exposed soil and water samples (42 × 10(4) CFU/g and 5.6 × 10(4) CFU/ml respectively), compared to the THB of cultivable area soil and water samples (98 × 10(7) CFU/g and 38.6 × 10(7) CFU/ml). The generic composition the THB of the pyrochemicals exposed samples too exhibited considerable change compared to other samples. Pseudomonas sp. was the predominant one (41.6%) followed by Achromobacter sp. (25%) in pyrochemical exposed soil and Pseudomonas sp. was the predominant one (25%) in pyrochemical exposed water samples followed by Bacillus sp. (25%) and Micrococcus sp. (16.6%). It was observed that Cornybacterium sp. and Micrococcus sp. were absent completely in pyrochemical exposed soil and Achromobacter sp. was missing in the pyrochemical exposed water samples, which were present in the other samples. The outcome of this study clearly demonstrates that pollutants such as chemicals used in pyrotechniques affect the microbial biodiversity and suitable measures have to be taken to control the pollution level and to save biodiversity.

  18. KACC: An identification and characterization for microbial resources ...

    African Journals Online (AJOL)

    Korean Agricultural Culture Collection (KACC) is an authorized organizer and the official depository for microbial resources in Korea. The KACC has developed a web-based database system to provide integrated information about microbial resources. It includes not only simple text information on individual microbe but ...

  19. Producing health, producing safety. Developing a collective safety culture in radiotherapy

    International Nuclear Information System (INIS)

    Nascimento, Adelaide

    2009-01-01

    This research thesis aims at a better understanding of safety management in radiotherapy and at proposing improvements for patient safety through the development of a collective safety culture. A first part presents the current context in France and abroad, addresses the transposition of other safety methods to the medical domain, and discusses the peculiarities of radiotherapy in terms of risks and the existing quality-assurance approaches. The second part presents the theoretical framework by commenting the intellectual evolution with respect to system safety and the emergence of the concept of safety culture, and by presenting the labour collective aspects and their relationship with system safety. The author then comments the variety of safety cultures among the different professions present in radiotherapy, highlights the importance of the collective dimension in correcting discrepancies at the end of the treatment process, and highlights how physicians take their colleagues work into account. Recommendations are made to improve patient safety in radiotherapy

  20. A vast collection of microbial genes that are toxic to bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Kimelman, Aya; Levy, Asaf; Sberro, Hila; Kidron, Shahar; Leavitt, Azita; Amitai, Gil; Yoder-Himes, Deborah; Wurtzel, Omri; Zhu, Yiwen; Rubin, Edward M; Sorek, Rotem

    2012-02-02

    In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes our assays revealed novel toxins and restriction enzymes, and new classes of small non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short toxic DNA fragments that were predicted to suppress E. coli growth by interacting with the replication initiator dnaA. Our results show that cloning gaps, once considered the result of technical problems, actually serve as a rich source for the discovery of biotechnologically valuable functions, and suggest new modes of antimicrobial interventions.

  1. Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities

    Science.gov (United States)

    Yusufaly, Tahir I.; Boedicker, James Q.

    2017-08-01

    Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. AI molecules bind to ‘cognate’ receptors, but also to ‘non-cognate’ receptors found in other strains, resulting in inter-strain crosstalk. Understanding these interactions is a prerequisite for deciphering the consequences of crosstalk in real ecosystems, where multiple AIs are regularly present in the same environment. As a step towards this goal, we map crosstalk in a heterogeneous community of variant QS strains onto an artificial neural network model. This formulation allows us to systematically analyze how crosstalk regulates the community’s capacity for flexible decision making, as quantified by the Boltzmann entropy of all QS gene expression states of the system. In a mean-field limit of complete cross-inhibition between variant strains, the model is exactly solvable, allowing for an analytical formula for the number of variants that maximize capacity as a function of signal kinetics and activation parameters. An analysis of previous experimental results on the Staphylococcus aureus two-component Agr system indicates that the observed combination of variant numbers, gene expression rates and threshold concentrations lies near this critical regime of parameter space where capacity peaks. The results are suggestive of a potential evolutionary driving force for diversification in certain QS systems.

  2. Characterization of Microbial Communities in Chinese Rice Wine Collected at Yichang City and Suzhou City in China.

    Science.gov (United States)

    Lü, Yucai; Gong, Yanli; Li, Yajie; Pan, Zejiang; Yao, Yi; Li, Ning; Guo, Jinling; Gong, Dachun; Tian, Yihong; Peng, Caiyun

    2017-08-28

    Two typical microbial communities from Chinese rice wine fermentation collected in Yichang city and Suzhou city in China were investigated. Both communities could ferment glutinous rice to rice wine in 2 days. The sugar and ethanol contents were 198.67 and 14.47 mg/g, respectively, for rice wine from Yichang city, and 292.50 and 12.31 mg/g, respectively, for rice wine from Suzhou city. Acetic acid and lactic acid were the most abundant organic acids. Abundant fungi and bacteria were detected in both communities by high-throughput sequencing. Saccharomycopsis fibuligera and Rhizopus oryzae were the dominant fungi in rice wine from Suzhou city, compared with R. oryzae , Wickerhamomyces anomalus, Saccharomyces cerevisiae, Mucor indicus , and Rhizopus microsporus in rice wine from Yichang city. Bacterial diversity was greater than fungal diversity in both communities. Citrobacter was the most abundant genus. Furthermore, Exiguobacterium, Aeromonas, Acinetobacter, Pseudomonas, Enterobacter, Bacillus , and Lactococcus were highly abundant in both communities.

  3. A simple laser-based device for simultaneous microbial culture and absorbance measurement

    Science.gov (United States)

    Abrevaya, X. C.; Cortón, E.; Areso, O.; Mauas, P. J. D.

    2013-07-01

    In this work we present a device specifically designed to study microbial growth with several applications related to environmental microbiology and other areas of research as astrobiology. The Automated Measuring and Cultivation device (AMC-d) enables semi-continuous absorbance measurements directly during cultivation. It can measure simultaneously up to 16 samples. Growth curves using low and fast growing microorganism were plotted, including Escherichia coli and Haloferax volcanii, a halophilic archaeon.

  4. A Simple Laser-Based Device for Simultaneous Microbial Culture and Absorbance Measurement

    OpenAIRE

    Abrevaya, X. C.; Cortón, E.; Areso, O.; Mauas, P. J. D.

    2012-01-01

    In this work we present a device specifically designed to study microbial growth with several applications related to environmental microbiology and other areas of research as astrobiology. The Automated Measuring and Cultivation device (AMC-d) enables semi-continuous absorbance measurements directly during cultivation. It can measure simultaneously up to 16 samples. Growth curves using low and fast growing microorganism were plotted, including Escherichia coli and Haloferax volcanii, a halop...

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

    Science.gov (United States)

    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

  6. Egypt’s Red Sea Coast: Phylogenetic analysis of cultured microbial consortia in industrialized sites

    Directory of Open Access Journals (Sweden)

    Ghada A. Mustafa

    2014-08-01

    Full Text Available The Red Sea has a unique geography and ecosystem and its shores are very rich in mangrove, macro-algae and coral reefs. Different sources of pollution are affecting the Red Sea shores and waters which impacts biological life including microbial life. We assessed the effects of industrialization, along the Egyptian Red Sea coast in eight coastal sites and two lakes, on microbial life. The bacterial community in sediment samples was analyzed using bacterial 16S rDNApyrosequencing of V6-V4 hypervariable regions. Taxonomical assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled Red Sea sites. This includes Proteobacteria (68%, Firmicutes (13%, Fusobacteria (12%, Bacteriodetes (6% and Spirochetes (0.03%. Further analysis revealed distinct bacterial consortium formed mainly of: 1 marine Vibrio’s- suggesting a Marine Vibrio phenomenon 2 potential human pathogens and 3 oil-degrading bacteria. We discuss a distinct microbial consortium in Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; revealing the highest abundance of human pathogens versus no pathogens, respectively. Our results draw attention to the affects of industrialization on the Red Sea, and suggest further analysis to overcome hazardous affects on the impacted sites.

  7. Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity.

    Science.gov (United States)

    Velmourougane, Kulandaivelu

    2016-01-01

    A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system.

  8. Characterization of fungi in office dust: Comparing results of microbial secondary metabolites, fungal internal transcribed spacer region sequencing, viable culture and other microbial indices.

    Science.gov (United States)

    Park, J-H; Sulyok, M; Lemons, A R; Green, B J; Cox-Ganser, J M

    2018-05-04

    Recent developments in molecular and chemical methods have enabled the analysis of fungal DNA and secondary metabolites, often produced during fungal growth, in environmental samples. We compared 3 fungal analytical methods by analysing floor dust samples collected from an office building for fungi using viable culture, internal transcribed spacer (ITS) sequencing and secondary metabolites using liquid chromatography-tandem mass spectrometry. Of the 32 metabolites identified, 29 had a potential link to fungi with levels ranging from 0.04 (minimum for alternariol monomethylether) to 5700 ng/g (maximum for neoechinulin A). The number of fungal metabolites quantified per sample ranged from 8 to 16 (average = 13/sample). We identified 216 fungal operational taxonomic units (OTUs) with the number per sample ranging from 6 to 29 (average = 18/sample). We identified 37 fungal species using culture, and the number per sample ranged from 2 to 13 (average = 8/sample). Agreement in identification between ITS sequencing and culturing was weak (kappa = -0.12 to 0.27). The number of cultured fungal species poorly correlated with OTUs, which did not correlate with the number of metabolites. These suggest that using multiple measurement methods may provide an improved understanding of fungal exposures in indoor environments and that secondary metabolites may be considered as an additional source of exposure. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Culturable microbial diversity and the impact of tourism in Kartchner Caverns, Arizona.

    Science.gov (United States)

    Ikner, Luisa A; Toomey, Rickard S; Nolan, Ginger; Neilson, Julia W; Pryor, Barry M; Maier, Raina M

    2007-01-01

    Kartchner Caverns in Benson, AZ, was opened for tourism in 1999 after a careful development protocol that was designed to maintain predevelopment conditions. As a part of an ongoing effort to determine the impact of humans on this limestone cave, samples were collected from cave rock surfaces along the cave trail traveled daily by tour groups (200,000 visitors year-1) and compared to samples taken from areas designated as having medium (30-40 visitors year-1) and low (2-3 visitors year-1) levels of human exposure. Samples were also taken from fiberglass moldings installed during cave development. Culturable bacteria were recovered from these samples and 90 unique isolates were identified by using 16S rRNA polymerase chain reaction and sequencing. Diversity generally decreased as human impact increased leading to the isolation of 32, 27, and 22 strains from the low, medium, and high impact areas, respectively. The degree of human impact was also reflected in the phylogeny of the isolates recovered. Although most isolates fell into one of three phyla: Actinobacteria, Firmicutes, or Proteobacteria, the Proteobacteria were most abundant along the cave trail (77% of the isolates), while Firmicutes predominated in the low (66%) and medium (52%) impact areas. Although the abundance of Proteobacteria along the cave trail seems to include microbes of environmental rather than of anthropogenic origin, it is likely that their presence is a consequence of increased organic matter availability due to lint and other organics brought in by cave visitors. Monitoring of the cave is still in progress to determine whether these bacterial community changes may impact the future development of cave formations.

  10. Substrate interactions of benzene, toluene, and para-xylene during microbial degradation by pure cultures and mixed culture aquifer slurries

    International Nuclear Information System (INIS)

    Alvarez, P.J.J.; Vogel, T.M.

    1991-01-01

    Release of petroleum hydrocarbons in the environment is a widespread occurrence. One particular concern is the contamination of drinking water sources by the toxic, water-soluble, and mobile petroleum components benzene, toluene, and xylene (BTX). Benzene, toluene, and p-xylene (BTX) were degraded by indigenous mixed cultures in sandy aquifer material and by two pure cultures isolated from the same site. Although BTX compounds have a similar chemical structure, the fate of individual BTX compounds differed when the compounds were fed to each pure culture and mixed culture aquifer slurries. The identification of substrate interactions aided the understanding of this behavior. Beneficial substrate interactions included enhanced degradation of benzene-dependent degradation of toluene and p-xylene by Arthrobacter sp. strain HCB. Detrimental substrate interactions included retardation in benzene and toluene degradation by the presence of p-xylene in both aquifer slurries and Pseudomonas incubations. The catabolic diversity of microbes in the environment precludes generalizations about the capacity of individual BTX compounds to enhance or inhibit the degradation of other BTX compounds

  11. Mapping the microbial universe : the importance of living collections for fungal systematics

    Science.gov (United States)

    F.M. Dugan; K.K. Nakasone

    1998-01-01

    The destruction of natural habitats has motivated scientists and environmentalists to collect, measure, and--one hopes--ultimately preserve as much of this planet's diverse biota as possible. Simultaneously, growing human populations have impelled research into how components of this biota can be manipulated to avert a crisis in human food, shelter, and health....

  12. Reconciling long-term cultural diversity and short-term collective social behavior.

    Science.gov (United States)

    Valori, Luca; Picciolo, Francesco; Allansdottir, Agnes; Garlaschelli, Diego

    2012-01-24

    An outstanding open problem is whether collective social phenomena occurring over short timescales can systematically reduce cultural heterogeneity in the long run, and whether offline and online human interactions contribute differently to the process. Theoretical models suggest that short-term collective behavior and long-term cultural diversity are mutually excluding, since they require very different levels of social influence. The latter jointly depends on two factors: the topology of the underlying social network and the overlap between individuals in multidimensional cultural space. However, while the empirical properties of social networks are intensively studied, little is known about the large-scale organization of real societies in cultural space, so that random input specifications are necessarily used in models. Here we use a large dataset to perform a high-dimensional analysis of the scientific beliefs of thousands of Europeans. We find that interopinion correlations determine a nontrivial ultrametric hierarchy of individuals in cultural space. When empirical data are used as inputs in models, ultrametricity has strong and counterintuitive effects. On short timescales, it facilitates a symmetry-breaking phase transition triggering coordinated social behavior. On long timescales, it suppresses cultural convergence by restricting it within disjoint groups. Moreover, ultrametricity implies that these results are surprisingly robust to modifications of the dynamical rules considered. Thus the empirical distribution of individuals in cultural space appears to systematically optimize the coexistence of short-term collective behavior and long-term cultural diversity, which can be realized simultaneously for the same moderate level of mutual influence in a diverse range of online and offline settings.

  13. [Neuroscience and collective memory: memory schemas linking brain, societies and cultures].

    Science.gov (United States)

    Legrand, Nicolas; Gagnepain, Pierre; Peschanski, Denis; Eustache, Francis

    2015-01-01

    During the last two decades, the effect of intersubjective relationships on cognition has been an emerging topic in cognitive neurosciences leading through a so-called "social turn" to the formation of new domains integrating society and cultures to this research area. Such inquiry has been recently extended to collective memory studies. Collective memory refers to shared representations that are constitutive of the identity of a group and distributed among all its members connected by a common history. After briefly describing those evolutions in the study of human brain and behaviors, we review recent researches that have brought together cognitive psychology, neuroscience and social sciences into collective memory studies. Using the reemerging concept of memory schema, we propose a theoretical framework allowing to account for collective memories formation with a specific focus on the encoding process of historical events. We suggest that (1) if the concept of schema has been mainly used to describe rather passive framework of knowledge, such structure may also be implied in more active fashions in the understanding of significant collective events. And, (2) if some schema researches have restricted themselves to the individual level of inquiry, we describe a strong coherence between memory and cultural frameworks. Integrating the neural basis and properties of memory schema to collective memory studies may pave the way toward a better understanding of the reciprocal interaction between individual memories and cultural resources such as media or education. © Société de Biologie, 2016.

  14. The impact of culture collections on molecular identification, taxonomy, and solving real problems

    Science.gov (United States)

    Among the fungi, Fusarium has stood out as a major focus for culture collection resource development over the last century. This has facilitated unprecedented molecular taxonomic advancements, which in turn has led to problem solving in plant pathology, mycotoxicology, medical mycology, and basic re...

  15. Culture collection of fungi (CCF) in Prague – original isolates accessed during 2003-05

    Czech Academy of Sciences Publication Activity Database

    Kubátová, A.; Kolařík, Miroslav

    2006-01-01

    Roč. 18, č. 5 (2006), s. 1-15 ISSN 0862-5158 R&D Projects: GA ČR GA522/02/1206 Institutional research plan: CEZ:AV0Z50200510 Keywords : ccf * culture collection * microscopic fungi Subject RIV: EE - Microbiology, Virology

  16. Teachers' Collective Efficacy, Job Satisfaction, and Job Stress in Cross-Cultural Context

    Science.gov (United States)

    Klassen, Robert M.; Usher, Ellen L.; Bong, Mimi

    2010-01-01

    This study examines how teachers' collective efficacy (TCE), job stress, and the cultural dimension of collectivism are associated with job satisfaction for 500 teachers from Canada, Korea (South Korea or Republic of Korea), and the United States. Multigroup path analysis revealed that TCE predicted job satisfaction across settings. Job stress was…

  17. Digital Collections, Digital Libraries and the Digitization of Cultural Heritage Information.

    Science.gov (United States)

    Lynch, Clifford

    2002-01-01

    Discusses the development of digital collections and digital libraries. Topics include digitization of cultural heritage information; broadband issues; lack of compelling content; training issues; types of materials being digitized; sustainability; digital preservation; infrastructure; digital images; data mining; and future possibilities for…

  18. Effect of biofilm and selective mixed culture on microbial fuel cell for the treatment of tempeh industrial wastewater

    Science.gov (United States)

    Arbianti, Rita; Surya Utami, Tania; Leondo, Vifki; Elisabeth; Andyah Putri, Syafira; Hermansyah, Heri

    2018-03-01

    Microbial Fuel Cell (MFC) provides a new alternative in the treatment of organic waste. MFC produces 50-90% less sludge to be disposed than other methods. MFC technology can utilize existing microorganisms in the waste as a catalyst to generate electricity and simultaneously also serves as a wastewater treatment unit itself. Tempeh wastewater is one of the abundant industrial wastewater which can be processed using MFC. Research using the selective mixed culture is very likely to do due to the good result on COD removals by adding mixed culture. Microorganisms in tempeh wastewater consist of bacteria gram positive and gram negative. This study focused on the aspects of waste treatment which is determined by decreased levels of COD and BOD. Variations in this study are the formation time of biofilm and the addition of selective gram. MFC operated for 50 hours. For a variation of biofilm formation, experiments were performed after incubation by replacing incubation substrates used in the formation of biofilms. Biofilm formation time in this study was 3 days, 5 days, 7 days and 14 days. Gram positive and gram negative bacteria were used in selective mixed culture experiments. Selective mixed culture added to the reactor by 1 mL and 5 mL. Selection of gram-positive or gram-negative bacteria carried by growing mixed culture on selective media. COD and BOD levels were measured in the wastewater before and after the experiment conducted in each variation. Biofilm formation optimum time is 7 days which decrease COD and BOD levels by 18.2% and 35.9%. The addition of gram negative bacteria decreases COD and BOD levels by 29.32% and 51.32%. Further research is needed in order to get a better result on decreasing levels of COD and BOD.

  19. Microbial identification and automated antibiotic susceptibility testing directly from positive blood cultures using MALDI-TOF MS and VITEK 2.

    Science.gov (United States)

    Wattal, C; Oberoi, J K

    2016-01-01

    The study addresses the utility of Matrix Assisted Laser Desorption/Ionisation Time-Of-Flight mass spectrometry (MALDI-TOF MS) using VITEK MS and the VITEK 2 antimicrobial susceptibility testing (AST) system for direct identification (ID) and timely AST from positive blood culture bottles using a lysis-filtration method (LFM). Between July and December 2014, a total of 140 non-duplicate mono-microbial blood cultures were processed. An aliquot of positive blood culture broth was incubated with lysis buffer before the bacteria were filtered and washed. Micro-organisms recovered from the filter were first identified using VITEK MS and its suspension was used for direct AST by VITEK 2 once the ID was known. Direct ID and AST results were compared with classical methods using solid growth. Out of the 140 bottles tested, VITEK MS resulted in 70.7 % correct identification to the genus and/ or species level. For the 103 bottles where identification was possible, there was agreement in 97 samples (94.17 %) with classical culture. Compared to the routine method, the direct AST resulted in category agreement in 860 (96.5 %) of 891 bacteria-antimicrobial agent combinations tested. The results of direct ID and AST were available 16.1 hours before those of the standard approach on average. The combined use of VITEK MS and VITEK 2 directly on samples from positive blood culture bottles using a LFM technique can result in rapid and reliable ID and AST results in blood stream infections to result in early institution of targeted treatment. The combination of LFM and AST using VITEK 2 was found to expedite AST more reliably.

  20. Language model: Extension to solve inconsistency, incompleteness, and short query in cultural heritage collection

    Science.gov (United States)

    Tan, Kian Lam; Lim, Chen Kim

    2017-10-01

    With the explosive growth of online information such as email messages, news articles, and scientific literature, many institutions and museums are converting their cultural collections from physical data to digital format. However, this conversion resulted in the issues of inconsistency and incompleteness. Besides, the usage of inaccurate keywords also resulted in short query problem. Most of the time, the inconsistency and incompleteness are caused by the aggregation fault in annotating a document itself while the short query problem is caused by naive user who has prior knowledge and experience in cultural heritage domain. In this paper, we presented an approach to solve the problem of inconsistency, incompleteness and short query by incorporating the Term Similarity Matrix into the Language Model. Our approach is tested on the Cultural Heritage in CLEF (CHiC) collection which consists of short queries and documents. The results show that the proposed approach is effective and has improved the accuracy in retrieval time.

  1. Egypt's Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites.

    Science.gov (United States)

    Mustafa, Ghada A; Abd-Elgawad, Amr; Abdel-Haleem, Alyaa M; Siam, Rania

    2014-01-01

    The Red Sea possesses a unique geography, and its shores are rich in mangrove, macro-algal and coral reef ecosystems. Various sources of pollution affect Red Sea biota, including microbial life. We assessed the effects of industrialization on microbes along the Egyptian Red Sea coast at eight coastal sites and two lakes. The bacterial communities of sediment samples were analyzed using bacterial 16S rDNA pyrosequencing of V6-V4 hypervariable regions. The taxonomic assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). Further analysis revealed distinct bacterial consortia that primarily included (1) marine Vibrio spp.-suggesting a "marine Vibrio phenomenon"; (2) potential human pathogens; and (3) oil-degrading bacteria. We discuss two divergent microbial consortia that were sampled from Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; these consortia contained the highest abundance of human pathogens and no pathogens, respectively. Our results draw attention to the effects of industrialization on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites.

  2. Microbial culture selection for bio-hydrogen production from waste ground wheat by dark fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Argun, Hidayet; Kargi, Fikret; Kapdan, Ilgi K. [Department of Environmental Engineering, Dokuz Eylul University, Buca, Izmir (Turkey)

    2009-03-15

    Hydrogen formation performances of different anaerobic bacteria were investigated in batch dark fermentation of waste wheat powder solution (WPS). Serum bottles containing wheat powder were inoculated with pure cultures of Clostridium acetobutylicum (CAB), Clostridium butyricum (CB), Enterobacter aerogenes (EA), heat-treated anaerobic sludge (ANS) and a mixture of those cultures (MIX). Cumulative hydrogen formation (CHF), hydrogen yield (HY) and specific hydrogen production rate (SHPR) were determined for every culture. The heat-treated anaerobic sludge was found to be the most effective culture with a cumulative hydrogen formation of 560 ml, hydrogen yield of 223 ml H{sub 2} g{sup -1} starch and a specific hydrogen production rate of 32.1 ml H{sub 2} g{sup -1} h{sup -1}. (author)

  3. [Microbial exposure in collection of residential garbage--results of field studies].

    Science.gov (United States)

    Neumann, H D; Balfanz, J

    1999-01-01

    Since 1995 the communal accident insurance carrier of the county Wetfalen-Lippe conducts investigations into the exposure to biological agents related to refuse collection. Total fungal exposure during refuse collection turned out to range from 10,000 up to 750,000 colony forming units per cubic meter. Most of the measurement values exceeded the limit of 50,000. During hot periods in the summertime, the concentration of Aspergillus fumigatus increased up to 90,000 cfu/m3. The mean values of the bacterial concentrations ranged from 15,000 up to 50,000 cfu/m3, the endotoxin concentration from 12 up to 59 EU/m3. In the driver's cabin fungal exposure sometimes exceeded 10,000 cfu/m3 especially in autumn and winter. Maximum values were 5,000 cfu/m3 for bacteria and 15 EU/m3 for endotoxins. High values were measured irrespective of the kind of refuse.

  4. The role of lactic acid bacteria (Lactobacillus sp yel133) from beef in inhibiting of microbial contaminants on various fillers of starter culture

    Science.gov (United States)

    Yunilas; Mirwandhono, E.

    2018-02-01

    The role of Lactic Acid Bacteria (LAB) on the starter culture can be seen from the ability to grow and suppress the growth of microbial contaminants (fungi). The research aimed to investigate the role of LAB (Lactobacillus sp YEL133) in inhibiting microbial contaminants (fungi) on starter cultures of various fillers. The materials used in this research was Lactobacillus sp YEL133 from beef and various fillers (rice flour, corn starch and wheat flour). The research methods used completely randomized design (CRD) with 3 treatments and 4 replications. The treatments of this research was P1(rice flour), P2 (corn starch) and P3 (wheat flour) that inoculated with Lactobacillus sp YEL133. Parameters which is observed such as: growth of lactic acid bacteria, total microbes and total fungi as microbial contaminants. The results showed that the starter culture with a filler material of rice flour produce lactic acid bacteria and microbes were highly significant (P wheat flour, as well as able to suppress the growth of microbial contaminants (fungi). The conclusion of the research is the use Lactobacillus sp YEL133 can suppress the growth of fungi on the starter culture using rice flour.

  5. Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology.

    Science.gov (United States)

    Zhang, L; Zhou, R; Niu, M; Zheng, J; Wu, C

    2015-11-01

    Artificial pit muds (APMs) is produced by peats, aged pit muds, yellow and black clays etc. and is one of essential factors for Luzhou-flavour liquor production. The microbial community of APMs significantly influence the quality of Luzhou-flavour liquor. The aim of this study was to investigate the differences in bacterial, archaeal and fungal community of APMs, starters and materials. Multiphase culture-independent technology were employed in this study, including nested PCR-denaturing gradient gel electrophoresis (nested PCR-DGGE), phospholipid fatty acid (PLFA), phospholipid ether lipids (PLEL) and fluorescence in situ hybridization (FISH) analysis. Results suggested that the microbial diversity significantly changed under environmental stress and different culture patterns during APMs cultivation. The dominant bacteria in APMs mainly fell into Clostridiales, Lactobacillales, Bacteroidales and Rhizobiales, Archaea affiliated with Methanomicrobiales and Methanosarcinales, and fungi belonged to Saccharomycetales and Eurotiales. Furthermore, the microbial community structures of APMs cultured by ground pile pattern were more similar with that of aged pit muds, meanwhile, the relative bands intensities of microbes, which are the main contributors for liquor brewing, increased with the culture times. Not only the niche selection and biogeochemical properties of APMs, but also the mutual collaboration and constraint between different microbes may result in enriching different liquor-brewing microbes into APMs. APM cultivation technology was necessary to promote enriching functional liquor-brewing microbes into APMs. These results may facilitate understanding the microbial succession during APMs manufacture. © 2015 The Society for Applied Microbiology.

  6. Microbial transformation of tannin-rich substrate to gallic acid through co-culture method.

    Science.gov (United States)

    Banerjee, Rintu; Mukherjee, Gargi; Patra, Krushna Chandra

    2005-05-01

    Modified solid-state fermentation (MSSF) of tannin-rich substrate yielding tannase and gallic acid was carried out using a co-culture of the filamentous fungi, Rhizopus oryzae (RO IIT RB-13, NRRL 21498) and Aspergillus foetidus (GMRB013 MTCC 3557). Powdered fruits of Terminalia chebula and powdered pod cover of Caesalpinia digyna was used in the process and the different process parameters for maximum production of tannase and gallic acid by co-culture method were optimized through media engineering. MSSF was carried out at the optimum conditions of 30 degrees C and 80% relative humidity. The optimal pH and incubation period was 5.0 and 48 h respectively. Through the co-culture technique the maximum yield of tannase and gallic acid was found to be 41.3 U/ml and 94.8% respectively.

  7. Awe, the diminished self, and collective engagement: Universals and cultural variations in the small self.

    Science.gov (United States)

    Bai, Yang; Maruskin, Laura A; Chen, Serena; Gordon, Amie M; Stellar, Jennifer E; McNeil, Galen D; Peng, Kaiping; Keltner, Dacher

    2017-08-01

    Awe has been theorized as a collective emotion, one that enables individuals to integrate into social collectives. In keeping with this theorizing, we propose that awe diminishes the sense of self and shifts attention away from individual interests and concerns. In testing this hypothesis across 6 studies (N = 2137), we first validate pictorial and verbal measures of the small self; we then document that daily, in vivo, and lab experiences of awe, but not other positive emotions, diminish the sense of the self. These findings were observed across collectivist and individualistic cultures, but also varied across cultures in magnitude and content. Evidence from the last 2 studies showed that the influence of awe upon the small self accounted for increases in collective engagement, fitting with claims that awe promotes integration into social groups. Discussion focused on how the small self might mediate the effects of awe on collective cognition and behavior, the need to study more negatively valenced varieties of awe, and other potential cultural variations of the small self. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  8. Acting and Collecting: Imagining Asia through material culture and musical theatre

    Directory of Open Access Journals (Sweden)

    Peter Thorley

    2015-07-01

    Full Text Available This paper explores the link between Asian-inspired material culture and musical theatre through the collections of Anglo-Australian performer Herbert Browne (1895-1975. Brown played lead roles in 1920s Australian musical theatre productions of The Mikado and Chu Chin Chow and re-lived his connection with oriental theatre by collecting and responding to objects performatively in the Chinoiserie room of his Melbourne home. Oriental musical theatre blended exotic cultures and locales in visually spectacular productions which bore little resemblance to reality. The taste for escapist fiction in the theatre took place against a backdrop of museum collecting which aimed to reproduce authentic Asian and Other cultures. In this paper, I draw on French philosopher Merleau-Ponty’s observations on the relationship between thought and the body’s interaction with space to interpret the influence of Browne’s theatricality on collecting choices. From this perspective, objects materialize particular understandings of the world which originate in the body and the body’s performative engagement with space.

  9. 77 FR 52610 - Pesticides; Microbial Pesticide Definitions and Applicability; Clarification and Availability of...

    Science.gov (United States)

    2012-08-30

    ... corrections to words and references. Finally, EPA is announcing the availability of a final microbial... nationally recognized culture collection. Collectively, the final rule clarifications and revisions, as well... sample in a nationally recognized culture collection, did not have an accompanying test guideline and...

  10. Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media.

    Science.gov (United States)

    Wu, Manli; Chen, Liming; Tian, Yongqiang; Ding, Yi; Dick, Warren A

    2013-07-01

    A consortium composed of many different bacterial species is required to efficiently degrade polycyclic aromatic hydrocarbons (PAH) in oil-contaminated soil. We obtained six PAH-degrading microbial consortia from three oil-contaminated soils using two different isolation culture media. Denaturing gradient gel electrophoresis (DGGE) and sequence analyses of amplified 16s rRNA genes confirmed the bacterial community was greatly affected by both the culture medium and the soil from which the consortia were enriched. Three bacterial consortia enriched using malt yeast extract (MYE) medium showed higher degradation rates of PAHs than consortia enriched using Luria broth (LB) medium. Consortia obtained from a soil and then added back to that same soil was more effective in degrading PAHs than adding, to the same soil, consortia isolated from other, unrelated soils. This suggests that inoculum used for bioremediation should be from the same, or very similar nearby soils, as the soil that is actually being bioremediated. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Optimization of culture conditions and electricity generation using Geobacter sulfurreducens in a dual-chambered microbial fuel-cell

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Mi-Sun; Lee, Yu-jin [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-343 (Korea, Republic of)

    2010-12-15

    The promise of generating electricity from the oxidation of organic substances using metal-reducing bacteria is drawing attention as an alternate form of bio-technology with positive environmental implications. In this study, we examined various experimental factors to obtain the maximum power output in a dual-chamber mediator-less microbial fuel-cell (MFC) using Geobacter sulfurreducens and acetate as an electron donor in a semi-continuous mode. The G. sulfurreducens culture conditions were optimized in a nutrient buffer containing 20 mM of acetate and 50 mM of fumarate at pH 6.8 and 30 C. For use in the MFC system, electrodes were made with carbon paper (area: 11.5 cm{sup 2}) and spaced 1.5 cm apart. Once the MFC was inoculated with the pre-cultured G. sulfurreducens in the anode chamber and while air was continuously sparged to the cathode chamber, the cells produced electricity stably over 60 days with the regular addition of 20 mM acetate, generating the maximum power density of 7 mW/m{sup 2} with a 5000 and ohm; load. The current output was significantly increased, by 1.6 times after 20 days of incubation under the same experimental conditions, when the carbon-paper anode was coated with carbon nanotubes. (author)

  12. The influence of Staphylococcus aureus on gut microbial ecology in an in vitro continuous culture human colonic model system.

    Science.gov (United States)

    Sannasiddappa, Thippeswamy H; Costabile, Adele; Gibson, Glenn R; Clarke, Simon R

    2011-01-01

    An anaerobic three-stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine, was used to study the effect of S. aureus infection of the gut on the resident faecal microbiota. Studies on the development of the microbiota in the three vessels were performed and bacteria identified by culture independent fluorescence in situ hybridization (FISH). Furthermore, short chain fatty acids (SCFA), as principal end products of gut bacterial metabolism, were measured along with a quantitative assessment of the predominant microbiota. During steady state conditions, numbers of S. aureus cells stabilised until they were washed out, but populations of indigenous bacteria were transiently altered; thus S. aureus was able to compromise colonisation resistance by the colonic microbiota. Furthermore, the concentration of butyric acid in the vessel representing the proximal colon was significantly decreased by infection. Thus infection by S. aureus appears to be able to alter the overall structure of the human colonic microbiota and the microbial metabolic profiles. This work provides an initial in vitro model to analyse interactions with pathogens.

  13. EvoBot: Towards a Robot-Chemostat for Culturing and Maintaining Microbial Fuel Cells (MFCs)

    DEFF Research Database (Denmark)

    Theodosiou, Pavlina; Faina, Andres; Nejatimoharrami, Farzad

    2017-01-01

    , which is akin to a chemostat. The chemostat is a well-known microbiology method for culturing bacterial cells under controlled conditions with continuous nutrient supply. EvoBot is perhaps the first pioneering attempt at functionalizing the 3D printing technology by combining it with the chemostat...

  14. Simple Sample Preparation Method for Direct Microbial Identification and Susceptibility Testing From Positive Blood Cultures.

    Science.gov (United States)

    Pan, Hong-Wei; Li, Wei; Li, Rong-Guo; Li, Yong; Zhang, Yi; Sun, En-Hua

    2018-01-01

    Rapid identification and determination of the antibiotic susceptibility profiles of the infectious agents in patients with bloodstream infections are critical steps in choosing an effective targeted antibiotic for treatment. However, there has been minimal effort focused on developing combined methods for the simultaneous direct identification and antibiotic susceptibility determination of bacteria in positive blood cultures. In this study, we constructed a lysis-centrifugation-wash procedure to prepare a bacterial pellet from positive blood cultures, which can be used directly for identification by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and antibiotic susceptibility testing by the Vitek 2 system. The method was evaluated using a total of 129 clinical bacteria-positive blood cultures. The whole sample preparation process could be completed in identification was 96.49% for gram-negative bacteria and 97.22% for gram-positive bacteria. Vitek 2 antimicrobial susceptibility testing of gram-negative bacteria showed an agreement rate of antimicrobial categories of 96.89% with a minor error, major error, and very major error rate of 2.63, 0.24, and 0.24%, respectively. Category agreement of antimicrobials against gram-positive bacteria was 92.81%, with a minor error, major error, and very major error rate of 4.51, 1.22, and 1.46%, respectively. These results indicated that our direct antibiotic susceptibility analysis method worked well compared to the conventional culture-dependent laboratory method. Overall, this fast, easy, and accurate method can facilitate the direct identification and antibiotic susceptibility testing of bacteria in positive blood cultures.

  15. Simple Sample Preparation Method for Direct Microbial Identification and Susceptibility Testing From Positive Blood Cultures

    Directory of Open Access Journals (Sweden)

    Hong-wei Pan

    2018-03-01

    Full Text Available Rapid identification and determination of the antibiotic susceptibility profiles of the infectious agents in patients with bloodstream infections are critical steps in choosing an effective targeted antibiotic for treatment. However, there has been minimal effort focused on developing combined methods for the simultaneous direct identification and antibiotic susceptibility determination of bacteria in positive blood cultures. In this study, we constructed a lysis-centrifugation-wash procedure to prepare a bacterial pellet from positive blood cultures, which can be used directly for identification by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS and antibiotic susceptibility testing by the Vitek 2 system. The method was evaluated using a total of 129 clinical bacteria-positive blood cultures. The whole sample preparation process could be completed in <15 min. The correct rate of direct MALDI-TOF MS identification was 96.49% for gram-negative bacteria and 97.22% for gram-positive bacteria. Vitek 2 antimicrobial susceptibility testing of gram-negative bacteria showed an agreement rate of antimicrobial categories of 96.89% with a minor error, major error, and very major error rate of 2.63, 0.24, and 0.24%, respectively. Category agreement of antimicrobials against gram-positive bacteria was 92.81%, with a minor error, major error, and very major error rate of 4.51, 1.22, and 1.46%, respectively. These results indicated that our direct antibiotic susceptibility analysis method worked well compared to the conventional culture-dependent laboratory method. Overall, this fast, easy, and accurate method can facilitate the direct identification and antibiotic susceptibility testing of bacteria in positive blood cultures.

  16. Collective animal navigation and migratory culture: from theoretical models to empirical evidence

    Science.gov (United States)

    Dell, Anthony I.

    2018-01-01

    Animals often travel in groups, and their navigational decisions can be influenced by social interactions. Both theory and empirical observations suggest that such collective navigation can result in individuals improving their ability to find their way and could be one of the key benefits of sociality for these species. Here, we provide an overview of the potential mechanisms underlying collective navigation, review the known, and supposed, empirical evidence for such behaviour and highlight interesting directions for future research. We further explore how both social and collective learning during group navigation could lead to the accumulation of knowledge at the population level, resulting in the emergence of migratory culture. This article is part of the theme issue ‘Collective movement ecology’. PMID:29581394

  17. X-ray spectroscopic studies of uranium transformations in microbial cultures

    International Nuclear Information System (INIS)

    Dodge, C.J.; Francis, A.J.; Clayton, C.R.

    1995-01-01

    Microbial transformations of uranyl nitrate, U:citric acid, and mixed metal U:Fe:citric acid complex were investigated. X-ray photoelectron spectroscopy (XPS) and X-ray absorption near edge structure (XANES) analyses showed that soluble U 6+ was reduced to insoluble U 4+ by Clostridium sp. and was associated with the bacterial surface, whereas U 3+ was observed within the biomass. Uranium forms a binuclear complex with citric acid involving two carboxylic acid groups and the hydroxyl group. Biodegradation studies of U:citric acid and U:Fe:citric acid complexes using Pseudomonas fluorescens showed they were recalcitrant. The lack of biodegradation was due to the nature of the metal-citrate complex species and not due to toxicity. Characterization of the mixed metal U:Fe:citric acid complex by extended X-ray absorption fine structure (EXAFS) indicated that Fe was associated with the U and citric acid, resulting in formation of a bionuclear mixed metal citrate complex

  18. Simulation of Feedforward-Feedback Control of Dissolved Oxygen of Microbial Repeated Fed-batch Culture

    Directory of Open Access Journals (Sweden)

    Ling Gao

    2016-09-01

    Full Text Available Fed-batch culture is often used in industry, and dissolved oxygen (DO concentration control is important in fermentation process control. DO control is often applied by using feedback (FB control strategy. But, feedforward-feedback (FF-FB control has the advantage in dealing with the time-varying characteristics resulted from the cell growth during the fermentation process. Mathematical modeling and computer simulation is a useful tool in analysis of the control system.  In this research, the FF-FB DO control and FB substrate control of repeated fed-batch culture process is modeled and simulated. The results showed the feasibility of the control strategy. These results are useful for control system development and process analyses and optimization.

  19. Removal of hydrocarbon from refinery tank bottom sludge employing microbial culture.

    Science.gov (United States)

    Saikia, Rashmi Rekha; Deka, Suresh

    2013-12-01

    Accumulation of oily sludge is becoming a serious environmental threat, and there has not been much work reported for the removal of hydrocarbon from refinery tank bottom sludge. Effort has been made in this study to investigate the removal of hydrocarbon from refinery sludge by isolated biosurfactant-producing Pseudomonas aeruginosa RS29 strain and explore the biosurfactant for its composition and stability. Laboratory investigation was carried out with this strain to observe its efficacy of removing hydrocarbon from refinery sludge employing whole bacterial culture and culture supernatant to various concentrations of sand-sludge mixture. Removal of hydrocarbon was recorded after 20 days. Analysis of the produced biosurfactant was carried out to get the idea about its stability and composition. The strain could remove up to 85 ± 3 and 55 ± 4.5 % of hydrocarbon from refinery sludge when whole bacterial culture and culture supernatant were used, respectively. Maximum surface tension reduction (26.3 mN m(-1)) was achieved with the strain in just 24 h of time. Emulsification index (E24) was recorded as 100 and 80 % with crude oil and n-hexadecane, respectively. The biosurfactant was confirmed as rhamnolipid containing C8 and C10 fatty acid components and having more mono-rhamnolipid congeners than the di-rhamnolipid ones. The biosurfactant was stable up to 121 °C, pH 2-10, and up to a salinity value of 2-10 % w/v. To our knowledge, this is the first report showing the potentiality of a native strain from the northeast region of India for the efficient removal of hydrocarbon from refinery sludge.

  20. In vitro anti-microbial activity of extracts from the callus cultures of some Nigella species

    Czech Academy of Sciences Publication Activity Database

    Landa, P.; Maršík, Petr; Vaněk, Tomáš; Rada, V.; Kokoška, L.

    2006-01-01

    Roč. 61, č. 3 (2006), s. 285-288 ISSN 0006-3088 R&D Projects: GA ČR(CZ) GA525/02/0257; GA MŠk(CZ) 1P04OC926.001 Institutional research plan: CEZ:AV0Z40550506 Keywords : Nigella * callus culture * antimicrobial activity Subject RIV: CC - Organic Chemistry Impact factor: 0.213, year: 2006

  1. A Cultural Psychological Analysis of Collective Memory as Mediated Action: Constructions of Indian History

    Directory of Open Access Journals (Sweden)

    Sahana Mukherjee

    2018-01-01

    Full Text Available The present research applies a cultural psychological perspective on collective memory as mediated action to examine how constructions of a national past serve as tools that both reflect and shape national identity concerns. We employ a situation-sampling method to investigate collective memory in a series of studies concerning intergroup relations in the Indian context. In Study 1, participants (N = 55 generated three historical events that they considered important/relevant for Indian history. In Study 2, participants (N = 95 rated the importance and relevance of these events in a within-participant design. Illuminating the psychological constitution of cultural reality, frequency of recall (Study 1 and ratings of importance/relevance (Study 2 were greater for nation-glorifying events celebrating ingroup triumph than for typically silenced, critical events acknowledging ingroup wrongdoing. Moreover, these patterns were stronger among participants who scored higher in national identification. In Studies 3 (N = 65 and 4 (N = 160, we exposed participants to different categories of events in a between-participants design. Illuminating the cultural constitution of psychological experience, participants exposed to typically silenced, critical events reported lower national identification and greater perception of injustice against marginalized groups than did participants exposed to nation-glorifying events. Together, results illuminate a conception of collective memory as mediated action. Producers invest memory products with an identity-interested charge that directs subsequent intergroup relations toward identity-consistent ends.

  2. Characterization of bacteriophages infecting clinical isolates of Pseudomonas aeruginosa stored in a culture collection

    Directory of Open Access Journals (Sweden)

    C.C.S. Zanetti

    2013-08-01

    Full Text Available Some clinical isolates of Pseudomonas aeruginosa stored in our culture collection did not grow or grew poorly and showed lysis on the culture plates when removed from the collection and inoculated on MacConkey agar. One hypothesis was that bacteriophages had infected and killed those clinical isolates. To check the best storage conditions to maintain viable P. aeruginosa for a longer time, clinical isolates were stored at various temperatures and were grown monthly. We investigated the presence of phage in 10 clinical isolates of P. aeruginosa stored in our culture collection. Four strains of P. aeruginosa were infected by phages that were characterized by electron microscopy and isolated to assess their ability to infect. The best condition to maintain the viability of the strains during storage was in water at room temperature. Three Siphoviridae and two Myoviridae phages were visualized and characterized by morphology. We confirmed the presence of bacteriophages infecting clinical isolates, and their ability to infect and lyse alternative hosts. Strain PAO1, however, did not show lysis to any phage. Mucoid and multidrug resistant strains of P. aeruginosa showed lysis to 50% of the phages tested.

  3. Direct conversion of sorghum carbohydrates to ethanol by a mixed microbial culture

    Energy Technology Data Exchange (ETDEWEB)

    Christakopoulos, Paul; Lianwu Li; Kekos, Dimitris; Macris, B.J. (National Technical Univ. of Athens (Greece). Dept. of Chemical Engineering)

    1993-01-01

    The carbohydrates of sweet sorghum were directly converted to ethanol by a mixed culture of Fusarium oxysporum F3 and Saccharomyces cerevisiae 2541. A number of factors affecting this bioconversion was studied. Optimum ethanol yields of 33.2 g/100 g of total sorghum carbohydrates, corresponding to 10.3 g/100 g of fresh stalks, were obtained. These values represented 68.6% of the theoretical yield based on total polysaccharides and exceeded that based on oligosaccharides of sorghum by 53.7%. The results demonstrated that more than half of the sorghum polysaccharides were directly fermented to ethanol, thus making the process worthy of further investigation. (author)

  4. Microscale validation of 4-aminoantipyrine test method for quantifying phenolic compounds in microbial culture

    International Nuclear Information System (INIS)

    Justiz Mendoza, Ibrahin; Aguilera Rodriguez, Isabel; Perez Portuondo, Irasema

    2014-01-01

    Validation of test methods microscale is currently of great importance due to the economic and environmental advantages possessed, which constitutes a prerequisite for the performance of services and quality assurance of the results to provide customer. This paper addresses the microscale validation of 4-aminoantipyrine spectrophotometric method for the quantification of phenolic compounds in culture medium. Parameters linearity, precision, regression, accuracy, detection limits, quantification limits and robustness were evaluated, addition to the comparison test with no standardized method for determining polyphenols (Folin Ciocalteu). The results showed that both methods are feasible for determining phenols

  5. Environmental Remediation Full-Scale Implementation: Back to Simple Microbial Massive Culture Approaches

    Directory of Open Access Journals (Sweden)

    Agung Syakti

    2010-10-01

    Full Text Available Using bioaugmentation and biostimulation approach for contaminated soil bioremediation were investigated and implemented on field scale. We combine those approaches by culturing massively the petrophilic indigenous microorganisms from chronically contaminated soil enriched by mixed manure. Through these methods, bioremediation performance revealed promising results in removing the petroleum hydrocarbons comparatively using metabolite by product such as biosurfactant, specific enzymes and other extra-cellular product which are considered as a difficult task and will impact on cost increase.

  6. Connecting Local Cultural Heritage Collections with ICT: the Case of ZBORZBIRK

    Directory of Open Access Journals (Sweden)

    Špela Ledinek Lozej

    2014-12-01

    Full Text Available AbstractPurpose: The article discusses the digitisation and inventory of 34 local cultural heritage collections in the border region between the Alps and the Karst, and the establishment of a network of owners, guardians of collections and professionals from the field of museology, ethnology, digital humanities and informatics.Methodology/approach: In the framework of the project “ZBORZBIRK – Cultural heritage between the Alps and the Karst” 34 collections of cultural heritage of different type and contents, until then inaccessible to the general public and experts, were catalogued, contextualised and presented to the general and expert public in different media and on the project website.Results: A unified repository with metadata on objects (units was established containing also digital photographs and scans of images and textual objects (digital objects. There are 4583 units and 5190 digital objects in the repository. It is designed for researchers, experts and students from the fields of ethnology, cultural anthropology, history, linguistics as well for the general public, and above all to achieve greater recognisability of the region.Research limitation: The research and the results were limited by the material itself, i.e. the collections included into the project, as well as by different aspirations of collectors and various levels of specialised skills of registrars and recorders who documented and digitised the units and entered the data in the metadata database. The project addresses a wide scope of potential users thus the implementation of different solutions gave rise to the conflict of interests among target groups. The question was whether it should serve as a virtual museum or as a research archival repository. More attention was focused on archival and research standards than on presentation technologies.Originality/practical implications: The project ZBORZBIRK is one of the first projects in the Italian and Slovenian

  7. Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS

    Directory of Open Access Journals (Sweden)

    Ali M. Bazzi

    2017-05-01

    Full Text Available Summary: Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients.In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2 with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1; 100% ethanol treatment (method 3, and picking colonies from 90 to 180 min subculture plates (method 4. Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations. Keywords: MALDI-TOF, Gram-negative, Gram-positive, Sepsis, Blood culture

  8. Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

    Science.gov (United States)

    Hamet, Maria Fernanda; Londero, Alejandra; Medrano, Micaela; Vercammen, Elisabeth; Van Hoorde, Koenraad; Garrote, Graciela L; Huys, Geert; Vandamme, Peter; Abraham, Analía G

    2013-12-01

    The biological and technological characteristics of kefiran as well as its importance in grain integrity led us to analyze the microbial kefir grain consortium with focus on Lactobacillus kefiranofaciens. The presence of L. kefiranofaciens in the nine kefir grains studied was demonstrated by denaturing gradient gel electrophoresis. By culture dependent methods applying a methodology focused on the search of this species, 22 isolates with typical morphology were obtained and identified applying a combination of SDS-PAGE of whole cell proteins, (GTG)5-PCR and sequence analysis of the housekeeping gene encoding the α-subunit of bacterial phenylalanyl-tRNA synthase (pheS). This polyphasic approach allowed the reliable identification of 11 L. kefiranofaciens, 5 Lactobacillus paracasei, 4 Lactobacillus kefiri and 2 Lactobacillus parakefiri isolates. Isolated L. kefiranofaciens strains produced polysaccharide in strain-dependent concentrations and EPS produced by them also differed in the degree of polymerization. The isolation and accurate identification of L. kefiranofaciens is relevant taking into account the important role of this microorganism in the grain ecosystem as well as its potential application as starter in food fermentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. N-acyl homoserine lactone-degrading microbial enrichment cultures isolated from Penaeus vannamei shrimp gut and their probiotic properties in Brachionus plicatilis cultures.

    Science.gov (United States)

    Tinh, Nguyen Thi Ngoc; Asanka Gunasekara, R A Y S; Boon, Nico; Dierckens, Kristof; Sorgeloos, Patrick; Bossier, Peter

    2007-10-01

    Three bacterial enrichment cultures (ECs) were isolated from the digestive tract of Pacific white shrimp Penaeus vannamei, by growing the shrimp microbial communities in a mixture of N-acyl homoserine lactone (AHL) molecules. The ECs, characterized by denaturing gradient gel electrophoresis analysis and subsequent rRNA sequencing, degraded AHL molecules in the degradation assays. Apparently, the resting cells of the ECs also degraded one of the three types of quorum-sensing signal molecules produced by Vibrio harveyi in vitro [i.e. harveyi autoinducer 1 (HAI-1)]. The most efficient AHL-degrading ECs, EC5, was tested in Brachionus experiments. EC5 degraded the V. harveyi HAI-1 autoinducer in vivo, neutralizing the negative effect of V. harveyi autoinducer 2 (AI-2) mutant, in which only the HAI-1- and CAI-1-mediated components of the quorum-sensing system are functional on the growth of Brachionus. This suggests that EC5 interferes with HAI-1-regulated metabolism in V. harveyi. These AHL-degrading ECs need to be tested in other aquatic systems for their probiotic properties, preferably in combination with specific AI-2-degrading bacteria.

  10. Co-culture microorganisms with different initial proportions reveal the mechanism of chalcopyrite bioleaching coupling with microbial community succession.

    Science.gov (United States)

    Ma, Liyuan; Wang, Xingjie; Feng, Xue; Liang, Yili; Xiao, Yunhua; Hao, Xiaodong; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan

    2017-01-01

    The effect of co-culture microorganisms with different initial proportions on chalcopyrite bioleaching was investigated. Communities were rebuilt by six typical strains isolated from the same habitat. The results indicated, by community with more sulfur oxidizers at both 30 and 40°C, the final copper extraction rate was 19.8% and 6.5% higher, respectively, than that with more ferrous oxidizers. The variations of pH, redox potential, ferrous and copper ions in leachate also provided evidences that community with more sulfur oxidizers was more efficient. Community succession of free and attached cells revealed that initial proportions played decisive roles on community dynamics at 30°C, while communities shared similar structures, not relevant to initial proportions at 40°C. X-ray diffraction analysis confirmed different microbial functions on mineral surface. A mechanism model for chalcopyrite bioleaching was established coupling with community succession. This will provide theoretical basis for reconstructing an efficient community in industrial application. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Web-based experiments for the study of collective social dynamics in cultural markets.

    Science.gov (United States)

    Salganik, Matthew J; Watts, Duncan J

    2009-07-01

    Social scientists are often interested in understanding how the dynamics of social systems are driven by the behavior of individuals that make up those systems. However, this process is hindered by the difficulty of experimentally studying how individual behavioral tendencies lead to collective social dynamics in large groups of people interacting over time. In this study, we investigate the role of social influence, a process well studied at the individual level, on the puzzling nature of success for cultural products such as books, movies, and music. Using a "multiple-worlds" experimental design, we are able to isolate the causal effect of an individual-level mechanism on collective social outcomes. We employ this design in a Web-based experiment in which 2,930 participants listened to, rated, and downloaded 48 songs by up-and-coming bands. Surprisingly, despite relatively large differences in the demographics, behavior, and preferences of participants, the experimental results at both the individual and collective levels were similar to those found in Salganik, Dodds, and Watts (2006). Further, by comparing results from two distinct pools of participants, we are able to gain new insights into the role of individual behavior on collective outcomes. We conclude with a discussion of the strengths and weaknesses of Web-based experiments to address questions of collective social dynamics. Copyright © 2009 Cognitive Science Society, Inc.

  12. Change of lactose content after milk fermentation using various microbial cultures

    Directory of Open Access Journals (Sweden)

    Ivana Vinko

    2011-06-01

    Full Text Available The purpose of this study was to determine lactose and lactic acid content and acidity changes in typified milk prior to fermentation and in dairy products on 1st and 28th day of their storage at 8 °C in cold environment. In this study 5 different dairy products were observed: yogurt, extra lactose yogurt, bifido milk, sour cream and sour milk. The enzymatic method for determination of lactose has been used. The biggest change in lactose and lactic acid content, according to study results, has happened in the process of fermentation, as expected. About 16-20 % of lactose has been converted by mesophilus, while significantly bigger part (round 30 % of lactose to lactic acid has been converted by thermophilus. The smallest part of lactose conversion was performed by Bifidobacterium therapy culture (just 15 % after the first day and 19 % on 28th day of cold storage which is due to the greater adjustment period of Bifidobacterium in milk for lactose fermentation.

  13. Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS.

    Science.gov (United States)

    Bazzi, Ali M; Rabaan, Ali A; El Edaily, Zeyad; John, Susan; Fawarah, Mahmoud M; Al-Tawfiq, Jaffar A

    Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients. In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2) with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1); 100% ethanol treatment (method 3)), and picking colonies from 90 to 180min subculture plates (method 4). Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations. Copyright © 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

  14. Dynamics of the Content of Lactobacilli, Microbial Metabolites and Antimicrobial Activity of Growing Culture of Lactobacillus Plantarum 8P-A3

    Directory of Open Access Journals (Sweden)

    I. Yu. Chicherin

    2013-01-01

    Full Text Available The dynamics of the content of lactobacilli, microbial metabolites and antimicrobial activity of growing cultures of Lactobacillus plantarum 8Р-А3 was studied. Lactobacilli L. plantarum 8Р-А3 and test microorganisms isolated from the intestinal contents of patients with dysbacteriosis were used in experiments. Study of the component composition of growing culture supernatant of lactobacilli was carried out by gas liquid chromatography with mass selective detection. By 54 h of cultivation the content of viable microbial cells in the native culture of Lactobacillus achieves 3,0·109 in 1 mL without further increase during the cultivation. The principal component of lactobacilli culture medium possessing antibacterial activity is lactic acid. In addition to lactic acid, which accounts for 70% of the total metabolites, the culture medium and the supernatant contain salts of phosphoric acid (14% as well as amino acids, carboxylic acids, fatty acids, sugars and polyhydric alcohol constituting of up to 16% of the total metabolites. It is found that during the cultivation in liquid medium lactobacilli produce metabolites which possess antibacterial activity against pathogenic bacteria that cause intestinal infections.

  15. The mind-body-microbial continuum

    OpenAIRE

    Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J.; Gordon, Jeffrey I.; Knight, Rob

    2011-01-01

    Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent ?metagenomic? techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A ce...

  16. Combination of image descriptors for the exploration of cultural photographic collections

    Science.gov (United States)

    Bhowmik, Neelanjan; Gouet-Brunet, Valérie; Bloch, Gabriel; Besson, Sylvain

    2017-01-01

    The rapid growth of image digitization and collections in recent years makes it challenging and burdensome to organize, categorize, and retrieve similar images from voluminous collections. Content-based image retrieval (CBIR) is immensely convenient in this context. A considerable number of local feature detectors and descriptors are present in the literature of CBIR. We propose a model to anticipate the best feature combinations for image retrieval-related applications. Several spatial complementarity criteria of local feature detectors are analyzed and then engaged in a regression framework to find the optimal combination of detectors for a given dataset and are better adapted for each given image; the proposed model is also useful to optimally fix some other parameters, such as the k in k-nearest neighbor retrieval. Three public datasets of various contents and sizes are employed to evaluate the proposal, which is legitimized by improving the quality of retrieval notably facing classical approaches. Finally, the proposed image search engine is applied to the cultural photographic collections of a French museum, where it demonstrates its added value for the exploration and promotion of these contents at different levels from their archiving up to their exhibition in or ex situ.

  17. Dynamic collection and analysis of volatile organic compounds from the headspace of cell cultures.

    Science.gov (United States)

    Baranska, A; Smolinska, A; Boots, A W; Dallinga, J W; van Schooten, F J

    2015-10-15

    Exhaled breath has proven to be a valuable source of information about human bodies. Subtle differences between volatile organic compounds (VOCs) formed endogenously can be detected and become a base for a potential monitoring tool for health and disease. Until now, there has been a lack of biological and mechanistic knowledge of the processes involved in the production of relevant VOCs. Among the possible sources of health-related and disease-related VOCs are microorganisms found in the respiratory tract and in the gut. Other VOCs in the body are produced by cells that are influenced by the disease, for instance, due to metabolic disorders and/or inflammation. To gain insight into the in vivo production of VOCs by human cells and thus the exhaled breath composition, in vitro experiments involving relevant cells should be studied because they may provide valuable information on the production of VOCs by the affected cells. To this aim we developed and validated a system for dynamically (continuously) collecting headspace air in vitro using a Caco-2 cell line. The system allows the application of different cell lines as well as different experimental setups, including varying exposure times and treatment options while preserving cell viability. Significant correlation (p  ⩽  0.0001) between collection outputs within each studied group confirmed high reproducibility of the collection system. An example of such an application is presented here. We studied the influence of oxidative stress on the VOC composition of the headspace air of Caco-2 cells. By comparing the VOC composition of air flushed through empty culture flasks (n  =  35), flasks with culture medium (n  =  35), flasks with medium and cells (n  =  20), flasks with medium and an oxidative stressor (H2O2) (n  =  20), and flasks with medium, stressor, and cells (n  =  20), we were able to separate the effects from the stressor on the cells from all other

  18. Reducing unnecessary culturing: a systems approach to evaluating urine culture ordering and collection practices among nurses in two acute care settings

    Directory of Open Access Journals (Sweden)

    Robert Redwood

    2018-01-01

    Full Text Available Abstract Background Inappropriate ordering and acquisition of urine cultures leads to unnecessary treatment of asymptomatic bacteriuria (ASB. Treatment of ASB contributes to antimicrobial resistance particularly among hospital-acquired organisms. Our objective was to investigate urine culture ordering and collection practices among nurses to identify key system-level and human factor barriers and facilitators that affect optimal ordering and collection practices. Methods We conducted two focus groups, one with ED nurses and the other with ICU nurses. Questions were developed using the Systems Engineering Initiative for Patient Safety (SEIPS framework. We used iterative categorization (directed content analysis followed by summative content analysis to code and analyze the data both deductively (using SEIPS domains and inductively (emerging themes. Results Factors affecting optimal urine ordering and collection included barriers at the person, process, and task levels. For ED nurses, barriers included patient factors, physician communication, reflex culture protocols, the electronic health record, urinary symptoms, and ED throughput. For ICU nurses, barriers included physician notification of urinalysis results, personal protective equipment, collection technique, patient body habitus, and Foley catheter issues. Conclusions We identified multiple potential process barriers to nurse adherence with evidence-based recommendations for ordering and collecting urine cultures in the ICU and ED. A systems approach to identifying barriers and facilitators can be useful to design interventions for improving urine ordering and collection practices.

  19. Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training

    KAUST Repository

    Antunes, Andre; Stackebrandt, Erko; Lima, Nelson

    2015-01-01

    A survey of European Microbial Biological Resource Centers and their users provided an overview on microbiology education and training. The results identified future increases in demand despite several shortcomings and gaps in the current offer

  20. Comparison of Uriswab to alternative methods for urine culture collection and transport: confirmation of standard culture methodology for investigation of urinary tract infections.

    Science.gov (United States)

    Rennie, Robert P; Turnbull, Lee-Ann; Gauchier-Pitts, Kaylee; Bennett, Tracy; Dyrland, Debbie; Blonski, Susan

    2016-08-01

    The ability to isolate and identify causative agents of urinary tract infections relies primarily on the quality of the urine sample that is submitted to the microbiology. The most important factors are the method of collection, the maintenance of viability of the potential pathogens during transport, and standardization of the culturing of the urine sample. This report is a composite of several investigations comparing collection and transport on urine culture paddles, with a preservative urine sponge (Uriswab), and a comparison of Uriswab with the BD preservative transport tube as methods of preservation of urinary pathogens. Primary studies showed that Uriswab maintained significantly more urinary pathogens than the urine culture paddle with fewer mixed or contaminated cultures. The two preservative transport systems were comparable for maintenance of viability of the pathogens, but there were fewer mixed cultures when samples were collected with Uriswab. This study confirms the importance of a standard volume of 1 μL of urine for culture. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. ARTEFACT MOBILE DATA MODEL TO SUPPORT CULTURAL HERITAGE DATA COLLECTION AND INTERPRETATION

    Directory of Open Access Journals (Sweden)

    Z. S. Mohamed-Ghouse

    2012-07-01

    Full Text Available This paper discusses the limitation of existing data structures in mobile mapping applications to support archaeologists to manage the artefact (any object made or modified by a human culture, and later recovered by an archaeological endeavor details excavated at a cultural heritage site. Current limitations of data structure in the mobile mapping application allow archeologist to record only one artefact per test pit location. In reality, more than one artefact can be excavated from the same test pit location. A spatial data model called Artefact Mobile Data Model (AMDM was developed applying existing Relational Data Base Management System (RDBMS technique to overcome the limitation. The data model was implemented in a mobile database environment called SprintDB Pro which was in turn connected to ArcPad 7.1 mobile mapping application through Open Data Base Connectivity (ODBC. In addition, the design of a user friendly application built on top of AMDM to interpret and record the technology associated with each artefact excavated in the field is also discussed in the paper. In summary, the paper discusses the design and implementation of a data model to facilitate the collection of artefacts in the field using integrated mobile mapping and database approach.

  2. Self-sustaining, solar-driven bioelectricity generation in micro-sized microbial fuel cell using co-culture of heterotrophic and photosynthetic bacteria

    Science.gov (United States)

    Liu, Lin; Choi, Seokheun

    2017-04-01

    Among many energy harvesting techniques with great potential, microbial fuel cell (MFC) technology is arguably the most underdeveloped. Even so, excitement is building, as microorganisms can harvest electrical power from any biodegradable organic source (e.g. wastewater) that is readily available in resource-limited settings. Nevertheless, the requirement for endless introduction of organic matter imposes a limiting factor to this technology, demanding an active feeding system and additional power. Here, we demonstrated self-sustaining bioelectricity generation from a microliter-scale microbial fuel cell (MFC) by using the syntrophic interaction between heterotrophic exoelectrogenic bacteria and phototrophs. The MFC continuously generated light-responsive electricity from the heterotrophic bacterial metabolic respiration with the organic substrates produced by photosynthetic bacteria. Without additional organic fuel, the mixed culture in a 90-μL-chamber MFC generated self-sustained current for more than 13 days, while the heterotrophic culture produced current that decreased dramatically within a few hours. The current from the mixed culture was about 70 times greater than that of the device with only photosynthetic bacteria. The miniaturization provided a short start-up time, a well-controlled environment, and small internal resistance. Those advantages will become the general design platform for micropower generation.

  3. Crowdfunding and Cultural Industry: The new relations between production and consumption based on the culture of participation and collective funding

    Directory of Open Access Journals (Sweden)

    Vanessa Amália Dalpizol Valiati

    2013-04-01

    Full Text Available The configuration of a new standard of consumption and cultural production based on the participation of consumers through the Internet has become a feature of modern society (Jenkins, 2009; Shirky, 2011. Based on this premise, we intend to analyze the process of crowd funding, in which a mass of staff is united in the realization of cultural projects and to create a unique product, under the bias of the culturological theory. This work is also raising questions as to the timeliness of the concept of cultural industry in the face of new practices allowed by digital networks and a potential democratization, focusing the brazilian website Catarse.

  4. 76 FR 16029 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

    Science.gov (United States)

    2011-03-22

    ... Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture Evaluation Envoys... larger Sports and Culture Evaluation to conduct a survey of the envoys who participated in the Sports... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports...

  5. 76 FR 16031 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

    Science.gov (United States)

    2011-03-22

    ... & Culture Evaluation Sports Surveys, OMB Control Number 1405-xxxx ACTION: Notice of request for public... Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture Evaluation Sports... Sports and Culture Evaluation to conduct a survey of exchange participants who participated in either the...

  6. 76 FR 16033 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

    Science.gov (United States)

    2011-03-22

    ... Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture Evaluation BTL... larger Sports and Culture Evaluation to conduct a survey of exchange participants who participated in the... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports...

  7. Microbial electrosynthetic cells

    Energy Technology Data Exchange (ETDEWEB)

    May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

    2018-01-30

    Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

  8. Nifedipine-activated Ca(2+) permeability in newborn rat cortical collecting duct cells in primary culture.

    Science.gov (United States)

    Valencia, L; Bidet, M; Martial, S; Sanchez, E; Melendez, E; Tauc, M; Poujeol, C; Martin, D; Namorado, M D; Reyes, J L; Poujeol, P

    2001-05-01

    To characterize Ca(2+) transport in newborn rat cortical collecting duct (CCD) cells, we used nifedipine, which in adult rat distal tubules inhibits the intracellular Ca(2+) concentration ([Ca(2+)](i)) increase in response to hormonal activation. We found that the dihydropyridine (DHP) nifedipine (20 microM) produced an increase in [Ca(2+)](i) from 87.6 +/- 3.3 nM to 389.9 +/- 29.0 nM in 65% of the cells. Similar effects of other DHP (BAY K 8644, isradipine) were also observed. Conversely, DHPs did not induce any increase in [Ca(2+)](i) in cells obtained from proximal convoluted tubule. In CCD cells, neither verapamil nor diltiazem induced any rise in [Ca(2+)](i). Experiments in the presence of EGTA showed that external Ca(2+) was required for the nifedipine effect, while lanthanum (20 microM), gadolinium (100 microM), and diltiazem (20 microM) inhibited the effect. Experiments done in the presence of valinomycin resulted in the same nifedipine effect, showing that K(+) channels were not involved in the nifedipine-induced [Ca(2+)](i) rise. H(2)O(2) also triggered [Ca(2+)](i) rise. However, nifedipine-induced [Ca(2+)](i) increase was not affected by protamine. In conclusion, the present results indicate that 1) primary cultures of cells from terminal nephron of newborn rats are a useful tool for investigating Ca(2+) transport mechanisms during growth, and 2) newborn rat CCD cells in primary culture exhibit a new apical nifedipine-activated Ca(2+) channel of capacitive type (either transient receptor potential or leak channel).

  9. The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

    Science.gov (United States)

    Desroches, M; Royer, G; Roche, D; Mercier-Darty, M; Vallenet, D; Médigue, C; Bastard, K; Rodriguez, C; Clermont, O; Denamur, E; Decousser, J-W

    2018-01-01

    More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli , one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses. These differences are correlated with the phylogeographic history of the strain and were due to an unprecedented number of mutations in coding DNA repair functions such as mismatch repair (MutL) and oxidized guanine nucleotide pool cleaning (MutT), conferring a specific mutational spectrum and leading to a mutator phenotype. The mutator phenotype was probably acquired during subculturing and corresponded to second-order selection. Furthermore, all of the isolates exhibited hypersusceptibility to antibiotics due to mutations in efflux pump- and porin-encoding genes, as well as a specific mutation in the sigma factor-encoding gene rpoS . These defects reflect a self-preservation and nutritional competence tradeoff allowing survival under the starvation conditions imposed by storage. From a clinical point of view, dealing with such mutator strains can lead microbiologists to draw false conclusions about isolate relatedness and may impact therapeutic effectiveness. IMPORTANCE Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to

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

    Science.gov (United States)

    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.

  11. Study on chromosome aberrations test determinated by micro-whole blood culture in vacuum blood collection tube

    International Nuclear Information System (INIS)

    Zhong Zhihong; Han Fang'an; Ge Qinjuan; Wu Xiao; Chen Juan

    2006-01-01

    Objective: To develop an easier and efficient method of culturing the chromosome and analyzing the aberrations in peripheral lymphocytes. Methods: Micro whole was cultured for 54 hours in home-made vacuum blood collection tube, and then collection, slice-making, microscopy detection for the chromosome aberrations was done. The difference of the results was analysed by comparing with the common method. Results: For 60 radiologists and 30 contrasts, the chromosome aberrations in peripheral lymphocytes were examed by this system, the lymphocytes and chromosome were clear and alive and easier to analyse. Compared with the common method, there was no significantly difference between the two analyzing results. Conclusion: The chromosome aberrations test by micro whole blood culture in vacuum blood collection tube is easier and efficient, and is worthy of being widely popularized. (authors)

  12. Bacterial diversity analysis of larvae and adult midgut microflora using culture-dependent and culture-independent methods in lab-reared and field-collected Anopheles stephensi-an Asian malarial vector

    Directory of Open Access Journals (Sweden)

    Adak Tridibesh

    2009-05-01

    Full Text Available Abstract Background Mosquitoes are intermediate hosts for numerous disease causing organisms. Vector control is one of the most investigated strategy for the suppression of mosquito-borne diseases. Anopheles stephensi is one of the vectors of malaria parasite Plasmodium vivax. The parasite undergoes major developmental and maturation steps within the mosquito midgut and little is known about Anopheles-associated midgut microbiota. Identification and characterization of the mosquito midgut flora is likely to contribute towards better understanding of mosquito biology including longevity, reproduction and mosquito-pathogen interactions that are important to evolve strategies for vector control mechanisms. Results Lab-reared and field-collected A. stephensi male, female and larvae were screened by "culture-dependent and culture-independent" methods. Five 16S rRNA gene library were constructed form lab and field-caught A. stephensi mosquitoes and a total of 115 culturable isolates from both samples were analyzed further. Altogether, 68 genera were identified from midgut of adult and larval A. stephensi, 53 from field-caught and 15 from lab-reared mosquitoes. A total of 171 and 44 distinct phylotypes having 85 to 99% similarity with the closest database matches were detected among field and lab-reared A. stephensi midgut, respectively. These OTUs had a Shannon diversity index value of 1.74–2.14 for lab-reared and in the range of 2.75–3.49 for field-caught A. stephensi mosquitoes. The high species evenness values of 0.93 to 0.99 in field-collected adult and larvae midgut flora indicated the vastness of microbial diversity retrieved by these approaches. The dominant bacteria in field-caught adult male A. stephensi were uncultured Paenibacillaceae while in female and in larvae it was Serratia marcescens, on the other hand in lab-reared mosquitoes, Serratia marcescens and Cryseobacterium meninqosepticum bacteria were found to be abundant. Conclusion

  13. The Study about the Influence of the Pop Culture for the Japanese Fashion : The Historical Materials Collection about the Connection of Japanese Fashion and Pop Cultures after World War II

    OpenAIRE

    田中, 里尚; 中村, 仁; 梅原, 宏司; 齋木, 吉隆; 古賀, 令子

    2010-01-01

    The purpose of this research collect and arrange documents and historical materials to determine how pop culture influenced the fashion in Japan after World War II. In 2010, we firstly collected previous fashion and popular culture studies done in foreign countries. We found many intriguing studies, but we came upon one which was particularly noteworthy. As a means of clarifying the relationship between fashion and pop culture, we collected books written by Angela McRobbie. Second, we collect...

  14. Production of rhamnolipids by Pseudomonas aeruginosa is inhibited by H2S but resumes in a co-culture with P. stutzeri: applications for microbial enhanced oil recovery.

    Science.gov (United States)

    Zhao, Feng; Ma, Fang; Shi, Rongjiu; Zhang, Jie; Han, Siqin; Zhang, Ying

    2015-09-01

    Sulfate-reducing bacteria and H2S exist widely in oil production systems, and in situ production of rhamnolipids is promising for microbial enhanced oil recovery (MEOR). However, information of the effect of S(2-) on rhamnolipids production is scarce. Two facultative anaerobic rhamnolipids-producing bacterial strains, Pseudomonas aeruginosa SG and WJ-1, were used. Above 10 mg S(2-)/l, both cell growth and rhamnolipids production were inhibited. A large inoculum (9%, v/v) failed to completely relieve the inhibitory effect of 10 mg S(2-)/l. Below 30 mg S(2-)/l, both strains resumed rhamnolipid production through co-culturing with the denitrifying and sulphide-removing strain Pseudomonas stutzeri DQ1. H2S has a direct but reversible inhibitory effect on rhamnolipids production. Control of H2S in oilfields is indispensable to MEOR, and the co-culture method is effective in restoring rhamnolipid production in presence of S(2-).

  15. Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training

    KAUST Repository

    Antunes, Andre

    2015-12-23

    A survey of European Microbial Biological Resource Centers and their users provided an overview on microbiology education and training. The results identified future increases in demand despite several shortcomings and gaps in the current offer. Urgent adjustments are needed to match users\\' needs, integrate innovative programs, and adopt new technologies. © 2015 Elsevier Ltd.

  16. Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training.

    Science.gov (United States)

    Antunes, André; Stackebrandt, Erko; Lima, Nelson

    2016-02-01

    A survey of European Microbial Biological Resource Centers and their users provided an overview on microbiology education and training. The results identified future increases in demand despite several shortcomings and gaps in the current offer. Urgent adjustments are needed to match users' needs, integrate innovative programs, and adopt new technologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

    NARCIS (Netherlands)

    Besaury, L.; Marty, F.; Buquet, S.; Mesnage, V.; Muijzer, G.; Quillet, L.

    2013-01-01

    Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions,

  18. Culture, Materiality, Memory: Collective Ownership and Action In Romanian Mutual Funds

    Directory of Open Access Journals (Sweden)

    Narcis TULBURE

    2015-12-01

    Full Text Available The paper presents the tensions between collectivist and corporatist forms of ownership for Romanian mutual funds. Drawing on my research among retail investors of funds that ended up in bankruptcy throughout the postsocialist period, I document the material practices and graphic artefacts they deploy in litigation as ways to make claims and produce evidence regarding their ongoing financial involvement and the rights to compensations. I focus specifically on the files documenting their personal histories (providing moral reasons for pursuing “speculative” investments as well as those materializing the memory of their involvement with the capital market. I conclude that material practices are constitutive of vernacular forms of financial and legal knowledge. Furthermore, they engender specific types of property that serve as premises for the defense of investor rights and as grounds for emerging forms of collective action. Methodologically, the conclusion of the paper is that qualitative methods constitute alternative approaches and a valuable complement of quantitate research methods for the behaviors of mutual fund investors illustrating some of the cultural components giving specific dynamics to the popular participation to the capital market that can be subsequently quantified.

  19. 76 FR 16031 - 60-Day Notice of Proposed Information Collection: Bureau of Educational and Cultural Affairs...

    Science.gov (United States)

    2011-03-22

    ...: Kennedy Center (KC) Cultural Visitors Program participants conducted by ECA from 2005 through 2009... of Educational and Cultural Affairs, Office of Policy and Evaluation, Evaluation Division: Sports & Culture Evaluation Kennedy Center Visitors Survey, OMB Control Number 1405-xxxx ACTION: Notice of request...

  20. EVA Suit Microbial Leakage Investigation

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

  1. Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

    International Nuclear Information System (INIS)

    Lee, Duu-Jong; Lee, Chin-Yu; Chang, Jo-Shu

    2012-01-01

    Highlights: ► We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. ► Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. ► The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. ► The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

  2. Treatment and electricity harvesting from sulfate/sulfide-containing wastewaters using microbial fuel cell with enriched sulfate-reducing mixed culture

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Duu-Jong, E-mail: cedean@mail.ntust.edu.tw [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan (China); Lee, Chin-Yu [Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan (China); Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan (China); Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan (China); Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan (China)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer We started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture. Black-Right-Pointing-Pointer Sulfate-reducing bacteria and anode-respiring bacteria were enriched in anodic biofilms. Black-Right-Pointing-Pointer The MFC effectively remove sulfate to elementary sulfur in the presence of lactate. Black-Right-Pointing-Pointer The present device can treat sulfate laden wastewaters with electricity harvesting. - Abstract: Anaerobic treatment of sulfate-laden wastewaters can produce excess sulfide, which is corrosive to pipelines and is toxic to incorporated microorganisms. This work started up microbial fuel cell (MFC) using enriched sulfate-reducing mixed culture as anodic biofilms and applied the so yielded MFC for treating sulfate or sulfide-laden wastewaters. The sulfate-reducing bacteria in anodic biofilm effectively reduced sulfate to sulfide, which was then used by neighboring anode respiring bacteria (ARB) as electron donor for electricity production. The presence of organic carbons enhanced MFC performance since the biofilm ARB were mixotrophs that need organic carbon to grow. The present device introduces a route for treating sulfate laden wastewaters with electricity harvesting.

  3. Microbial Contamination of Date Rutab Collected from the Markets of Al-Hofuf City in Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Siddig H. Hamad

    2012-01-01

    Full Text Available The microbial contamination of 60 samples from six date cultivars in the rutab stage purchased from different retail outlets in AL-Hofuf City, Saudi Arabia was studied. All samples were found contaminated with aerobic mesophilic bacteria at loads in the order 102 to 105 cfu/cm2 with some significant differences among varieties that can be attributed to differences in the weather conditions during rutab season. Also all samples, except only one, were contaminated with molds and yeasts at loads in the order 102 to 103 cfu/cm2. Potentially pathogenic Staphylococcus aureus was detected in 57 samples and A. flavus/parasiticus in 13 samples, while coliforms were detected in 39 samples.

  4. The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing

    Directory of Open Access Journals (Sweden)

    Kevin McCluskey

    2017-08-01

    Full Text Available The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD. The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol.

  5. Polyhydroxyalkanoate synthesis by mixed microbial consortia cultured on fermented dairy manure: Effect of aeration on process rates/yields and the associated microbial ecology.

    Science.gov (United States)

    Coats, Erik R; Watson, Benjamin S; Brinkman, Cynthia K

    2016-12-01

    Polyhydroxyalkanoates (PHAs) are biodegradable polymers that can substitute for petroleum-based plastics in a variety of applications. One avenue to commercial PHA production involves coupling waste-based synthesis with the use of mixed microbial consortia (MMC). In this regard, production requires maximizing the enrichment of a MMC capable of feast-famine PHA synthesis, with the metabolic response induced through imposition of aerobic-dynamic feeding (ADF) conditions. However, the concept of PHA production in complex matrices remains unrefined; process operational improvements are needed, along with an enhanced understanding of the MMC. Research presented herein investigated the effect of aeration on feast-famine PHA synthesis, with four independent aeration state systems studied; MMC were fed volatile fatty acid (VFA)-rich fermented dairy manure. Regardless of the aeration state, all MMC exhibited a feast-famine response based on observed carbon cycling. Moreover, there was no statistical difference in PHA synthesis rates, with q PHA ranging from 0.10 to 0.19 CmmolPHA gVSS -1 min -1 ; VFA uptake rates exhibited similar statistical indifferences. PHA production assessments on the enriched MMC resulted in maximum intracellular concentrations ranging from 22.5 to 90.7% (mgPHA mgVSS -1 ); at maximum concentration, the mean hydroxyvalerate mol content was 73 ± 0.6%. While a typical feast-famine dissolved oxygen (DO) pattern was observed at maximum aeration, less resolution was observed at decreasing aeration rates, suggesting that DO may not be an optimal process monitoring parameter. At lower aeration states, nitrogen cycling patterns, supported by molecular investigations targeting AOBs and NOBs, indicate that NO 2 and NO 3 sustained feast-famine PHA synthesis. Next-generation sequencing analysis of the respective MMC revealed numerous and diverse genera exhibiting the potential to achieve PHA synthesis, suggesting functional redundancy embedded in the diverse

  6. Microbial acetate oxidation in horizontal rotating tubular bioreactor

    Indian Academy of Sciences (India)

    Unknown

    shaped partition walls that served as carriers for micro- bial biomass. Mixing ... from soil sample collected from Zagreb mountain. This microbial culture was ... HRTB was made of a plastic tube 1⋅8 m long with an inner diameter of 0⋅25 m.

  7. Collective Cultural Memory as a TV Guide : ‘Living’ History and Nostalgia on the Digital Television Platform

    NARCIS (Netherlands)

    Hagedoorn, Berber

    2017-01-01

    Collective Cultural Memory as a TV Guide: “Living” History and Nostalgia on the Digital Television Platform Berber Hagedoorn University of Groningen (NL) E-mail: b.hagedoorn@rug.nl Abstract: Modern audiences engage with representations of the past in a particular way via the medium of television,

  8. Cultural Codes as Catalysts for Collective Conscientisation in Environmental Adult Education: Mr. Floatie, Tree Squatting and Save-Our-Surfers

    Science.gov (United States)

    Walter, Pierre

    2012-01-01

    This study examines how cultural codes in environmental adult education can be used to "frame" collective identity, develop counterhegemonic ideologies, and catalyse "educative-activism" within social movements. Three diverse examples are discussed, spanning environmental movements in urban Victoria, British Columbia, Canada,…

  9. Taxonomic evaluation of unidentified Streptomyces isolates in the ARS Culture Collection (NRRL) using multi-locus sequence analysis

    Science.gov (United States)

    The ARS Culture Collection (NRRL) currently contains 7569 strains within the family Streptomycetaceae but 4368 of them have not been characterized to the species level. A gene sequence database using the Bacterial Isolate Genomic Sequence Database package (BIGSdb) (Jolley & Maiden, 2010) is availabl...

  10. Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS (NRRL) Culture Collection using multi-locus sequence analysis

    Science.gov (United States)

    Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 str...

  11. Simultaneous Transformation of Commingled Trichloroethylene, Tetrachloroethylene, and 1,4-Dioxane by a Microbially Driven Fenton Reaction in Batch Liquid Cultures

    Science.gov (United States)

    Sekar, Ramanan; Taillefert, Martial

    2016-01-01

    ABSTRACT Improper disposal of 1,4-dioxane and the chlorinated organic solvents trichloroethylene (TCE) and tetrachloroethylene (also known as perchloroethylene [PCE]) has resulted in widespread contamination of soil and groundwater. In the present study, a previously designed microbially driven Fenton reaction system was reconfigured to generate hydroxyl (HO˙) radicals for simultaneous transformation of source zone levels of single, binary, and ternary mixtures of TCE, PCE, and 1,4-dioxane. The reconfigured Fenton reaction system was driven by fed batch cultures of the Fe(III)-reducing facultative anaerobe Shewanella oneidensis amended with lactate, Fe(III), and contaminants and exposed to alternating anaerobic and aerobic conditions. To avoid contaminant loss due to volatility, the Fe(II)-generating, hydrogen peroxide-generating, and contaminant transformation phases of the microbially driven Fenton reaction system were separated. The reconfigured Fenton reaction system transformed TCE, PCE, and 1,4-dioxane either as single contaminants or as binary and ternary mixtures. In the presence of equimolar concentrations of PCE and TCE, the ratio of the experimentally derived rates of PCE and TCE transformation was nearly identical to the ratio of the corresponding HO˙ radical reaction rate constants. The reconfigured Fenton reaction system may be applied as an ex situ platform for simultaneous degradation of commingled TCE, PCE, and 1,4-dioxane and provides valuable information for future development of in situ remediation technologies. IMPORTANCE A microbially driven Fenton reaction system [driven by the Fe(III)-reducing facultative anaerobe S. oneidensis] was reconfigured to transform source zone levels of TCE, PCE, and 1,4-dioxane as single contaminants or as binary and ternary mixtures. The microbially driven Fenton reaction may thus be applied as an ex situ platform for simultaneous degradation of at least three (and potentially more) commingled contaminants

  12. Surface-to-surface biofilm transfer: a quick and reliable startup strategy for mixed culture microbial fuel cells.

    Science.gov (United States)

    Vogl, Andreas; Bischof, Franz; Wichern, Marc

    2016-01-01

    The startup of microbial fuel cells (MFCs) is known to be prone to failure or result in erratic performance impeding the research. The aim of this study was to advise a quick launch strategy for laboratory-scale MFCs that ensures steady operation performance in a short period of time. Different startup strategies were investigated and compared with membraneless single chamber MFCs. A direct surface-to-surface biofilm transfer (BFT) in an operating MFC proved to be the most efficient method. It provided steady power densities of 163 ± 13 mWm(-2) 4 days after inoculation compared to 58 ± 15 mWm(-2) after 30 days following a conventional inoculation approach. The in situ BFT eliminates the need for microbial acclimation during startup and reduces performance fluctuations caused by shifts in microbial biodiversity. Anaerobic pretreatment of the substrate and addition of suspended enzymes from an operating MFC into the new MFC proved to have a beneficial effect on startup and subsequent operation. Polarization methods were applied to characterize the startup phase and the steady state operation in terms of power densities, internal resistance and power overshoot during biofilm maturation. Applying this method a well-working MFC can be multiplied into an array of identically performing MFCs.

  13. Collection methods and quality assessment for Esche-richia coli, water quality, and microbial source tracking data within Tumacácori National Historical Park and the upper Santa Cruz River, Arizona, 2015-16

    Science.gov (United States)

    Paretti, Nicholas; Coes, Alissa L.; Kephart, Christopher M.; Mayo, Justine

    2018-03-05

    Tumacácori National Historical Park protects the culturally important Mission, San José de Tumacácori, while also managing a portion of the ecologically diverse riparian corridor of the Santa Cruz River. This report describes the methods and quality assurance procedures used in the collection of water samples for the analysis of Escherichia coli (E. coli), microbial source tracking markers, suspended sediment, water-quality parameters, turbidity, and the data collection for discharge and stage; the process for data review and approval is also described. Finally, this report provides a quantitative assessment of the quality of the E. coli, microbial source tracking, and suspended sediment data.The data-quality assessment revealed that bias attributed to field and laboratory contamination was minimal, with E. coli detections in only 3 out of 33 field blank samples analyzed. Concentrations in the field blanks were several orders of magnitude lower than environmental concentrations. The microbial source tracking (MST) field blank was below the detection limit for all MST markers analyzed. Laboratory blanks for E. coli at the USGS Arizona Water Science Center and laboratory blanks for MST markers at the USGS Ohio Water Microbiology Laboratory were all below the detection limit. Irreplicate data for E. coli and suspended sediment indicated that bias was not introduced to the data by combining samples collected using discrete sampling methods with samples collected using automatic sampling methods.The split and sequential E. coli replicate data showed consistent analytical variability and a single equation was developed to explain the variability of E. coli concentrations. An additional analysis of analytical variability for E. coli indicated analytical variability around 18 percent relative standard deviation and no trend was observed in the concentration during the processing and analysis of multiple split-replicates. Two replicate samples were

  14. Collaboration in Visual Culture Learning Communities: Towards a Synergy of Individual and Collective Creative Practice

    Science.gov (United States)

    Karpati, Andrea; Freedman, Kerry; Castro, Juan Carlos; Kallio-Tavin, Mira; Heijnen, Emiel

    2017-01-01

    A visual culture learning community (VCLC) is an adolescent or young adult group engaged in expression and creation outside of formal institutions and without adult supervision. In the framework of an international, comparative research project executed between 2010 and 2014, members of a variety of eight self-initiated visual culture groups…

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

    Science.gov (United States)

    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

  16. Establishment of 3D culture and induction of osteogenic differentiation of pre-osteoblasts using wet-collected aligned scaffolds

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Huifen [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China); Chongqing Affiliated Hospital of Stomatology, Chongqing University of Medical Sciences, Chongqing 400015 (China); Zhong, Junwen [Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074 (China); Xu, Fei; Song, Fangfang; Yin, Miao; Wu, Yanru; Hu, Qiyi [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China); Wang, Jiawei, E-mail: wangjwei@hotmail.com [Hubei-MOSTKLOS & KLOBM, School and Hospital of Stomatology, Wuhan University, Wuhan 430079 (China)

    2017-02-01

    Aligned fibrous scaffolds have attracted much interest in bone tissue engineering, because they are supposed to induce osteogenic differentiation. For the first time, aligned silk fibroin nanofibres were loosely packed using a novel wet-collection electrospinning method. Moreover, three-dimensional (3D) culture of MC3T3-E1 pre-osteoblasts was established on these fibrous scaffolds. Physicochemical properties of the scaffolds and the behaviour of MC3T3-E1 pre-osteoblasts on the scaffolds were analysed and compared with scaffolds obtained using traditional method. Ethanol bath improved the uniformity and alignment of the fibres and increased the thickness and porosity of the scaffolds. Structures of the fibres were well maintained after immediate crosslinking in ethanol. Cells on the wet-collected scaffolds exhibited more ordered arrangement and elongated morphology as well as faster and deeper infiltration. The ordered infiltration resulted in the establishment of the 3D culture of cells, promoting proliferation and osteogenic differentiation of the pre-osteoblasts. Thus, the wet-collected aligned scaffolds with improved topographical and physicochemical properties presents significant potential application in bone regeneration. - Highlights: • Aligned silk fibroin nanofibres were loosely packed using a novel wet-collection electrospinning method. • Structural properties of the aligned nanofibres were improved. • Three-dimensional culture of MC3T3-E1 pre-osteoblasts was established. • The arrangement, morphology, infiltration, proliferation and osteogenic differentiation of cells were enhanced.

  17. Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques.

    Science.gov (United States)

    Ryssel, Mia; Johansen, Pernille; Al-Soud, Waleed Abu; Sørensen, Søren; Arneborg, Nils; Jespersen, Lene

    2015-12-23

    Microbial successions on the surface and in the interior of surface ripened semi-hard Danish Danbo cheeses were investigated by culture-dependent and -independent techniques. Culture-independent detection of microorganisms was obtained by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture-independent techniques correlated, a higher number of genera were detected by pyrosequencing compared to DGGE. Additionally, minor parts of the microbiota, i.e. comprising surface and the interior of the cheeses diverged. During cheese production pyrosequencing determined Lactococcus as the dominating genus on cheese surfaces, representing on average 94.7%±2.1% of the OTUs. At day 6 Lactococcus spp. declined to 10.0% of the OTUs, whereas Staphylococcus spp. went from 0.0% during cheese production to 75.5% of the OTUs at smearing. During ripening, i.e. from 4 to 18 weeks, Corynebacterium was the dominant genus on the cheese surface (55.1%±9.8% of the OTUs), with Staphylococcus (17.9%±11.2% of the OTUs) and Brevibacterium (10.4%±8.3% of the OTUs) being the second and third most abundant genera. Other detected bacterial genera included Clostridiisalibacter (5.0%±4.0% of the OTUs), as well as Pseudoclavibacter, Alkalibacterium and Marinilactibacillus, which represented surface ripened semi-hard cheeses. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Organizational culture - a factor of potential positive influence on the collectivities of any organization

    Directory of Open Access Journals (Sweden)

    Ramona-Andreea MIHALACHE

    2016-07-01

    Full Text Available Organizational culture is a relatively new and rapidly expanding concept, but partly invisible and therefore very difficult analyze, offering in the same time the possibility to carry out complex studies. This paper was drawn up into two different organizations - Pentalog Romania, an IT service provider, and House of Dracula Hotel, a tourist unit - and it is based on a research carried out in order to highlight the importance of organizational culture within any entity. Considered a powerful strategic tool, the organizational culture can be used for focusing companies and their staff on joint goals, for mobilizing the initiatives, ensuring loyalty and facilitating intercommunication.

  19. Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel

    Directory of Open Access Journals (Sweden)

    C. Varrone

    2015-01-01

    Full Text Available Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs, able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable and stable MMC, trying to overcome inhibition problems and enhance substrate degradation efficiency, as well as generation of soluble fermentation products. Repeated transfers in small batches and fed-batch conditions have been applied, comparing the use of different inoculum, growth media, and Kinetic Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h and different dominant metabolic products were obtained, depending on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate. On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1,3-propanediol and butyrate production. Changes in microbial composition were monitored by means of Next Generation Sequencing, revealing a dominance of glycerol consuming species, such as Clostridium, Klebsiella, and Escherichia.

  20. Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel.

    Science.gov (United States)

    Varrone, C; Heggeset, T M B; Le, S B; Haugen, T; Markussen, S; Skiadas, I V; Gavala, H N

    2015-01-01

    Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs), able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable and stable MMC, trying to overcome inhibition problems and enhance substrate degradation efficiency, as well as generation of soluble fermentation products. Repeated transfers in small batches and fed-batch conditions have been applied, comparing the use of different inoculum, growth media, and Kinetic Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h) and different dominant metabolic products were obtained, depending on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate). On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1,3-propanediol and butyrate production. Changes in microbial composition were monitored by means of Next Generation Sequencing, revealing a dominance of glycerol consuming species, such as Clostridium, Klebsiella, and Escherichia.

  1. The culture collection and herbarium of the Center for Forest Mycology Research: A national resource

    Science.gov (United States)

    J.A. Glaeser; K.K. Nakasone; D.J. Lodge; B. Ortiz-Santana; D.L. Lindner

    2013-01-01

    The Center for Forest Mycology Research (CFMR), U.S. Forest Service, Northern Research Station, Madison, WI, is home to the world's largest collection of wood-inhabiting fungi. These collections constitute a library of the fungal kingdom that is used by researchers thoughout the world. The CFMR collections have many practical uses that have improved the lives of...

  2. Microbial flora analysis for the degradation of beta-cypermethrin.

    Science.gov (United States)

    Qi, Zhang; Wei, Zhang

    2017-03-01

    In the Xinjiang region of Eurasia, sustained long-term and continuous cropping of cotton over a wide expanse of land is practiced, which requires application of high levels of pyrethroid and other classes of pesticides-resulting in high levels of pesticide residues in the soil. In this study, soil samples were collected from areas of long-term continuous cotton crops with the aim of obtaining microbial resources applicable for remediation of pyrethroid pesticide contamination suitable for the soil type and climate of that area. Soil samples were first used to culture microbial flora capable of degrading beta-cypermethrin using an enrichment culture method. Structural changes and ultimate microbial floral composition during enrichment were analyzed by high-throughput sequencing. Four strains capable of degrading beta-cypermethrin were isolated and preliminarily classified. Finally, comparative rates and speeds of degradation of beta-cypermethrin between relevant microbial flora and single strains were determined. After continuous subculture for 3 weeks, soil sample microbial flora formed a new type of microbial flora by rapid succession, which showed stable growth by utilizing beta-cypermethrin as the sole carbon source (GXzq). This microbial flora mainly consisted of Pseudomonas, Hyphomicrobium, Dokdonella, and Methyloversatilis. Analysis of the microbial flora also permitted separation of four additional strains; i.e., GXZQ4, GXZQ6, GXZQ7, and GXZQ13 that, respectively, belonged to Streptomyces, Enterobacter, Streptomyces, and Pseudomonas. Under culture conditions of 37 °C and 180 rpm, the degradation rate of beta-cypermethrin by GXzq was as high as 89.84% within 96 h, which exceeded that achieved by the single strains GXZQ4, GXZQ6, GXZQ7, and GXZQ13 and their derived microbial flora GXh.

  3. Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel

    DEFF Research Database (Denmark)

    Varrone, Cristiano; Heggeset, T. M. B.; Le, S. B.

    2015-01-01

    Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs), able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable...... Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h) and different dominant metabolic products were obtained, depending...... on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate). On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1...

  4. Characterization of multiple antibiotic resistance of culturable microorganisms and metagenomic analysis of total microbial diversity of marine fish sold in retail shops in Mumbai, India.

    Science.gov (United States)

    Naik, Onkar A; Shashidhar, Ravindranath; Rath, Devashish; Bandekar, Jayant R; Rath, Archana

    2018-03-01

    Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g -1 . Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium. Most of these pathogens were resistant to multiple antibiotics such as erythromycin, kanamycin, neomycin, streptomycin, penicillin, cefotaxime, bacitracin, rifampicin, trimethoprim, ciprofloxacin, and doxycycline with a high multiple antibiotic resistance index of 0.54-0.77. The fish microflora showed high prevalence of AR genes like bla TEM , Class I integron, tetA, aph(3')-IIIa, ermB, aadA, and sul1. Nineteen of 26 AR isolates harbored Class I integrons showing high co-resistance to trimethoprim, kanamycin, doxycycline, and cefotaxime. Mobile R-plasmids from 6 of the 12 AR pathogens were transferred to recipient E. coli after conjugation. The transconjugants harbored the same R-plasmid carrying bla CTX-M , dfr1, tetA, bla TEM , and cat genes. This study confirms that fish is a potential carrier of AR pathogens which can enter the human gut via food chain. To the best of our knowledge, this is the first study in the Indian subcontinent reporting a direct evidence of spread of AR pathogens to humans from specific marine fish consumption.

  5. An epidemic of collective conversion and dissociation disorder in an indigenous group of Colombia: its relation to cultural change.

    Science.gov (United States)

    Piñeros, M; Rosselli, D; Calderon, C

    1998-06-01

    We describe a collective episode of psychogenic illness in an indigenous group (Embera) of Colombia, geographically isolated from its native homeland and surrounded by non-indigenous settlers. The condition, which affected three young adult men and six adolescent women, was attributed by them to a spell (maleficio). It was designated as ataques de locura (madness attacks) according to their traditional medical system; and as a conversive disorder with dissociative features by psychiatrists. Different therapeutic approaches, including antipsychotic medication, religious healers and traditional herbal remedies were unsuccessful. Contact with shamans of the same ethnic origin, on the other hand, proved to be an effective way of dealing with the symptoms. We interpret the situation as an expression of psychosocial stress secondary to cultural change. This medical problem bears close resemblance to other specific culture-bound syndromes such as ataques de nervios or possession syndromes and gives clues to ways of dealing with psychogenic expressions of cultural stress.

  6. Strategies for efficiently selecting PHA producing mixed microbial cultures using complex feedstocks: Feast and famine regime and uncoupled carbon and nitrogen availabilities.

    Science.gov (United States)

    Oliveira, Catarina S S; Silva, Carlos E; Carvalho, Gilda; Reis, Maria A

    2017-07-25

    Production of polyhydroxyalkanoates (PHAs) by open mixed microbial cultures (MMCs) has been attracting increasing interest as an alternative technology to PHA production by pure cultures, due to the potential for lower costs associated with the use of open systems (eliminating the requirement for sterile conditions) and the utilisation of cheap feedstock (industrial and agricultural wastes). Such technology relies on the efficient selection of an MMC enriched in PHA-accumulating organisms. Fermented cheese whey, a protein-rich complex feedstock, has been used previously to produce PHA using the feast and famine regime for selection of PHA accumulating cultures. While this selection strategy was found efficient when operated at relatively low organic loading rate (OLR, 2g-CODL -1 d -1 ), great instability and low selection efficiency of PHA accumulating organisms were observed when higher OLR (ca. 6g-CODL -1 d -1 ) was applied. High organic loading is desirable as a means to enhance PHA productivity. In the present study, a new selection strategy was tested with the aim of improving selection for high OLR. It was based on uncoupling carbon and nitrogen supply and was implemented and compared with the conventional feast and famine strategy. For this, two selection reactors were fed with fermented cheese whey applying an OLR of ca. 8.5g-CODL -1 (with 3.8g-CODL -1 resulting from organic acids and ethanol), and operated in parallel under similar conditions, except for the timing of nitrogen supplementation. Whereas in the conventional strategy nitrogen and carbon substrates were added simultaneously at the beginning of the cycle, in the uncoupled substrates strategy, nitrogen addition was delayed to the end of the feast phase (i.e. after exogenous carbon was exhausted). The two different strategies selected different PHA-storing microbial communities, dominated by Corynebacterium and a Xantomonadaceae, respectively with the conventional and the new approaches. The new

  7. Comparison of Vibrio harveyi strains isolated from shrimp farms and from culture collection in terms of toxicity and antibiotic resistance.

    Science.gov (United States)

    Nakayama, Tatsuya; Ito, Emi; Nomura, Nakao; Nomura, Nobuhiko; Matsumura, Masatoshi

    2006-05-01

    Vibrio harveyi strains isolated from shrimp farms (wild strains) were compared with those from culture collections in terms of minimum inhibitory concentration (MIC) and toxicity. Wild strains had higher MIC values for four antibiotics (kanamycin, carbenicillin, oxytetracycline and ampicillin) and also showed higher toxicity compared with culture collection strains. Vibrio harveyi with the lowest antibacterial resistance was chosen to test if a gradual increase in antibiotic concentration and frequent subculture would enhance its antibiotic resistance. Results showed that V. harveyi was able to develop resistance to oxytetracycline. The MIC value was 250 times higher compared with the MIC before subculturing. Moreover, the V. harveyi strain developed slightly higher toxicity. Therefore, it is possible that there is a relationship between antibiotic resistance and toxicity in V. harveyi.

  8. Effects of concentrate replacement by feed blocks on ruminal fermentation and microbial growth in goats and single-flow continuous-culture fermenters.

    Science.gov (United States)

    Molina-Alcaide, E; Pascual, M R; Cantalapiedra-Hijar, G; Morales-García, E Y; Martín-García, A I

    2009-04-01

    The effect of replacing concentrate with 2 different feed blocks (FB) on ruminal fermentation and microbial growth was evaluated in goats and in single-flow continuous-culture fermenters. Diets consisted of alfalfa hay plus concentrate and alfalfa hay plus concentrate with 1 of the 2 studied FB. Three trials were carried out with 6 rumen-fistulated Granadina goats and 3 incubation runs in 6 single-flow continuous-culture fermenters. Experimental treatments were assigned randomly within each run, with 2 repetitions for each diet. At the end of each in vivo trial, the rumen contents were obtained for inoculating the fermenters. For each incubation run, the fermenters were inoculated with ruminal fluid from goats fed the same diet supplied to the corresponding fermenter flask. The average pH values, total and individual VFA, and NH(3)-N concentrations, and acetate:propionate ratios in the rumen of goats were not affected (P >or= 0.10) by diet, whereas the microbial N flow (MNF) and efficiency were affected (P fermenters, the diet affected pH (Por= 0.05), and total (P=0.02), NH(3) (P=0.005), and non-NH(3) (P=0.02) N flows, whereas the efficiency of VFA production was not affected (P=0.75). The effect of diet on MNF and efficiency depended on the bacterial pellet used as a reference. An effect (Pfermenter contents and effluent were similar (P=0.05). Differences (Pfermentation variables and bacterial pellet compositions were found. Partial replacement of the concentrate with FB did not greatly compromise carbohydrate fermentation in unproductive goats. However, this was not the case for MNF and efficiency. Differences between the results obtained in vivo and in vitro indicate a need to identify conditions in fermenters that allow better simulation of fermentation, microbial growth, and bacterial pellet composition in vivo. Reduced feeding cost could be achieved with the inclusion of FB in the diets of unproductive goats without altering rumen fermentation.

  9. Occurrence and characterization of Candida nivariensis from a culture collection of Candida glabrata clinical isolates in Malaysia.

    Science.gov (United States)

    Tay, Sun Tee; Lotfalikhani, Azadeh; Sabet, Negar Shafiei; Ponnampalavanar, Sasheela; Sulaiman, Sofiah; Na, Shiang Ling; Ng, Kee Peng

    2014-10-01

    Candida nivariensis and C. bracarensis have been recently identified as emerging yeast pathogens which are phenotypically indistinguishable from C. glabrata. However, there is little data on the prevalence and antifungal susceptibilities of these species. This study investigated the occurrence of C. nivariensis and C. bracarensis in a culture collection of 185 C. glabrata isolates at a Malaysian teaching hospital. C. nivariensis was discriminated from C. glabrata using a PCR assay as described by Enache-Angoulvant et al. (J Clin Microbiol 49:3375-9, 2011). The identity of the isolates was confirmed by sequence analysis of the D1D2 domain and internal transcribed spacer region of the yeasts. The isolates were cultured on Chromogenic CHROMagar Candida (®) agar (Difco, USA), and their biochemical and enzymic profiles were determined. Antifungal susceptibilities of the isolates against amphotericin B, fluconazole, voriconazole and caspofungin were determined using E tests. Clotrimazole MICs were determined using a microbroth dilution method. There was a low prevalence (1.1 %) of C. nivariensis in our culture collection of C. glabrata. C. nivariensis was isolated from a blood culture and vaginal swab of two patients. C. nivariensis grew as white colonies on Chromogenic agar and demonstrated few positive reactions using biochemical tests. Enzymatic profiles of the C. nivariensis isolates were similar to that of C. glabrata. The isolates were susceptible to amphotericin B, fluconazole, voriconazole and caspofungin. Clotrimazole resistance is suspected in one isolate. This study reports for the first time the emergence of C. nivariensis in our clinical setting.

  10. Resistance to Cultural Intervention: Formation of Inhibitory Collective and children's Self-Defensive Regulation in a Chinese School.

    Science.gov (United States)

    Wu, Aruna; Li, Xiao-Wen; Zhou, Lihua; Zhang, Qian

    2017-09-01

    A sequel to the previous article "Roots of Excellence: The Releasing Effect of Individual Potentials through Educational Cultural Intervention in a Chinese School" (in press), the present study is on the unexpected reversal phenomena in the process of cultural intervention. The goal of the intervention is to construct the dynamics of Jiti (well-organized collective in Chinese) through creative activities to promote students' development. In the intervention, the releasing effect (Wu et al. 2016) emerged as well, but the teacher's concern about worsening discipline and academic performance evoked and reinforced his habitual notions and practices of education, turning the joint activities into a way of strengthening discipline. The energy that had been discharging at the beginning of the intervention was inhibited, so that many more problematic behaviors took shape. The whole class formed an inhibitory atmosphere, within which pupils formed self-defensive regulation strategies. By comparing with the productive collective in which intervention was effective and analyzing this unexpected reversal process, we can not only see pupils' self-construction status in the inhibitory culture but illuminate the formation of the teacher's resistance to educational and cultural transformation as well. Resistance is originated from teachers not being able to interpret pupils' inner developmental needs but instead anxious about the ongoing problems.

  11. Near-IR laser-triggered target cell collection using a carbon nanotube-based cell-cultured substrate.

    Science.gov (United States)

    Sada, Takao; Fujigaya, Tsuyohiko; Niidome, Yasuro; Nakazawa, Kohji; Nakashima, Naotoshi

    2011-06-28

    Unique near-IR optical properties of single-walled carbon nanotube (SWNTs) are of interest in many biological applications. Here we describe the selective cell detachment and collection from an SWNT-coated cell-culture dish triggered by near-IR pulse laser irradiation. First, HeLa cells were cultured on an SWNT-coated dish prepared by a spraying of an aqueous SWNT dispersion on a glass dish. The SWNT-coated dish was found to show a good cell adhesion behavior as well as a cellular proliferation rate similar to a conventional glass dish. We discovered, by near-IR pulse laser irradiation (at the laser power over 25 mW) to the cell under optical microscopic observation, a quick single-cell detachment from the SWNT-coated surface. Shockwave generation from the irradiated SWNTs is expected to play an important role for the cell detachment. Moreover, we have succeeded in catapulting the target single cell from the cultured medium when the depth of the medium was below 150 μm and the laser power was stronger than 40 mW. The captured cell maintained its original shape. The retention of the genetic information of the cell was confirmed by the polymerase chain reaction (PCR) technique. A target single-cell collection from a culture medium under optical microscopic observation is significant in wide fields of single-cell studies in biological areas.

  12. The use of physical and virtual infrastructures for the validation of algal cryopreservation methods in international culture collections

    Czech Academy of Sciences Publication Activity Database

    Day, J. G.; Lorenz, M.; Wilding, T.A.; Friedl, T.; Harding, K.; Pröschold, T.; Brennan, D.; Müller, J.; Santos, L. M. A.; Santos, M. F.; Osório, H.C.; Amaral, R.; Lukešová, Alena; Hrouzek, Pavel; Lukeš, Martin; Elster, Josef; Lukavský, Jaromír; Probert, I.; Ryan, M.J.; Benson, E. E.

    2007-01-01

    Roč. 28, č. 5 (2007), s. 359-376 ISSN 0143-2044 Grant - others:Evropská unie(XE) QLRT-2000-01645 (Cobra) Institutional research plan: CEZ:AV0Z60660521; CEZ:AV0Z60050516 Source of funding: V - iné verejné zdroje Keywords : cryopreservation * storage * culture collections Subject RIV: EH - Ecology, Behaviour Impact factor: 1.141, year: 2007

  13. Objects of utility: cultural responses to industrial collections in municipal museums 1845-1914

    Directory of Open Access Journals (Sweden)

    Robert Snape

    2010-03-01

    Full Text Available Between 1845 and 1914 several municipal museums in Great Britain established an industrial collection of objects relevant to local manufacture. The origins of these collections are found in the 1830s and the reform of design education. Industrial collections assigned an economic function to museums and were contested by critics who maintained that museums should be concerned primarily with fine rather than applied art. It is argued that curatorial decisions on the adoption of industrial collections can be evaluated with reference to contemporary debates on art, design education and the relative values of liberal and applied knowledge. Through case studies of the municipal museums of Birmingham and Preston, this paper assesses contrasting curatorial responses to industrial collections. Adopting Matthew Arnold’s categories of Hebraism and Hellenism as an exploratory framework, it concludes that industrial collections represented materialistic values associated with Hebraism that were directly opposed to the spiritual values associated with Hellenism.

  14. Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: Model validation and sensitivity analysis

    Science.gov (United States)

    Chen, Mingjie; Abriola, Linda M.; Amos, Benjamin K.; Suchomel, Eric J.; Pennell, Kurt D.; Löffler, Frank E.; Christ, John A.

    2013-08-01

    Reductive dechlorination catalyzed by organohalide-respiring bacteria is often considered for remediation of non-aqueous phase liquid (NAPL) source zones due to cost savings, ease of implementation, regulatory acceptance, and sustainability. Despite knowledge of the key dechlorinators, an understanding of the processes and factors that control NAPL dissolution rates and detoxification (i.e., ethene formation) is lacking. A recent column study demonstrated a 5-fold cumulative enhancement in tetrachloroethene (PCE) dissolution and ethene formation (Amos et al., 2009). Spatial and temporal monitoring of key geochemical and microbial (i.e., Geobacter lovleyi and Dehalococcoides mccartyi strains) parameters in the column generated a data set used herein as the basis for refinement and testing of a multiphase, compositional transport model. The refined model is capable of simulating the reactive transport of multiple chemical constituents produced and consumed by organohalide-respiring bacteria and accounts for substrate limitations and competitive inhibition. Parameter estimation techniques were used to optimize the values of sensitive microbial kinetic parameters, including maximum utilization rates, biomass yield coefficients, and endogenous decay rates. Comparison and calibration of model simulations with the experimental data demonstrate that the model is able to accurately reproduce measured effluent concentrations, while delineating trends in dechlorinator growth and reductive dechlorination kinetics along the column. Sensitivity analyses performed on the optimized model parameters indicate that the rates of PCE and cis-1,2-dichloroethene (cis-DCE) transformation and Dehalococcoides growth govern bioenhanced dissolution, as long as electron donor (i.e., hydrogen flux) is not limiting. Dissolution enhancements were shown to be independent of cis-DCE accumulation; however, accumulation of cis-DCE, as well as column length and flow rate (i.e., column residence time

  15. An Automated Sample Preparation Instrument to Accelerate Positive Blood Cultures Microbial Identification by MALDI-TOF Mass Spectrometry (Vitek®MS

    Directory of Open Access Journals (Sweden)

    Patrick Broyer

    2018-05-01

    Full Text Available Sepsis is the leading cause of death among patients in intensive care units (ICUs requiring an early diagnosis to introduce efficient therapeutic intervention. Rapid identification (ID of a causative pathogen is key to guide directed antimicrobial selection and was recently shown to reduce hospitalization length in ICUs. Direct processing of positive blood cultures by MALDI-TOF MS technology is one of the several currently available tools used to generate rapid microbial ID. However, all recently published protocols are still manual and time consuming, requiring dedicated technician availability and specific strategies for batch processing. We present here a new prototype instrument for automated preparation of Vitek®MS slides directly from positive blood culture broth based on an “all-in-one” extraction strip. This bench top instrument was evaluated on 111 and 22 organisms processed using artificially inoculated blood culture bottles in the BacT/ALERT® 3D (SA/SN blood culture bottles or the BacT/ALERT VirtuoTM system (FA/FN Plus bottles, respectively. Overall, this new preparation station provided reliable and accurate Vitek MS species-level identification of 87% (Gram-negative bacteria = 85%, Gram-positive bacteria = 88%, and yeast = 100% when used with BacT/ALERT® 3D and of 84% (Gram-negative bacteria = 86%, Gram-positive bacteria = 86%, and yeast = 75% with Virtuo® instruments, respectively. The prototype was then evaluated in a clinical microbiology laboratory on 102 clinical blood culture bottles and compared to routine laboratory ID procedures. Overall, the correlation of ID on monomicrobial bottles was 83% (Gram-negative bacteria = 89%, Gram-positive bacteria = 79%, and yeast = 78%, demonstrating roughly equivalent performance between manual and automatized extraction methods. This prototype instrument exhibited a high level of performance regardless of bottle type or BacT/ALERT system. Furthermore, blood culture workflow could

  16. Culture.

    Science.gov (United States)

    Smith, Timothy B; Rodríguez, Melanie Domenech; Bernal, Guillermo

    2011-02-01

    This article summarizes the definitions, means, and research of adapting psychotherapy to clients' cultural backgrounds. We begin by reviewing the prevailing definitions of cultural adaptation and providing a clinical example. We present an original meta-analysis of 65 experimental and quasi-experimental studies involving 8,620 participants. The omnibus effect size of d = .46 indicates that treatments specifically adapted for clients of color were moderately more effective with that clientele than traditional treatments. The most effective treatments tended to be those with greater numbers of cultural adaptations. Mental health services targeted to a specific cultural group were several times more effective than those provided to clients from a variety of cultural backgrounds. We recommend a series of research-supported therapeutic practices that account for clients' culture, with culture-specific treatments being more effective than generally culture-sensitive treatments. © 2010 Wiley Periodicals, Inc.

  17. Evaluation of shiitake (Lentinula edodes) strains of the culture collection of Applied Plant Research

    NARCIS (Netherlands)

    Sonnenberg, A.S.M.; Amsing, J.G.M.

    2005-01-01

    Applied Plant Research (PPO), Mushroom Research Unit, has a unique collection of fungi that is used for research in edible mushrooms. The collection contains approximately 6600 strains representing more than 100 species. Most of the species are represented by Agaicus bisporus (button mushroom) and

  18. A 3D-printed microbial cell culture platform with in situ PEGDA hydrogel barriers for differential substrate delivery.

    Science.gov (United States)

    Kadilak, Andrea L; Rehaag, Jessica C; Harrington, Cameron A; Shor, Leslie M

    2017-09-01

    Additive manufacturing, or 3D-printing techniques have recently begun to enable simpler, faster, and cheaper production of millifluidic devices at resolutions approaching 100-200  μ m. At this resolution, cell culture devices can be constructed that more accurately replicate natural environments compared with conventional culturing techniques. A number of microfluidics researchers have begun incorporating additive manufacturing into their work, using 3D-printed devices in a wide array of chemical, fluidic, and even some biological applications. Here, we describe a 3D-printed cell culture platform and demonstrate its use in culturing Pseudomonas putida KT2440 bacteria for 44 h under a differential substrate gradient. Polyethylene glycol diacrylate (PEGDA) hydrogel barriers are patterned in situ within a 3D-printed channel. Transport of the toluidine blue tracer dye through the hydrogel barriers is characterized. Nutrients and oxygen were delivered to cells in the culture region by diffusion through the PEGDA hydrogel barriers from adjacent media or saline perfusion channels. Expression of green fluorescent protein by P. putida KT2440 enabled real time visualization of cell density within the 3D-printed channel, and demonstrated cells were actively expressing protein over the course of the experiment. Cells were observed clustering near hydrogel barrier boundaries where fresh substrate and oxygen were being delivered via diffusive transport, but cells were unable to penetrate the barrier. The device described here provides a versatile and easy to implement platform for cell culture in readily controlled gradient microenvironments. By adjusting device geometry and hydrogel properties, this platform could be further customized for a wide variety of biological applications.

  19. Banking culture and collective responsibility: A memorandum to the UK Parliamentary Commission on Banking Standards

    NARCIS (Netherlands)

    N. Dorn (Nicholas)

    2013-01-01

    textabstractBasic assumptions • There is wide interest in connecting issues of (i) occupational culture, (ii) compliance/ misconduct, (iii) remuneration and (iv) clawback (the bonus/malus debate). • Individual-focussed measures (supervision, remuneration and measures in civil or criminal law) must

  20. Bioaccumulation of 137Cs by culture collection strains of bacteria and fungi

    International Nuclear Information System (INIS)

    Pipiska, M.; Rozloznik, M.; Augustin, J.

    2003-01-01

    Soil decontamination of soil contaminated by low-level activities of radionuclides, mainly by caesium-137, which come from accidental releases by maintenance of nuclear devices and by liquid wastes reprocessing, is long-term and expensive technology. Knowledge of the causations, which control the processes of bioaccumulation of radionuclides, is a necessary condition for critical assessment and successful utilization of processes of bioremediation in situ in practise. The authors present the experimentally gained quantitative values of bioaccumulation of caesium-137 from water solutions by micro organism cultures of Rhodotorula aurantiaca CCY 20-9-1, Sacharomyces cerevisiae, Rhodococcus rhodochrous ATCC 15906, Streptomyces sp. DX-IX, Coriolus versicolor CCWDF-14 and Rhizopus sp. R-18. Intensively growing cultures reach the highest values of bioaccumulation; the cultures in non-growing phase reach several orders lower values. From researched micro organisms the highest values of bioaccumulation of Cs + 5.1 pmol/g (wet weight) at initial concentration of Cs + in solution co = 1 nmol/l (without carrier) and 29.2 μmol/g (wet weight) at co = 6 mmol/l Cs + (adding of carrier CsCl) were found out at growing culture S. cerevisiae as model of eukaryotic cell after an achievement of maximal stationary grow phase. Acquired information refer to the possible role of soil micro organisms at bioaccumulation of 137 Cs in contaminated soils and their potential utilization in lowering of radioactive contamination of environment (authors)

  1. Full Spectrum Tools for Collecting, Analyzing, and Using Cultural Data in Decision Making

    Science.gov (United States)

    2010-12-10

    self-sustaining system of relationships among social roles ( Malinowski , Radcliffe-Brown), a culturally consistent mode of thought (Nisbett) or set of...Introduction and critical Survey: Dover. Malinowski , B. (1984). Magic, Science, and Religion and Other Essays. Westport CT: Greenwood Press. Malle

  2. Mixed culture models for predicting intestinal microbial interactions between Escherichia coli and Lactobacillus in the presence of probiotic Bacillus subtilis.

    Science.gov (United States)

    Yang, J J; Niu, C C; Guo, X H

    2015-01-01

    Bacillus has been proposed as a probiotic due to its in vivo effectiveness in the gastrointestinal tract through antimicrobial activities. The present study investigates the effects of Lactobacillus alone or in the presence of Bacillus subtilis MA139 on the inhibition of pathogenic Escherichia coli K88. Mixed cultures were used to predict the possible interactions among these bacteria within the intestinal tract of animals. B. subtilis MA139 was first assayed for its inhibition against E. coli K88 both under shaking and static culture conditions. A co-culture assay was employed under static conditions to test the inhibitory effects of Lactobacillus reuteri on E. coli K88, with or without addition of B. subtilis MA139. The results showed that B. subtilis MA139 had marked inhibition against E. coli K88 under shaking conditions and weak inhibition under static conditions. Lactobacillus alone as well as in combination with B. subtilis MA139 spores exerted strong inhibition against E. coli K88 under static conditions. However, the inhibition by Lactobacillus in combination with B. subilis spores was much higher than that by Lactobacillus alone (Psubtilis MA139 significantly decreased the pH and oxidation-reduction potential values of the co-culture broth compared to that of Lactobacillus alone (Psubtilis MA139 because of significantly higher Lactobacillus counts and lower pH values in the broth (PBacillus in the mixed culture models suggests that Bacillus may produce beneficial effects by increasing the viability of lactobacilli and subsequently inhibiting the growth of pathogenic E. coli. Therefore, the combination of Bacillus and Lactobacillus species as a probiotic is recommended.

  3. Comparison of two apheresis systems for the collection of CD14+ cells intended to be used in dendritic cell culture.

    Science.gov (United States)

    Strasser, Erwin F; Berger, Thomas G; Weisbach, Volker; Zimmermann, Robert; Ringwald, Jürgen; Schuler-Thurner, Beatrice; Zingsem, Jürgen; Eckstein, Reinhold

    2003-09-01

    Monocytes collected by leukapheresis are increasingly used for dendritic cell (DC) culture in cell factories suitable for DC vaccination in cancer. Using modified MNC programs on two apheresis systems (Cobe Spectra and Fresenius AS.TEC204), leukapheresis components collected from 84 patients with metastatic malignant melanoma and from 31 healthy male donors were investigated. MNCs, monocytes, RBCs, and platelets (PLTs) in donors and components were analyzed by cell counters, WBC differential counts, and flow cytometry. In 5-L collections, Astec showed better results regarding monocyte collection rates (11.0 vs. 7.4 x 10(6)/min, p = 0.04) and efficiencies (collection efficiency, 51.9 vs. 31.9%; p Astec components contained high residual RBCs. Compared to components with low residual PLTs, high PLT concentration resulted in higher monocyte loss (48 vs. 20%, p Astec is more efficient in 5-L MNC collections compared to the Spectra. Components with high residual PLTs result in high MNC loss by purification procedures. Thus, optimizing MNC programs is essential to obtain components with high MNC yields and low residual cells as prerequisite for high DC yields.

  4. Effects of Culture and 2-Hydroxy-4-(Methylthio-Butanoic Acid on Rumen Fermentation and Microbial Populations between Different Roughage Sources

    Directory of Open Access Journals (Sweden)

    H. Sun

    2014-09-01

    Full Text Available An in vitro experiment was conducted to evaluate the effects of Aspergillus oryzae culture (AOC and 2-hydroxy-4-(methylthio-butanoic acid (HMB on rumen fermentation and microbial populations between different roughage sources. Two roughage sources (Chinese wild rye [CWR] vs corn silage [CS] were assigned in a 2×3 factorial arrangement with HMB (0 or 15 mg and AOC (0, 3, or 6 mg. Gas production (GP, microbial protein (MCP and total volatile fatty acid (VFA were increased in response to addition of HMB and AOC (p<0.01 for the two roughages. The HMB and AOC showed inconsistent effects on ammonia-N with different substrates. For CWR, neither HMB nor AOC had significant effect on molar proportion of individual VFA. For CS, acetate was increased (p = 0.02 and butyrate was decreased (p<0.01 by adding HMB and AOC. Increase of propionate was only occurred with AOC (p<0.01. Populations of protozoa (p≤0.03 and fungi (p≤0.02 of CWR were differently influenced by HMB and AOC. Percentages of F. succinogenes, R. albus, and R. flavefaciens (p<0.01 increased when AOC was added to CWR. For CS, HMB decreased the protozoa population (p = 0.01 and increased the populations of F. succinogenes and R. albus (p≤0.03. Populations of fungi, F. succinogenes (p = 0.02 and R. flavefacien (p = 0.03 were increased by adding AOC. The HMB×AOC interactions were noted in MCP, fungi and R. flavefacien for CWR and GP, ammonia-N, MCP, total VFA, propionate, acetate/propionate (A/P and R. albus for CS. It is inferred that addition of HMB and AOC could influence rumen fermentation of forages by increasing the number of rumen microbes.

  5. Effects of Aspergillus Oryzae Culture and 2-Hydroxy-4-(Methylthio)-Butanoic Acid on In vitro Rumen Fermentation and Microbial Populations between Different Roughage Sources.

    Science.gov (United States)

    Sun, H; Wu, Y M; Wang, Y M; Liu, J X; Myung, K H

    2014-09-01

    An in vitro experiment was conducted to evaluate the effects of Aspergillus oryzae culture (AOC) and 2-hydroxy-4-(methylthio)-butanoic acid (HMB) on rumen fermentation and microbial populations between different roughage sources. Two roughage sources (Chinese wild rye [CWR] vs corn silage [CS]) were assigned in a 2×3 factorial arrangement with HMB (0 or 15 mg) and AOC (0, 3, or 6 mg). Gas production (GP), microbial protein (MCP) and total volatile fatty acid (VFA) were increased in response to addition of HMB and AOC (p<0.01) for the two roughages. The HMB and AOC showed inconsistent effects on ammonia-N with different substrates. For CWR, neither HMB nor AOC had significant effect on molar proportion of individual VFA. For CS, acetate was increased (p = 0.02) and butyrate was decreased (p<0.01) by adding HMB and AOC. Increase of propionate was only occurred with AOC (p<0.01). Populations of protozoa (p≤0.03) and fungi (p≤0.02) of CWR were differently influenced by HMB and AOC. Percentages of F. succinogenes, R. albus, and R. flavefaciens (p<0.01) increased when AOC was added to CWR. For CS, HMB decreased the protozoa population (p = 0.01) and increased the populations of F. succinogenes and R. albus (p≤0.03). Populations of fungi, F. succinogenes (p = 0.02) and R. flavefacien (p = 0.03) were increased by adding AOC. The HMB×AOC interactions were noted in MCP, fungi and R. flavefacien for CWR and GP, ammonia-N, MCP, total VFA, propionate, acetate/propionate (A/P) and R. albus for CS. It is inferred that addition of HMB and AOC could influence rumen fermentation of forages by increasing the number of rumen microbes.

  6. Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments.

    Science.gov (United States)

    Besaury, Ludovic; Marty, Florence; Buquet, Sylvaine; Mesnage, Valérie; Muyzer, Gerard; Quillet, Laurent

    2013-02-01

    Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.

  7. Effect of Long Time Oxygen Exposure on Power Generation of Microbial Fuel Cell with Enriched Mixed Culture

    International Nuclear Information System (INIS)

    Mimi Hani Abu Bakar; Mimi Hani Abu Bakar; Mimi Hani Abu Bakar; Pasco, N.F.; Gooneratne, R.; Hong, K.B.; Hong, K.B.; Hong, K.B.

    2016-01-01

    In this study, we are interested in the effect of long time exposure of the microbial fuel cells (MFCs) to air on the electrochemical performance. Here, MFCs enriched using an effluent from a MFC operated for about eight months. After 30 days, the condition of these systems was reversed from aerobic to anaerobic and vice versa, and their effects were observed for 11 days. The results show that for anaerobic MFCs, power generation was reduced when the anodes were exposed to dissolved oxygen of 7.5 ppm. The long exposure of anodic biofilm to air led to poor electrochemical performance. The power generation recovered fully when air supply stopped entering the anode compartment with a reduction of internal resistance up to 53 %. The study was able to show that mixed facultative microorganism able to strive through the aerobic condition for about a month at 7.5 ppm oxygen or less. The anaerobic condition was able to turn these microbes into exoelectrogen, producing considerable power in relative to their aerobic state. (author)

  8. Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets

    Directory of Open Access Journals (Sweden)

    Kim Minseok

    2012-09-01

    Full Text Available Abstract Background The number and diversity of uncultured ruminal bacterial and archaeal species revealed by 16S rRNA gene (rrs sequences greatly exceeds that of cultured bacteria and archaea. However, the significance of uncultured microbes remains undetermined. The objective of this study was to assess the numeric importance of select uncultured bacteria and cultured bacteria and the impact of diets and microenvironments within cow rumen in a comparative manner. Results Liquid and adherent fractions were obtained from the rumen of Jersey cattle fed hay alone and Holstein cattle fed hay plus grain. The populations of cultured and uncultured bacteria present in each fraction were quantified using specific real-time PCR assays. The population of total bacteria was similar between fractions or diets, while total archaea was numerically higher in the hay-fed Jersey cattle than in the hay-grain-fed Holstein cattle. The population of the genus Prevotella was about one log smaller than that of total bacteria. The populations of Fibrobacter succinogenes, Ruminococcus flavefaciens, the genus Butyrivibrio, and R. albus was at least one log smaller than that of genus Prevotella. Four of the six uncultured bacteria quantified were as abundant as F. succinogenes, R. flavefaciens and the genus Butyrivibrio. In addition, the populations of several uncultured bacteria were significantly higher in the adherent fractions than in the liquid fractions. These uncultured bacteria may be associated with fiber degradation. Conclusions Some uncultured bacteria are as abundant as those of major cultured bacteria in the rumen. Uncultured bacteria may have important contribution to ruminal fermentation. Population dynamic studies of uncultured bacteria in a comparative manner can help reveal their ecological features and importance to rumen functions.

  9. Gamma radiation treatment applied to microbial decontamination of products derived from eggs collected from the retail market in São Paulo, SP, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Aquino, S.; Lui, C.C., E-mail: siaq06@hotmail.com [Universidade Nove de Julho (UNINOVE), São Paulo, SP (Brazil); Corrêa, B. [Universidade de São Paulo (USP), SP (Brazil)

    2017-11-15

    The quality of products derived from eggs depends on the quality of the raw material source and the industrial production. The contamination by fungi and bacteria can occur after exposure of the product in the retail market. The objective of this study was to evaluate the microbiological quality of 60 samples of derived egg products and evaluate the effects of gamma radiation of cobalt-60, using the dose of 5 and 10 kGy, for decontamination of products collected in the retail market in the São Paulo city. The bacterial count was performed by the most probable number (MPN) and the fungal counts by serial dilution after plating surface. It was observed a decrease in the humidity and water activity (Aw) values of irradiated whole egg powder and white egg powder samples (p<0.05), but there was no significant change in the pH of the same samples irradiated with 5 and 10 kGy (p>0.05). In the powdered yolk the values of pH and Aw presented a significant difference (p<0.05), but no significant difference in the humidity values of 5 and 10 kGy irradiated samples (p>0.05). Effective microbial sterilization of all products occurred at the dose of 10 kGy. (author)

  10. Gamma radiation treatment applied to microbial decontamination of products derived from eggs collected from the retail market in São Paulo, SP, Brazil

    International Nuclear Information System (INIS)

    Aquino, S.; Lui, C.C.; Corrêa, B.

    2017-01-01

    The quality of products derived from eggs depends on the quality of the raw material source and the industrial production. The contamination by fungi and bacteria can occur after exposure of the product in the retail market. The objective of this study was to evaluate the microbiological quality of 60 samples of derived egg products and evaluate the effects of gamma radiation of cobalt-60, using the dose of 5 and 10 kGy, for decontamination of products collected in the retail market in the São Paulo city. The bacterial count was performed by the most probable number (MPN) and the fungal counts by serial dilution after plating surface. It was observed a decrease in the humidity and water activity (Aw) values of irradiated whole egg powder and white egg powder samples (p<0.05), but there was no significant change in the pH of the same samples irradiated with 5 and 10 kGy (p>0.05). In the powdered yolk the values of pH and Aw presented a significant difference (p<0.05), but no significant difference in the humidity values of 5 and 10 kGy irradiated samples (p>0.05). Effective microbial sterilization of all products occurred at the dose of 10 kGy. (author)

  11. Biogenic selenium and tellurium nanoparticles synthesized by environmental microbial isolates efficaciously inhibit bacterial planktonic cultures and biofilms

    Directory of Open Access Journals (Sweden)

    Emanuele eZonaro

    2015-06-01

    Full Text Available The present study deals with Se0- and Te0-based nanoparticles bio-synthesized by two selenite- and tellurite-reducing bacterial strains, namely Stenotrophomonas maltophilia SeITE02 and Ochrobactrum sp. MPV1, isolated from polluted sites. We discovered that, by regulating culture conditions and exposure time to the selenite and tellurite oxyanions, differently sized zero-valent Se and Te nanoparticles were produced. The results revealed that these Se0 and Te0 nanoparticles possess antimicrobial and biofilm eradication activity against E. coli JM109, P. aeruginosa PAO1, and S. aureus ATCC 25923. In particular, Se0 nanoparticles exhibited antimicrobial activity at quite low concentrations, below that of selenite. Toxic effects of both Se0 and Te0 nanoparticles can be related to the production of reactive oxygen species upon exposure of the bacterial cultures. Evidence so far achieved suggests that the antimicrobial activity seems to be strictly linked to the dimensions of the nanoparticles: indeed, the highest activity was shown by nanoparticles of smaller sizes. In particular, it is worth noting how the bacteria tested in biofilm mode responded to the treatment by Se0 and Te0 nanoparticles with a susceptibility similar to that observed in planktonic cultures. This suggests a possible exploitation of both Se0 and Te0 nanoparticles as efficacious antimicrobial agents with a remarkable biofilm eradication capacity.

  12. Culture of uterine flushings, cervical mucus, and udder secretions collected post-abortion from heifers artificially exposed to Brucella abortus.

    Science.gov (United States)

    Stringfellow, D A; Scanlan, C M; Hannon, S S; Panangala, V S; Gray, B W; Galik, P A

    1983-07-01

    Uterine flushings, cervical mucus swabs and udder secretions collected at weekly intervals from five mixed breed beef cows (four Brucella abortus strain 19 vaccinates, and 1 non-vaccinate) were cultured for Brucella abortus . Prior to sampling, four of the five had aborted 7-to 8-month-old fetuses and one gave brith to a weak calf. The fetuses and/or udder secretions from the cows were culture positive for B. abortus at the time of parturition. Three of the cows developed persistent udder infections. Two of these cows were also shown to have brucellae in their cervical mucus for 10 and 20 days and in their uterine flushings for 17 and 41 days after parturition, respectively. One other cow had brucellae in the cervical mucus for 16 days and in the uterine flushings for up to 36 days post-abortion. All attempts to isolate the organism from this cow's udder secretions in culture were negative. In two cows with culture-positive uterine flushings, isolations of brucellae were made subsequent to normal postpabortion return to estrus.

  13. Interplay of differential cell mechanical properties, motility, and proliferation in emergent collective behavior of cell co-cultures

    Science.gov (United States)

    Sutter, Leo; Kolbman, Dan; Wu, Mingming; Ma, Minglin; Das, Moumita

    The biophysics of cell co-cultures, i.e. binary systems of cell populations, is of great interest in many biological processes including formation of embryos, and tumor progression. During these processes, different types of cells with different physical properties are mixed with each other, with important consequences for cell-cell interaction, aggregation, and migration. The role of the differences in their physical properties in their collective behavior remains poorly understood. Furthermore, until recently most theoretical studies of collective cell migration have focused on two dimensional systems. Under physiological conditions, however, cells often have to navigate three dimensional and confined micro-environments. We study a confined, three-dimensional binary system of interacting, active, and deformable particles with different physical properties such as deformability, motility, adhesion, and division rates using Langevin Dynamics simulations. Our findings may provide insights into how the differences in and interplay between cell mechanical properties, division, and motility influence emergent collective behavior such as cell aggregation and segregation experimentally observed in co-cultures of breast cancer cells and healthy breast epithelial cells. This work was partially supported by a Cottrell College Science Award.

  14. Negative Affect during a Collective (but Not an Individual Task Is Associated with Holistic Attention in East Asian Cultural Context

    Directory of Open Access Journals (Sweden)

    Hitoshi Tominaga

    2017-08-01

    Full Text Available Previous studies have suggested that individuals from East Asian cultures are more likely to show holistic attention—a pattern of attention that incorporates contextual information into focal stimuli—than individuals from North American cultures. Holistic attention is also prevalent in communities that require close cooperation. However, it is not yet known how cooperation is related to holistic attention. We theorized that holistic attention increases when people experience negative affect (e.g., worry, sadness, and frustration during collective tasks (but not during individual tasks because negative affect in social contexts signals the existence of potential threats to social harmony, thus indicating a need to restore social harmony. To examine this hypothesis, an experiment was conducted in which participants performed a musical duet either with another participant (a collective task requiring cooperation, or individually with a computer (an individual task. After the musical task, the Framed Line Task (FLT was administered to examine their holistic attention. Participants also reported their emotional states both before and after the music task. Results suggested that negative affect in the collective task—but not the individual task—was positively correlated with a holistic pattern of attention. The function of negative affect in social contexts as motivation to restore relationships and how this enhances holistic attention is discussed. The moderating effect of social context on the link between negative affect and cognition is also discussed.

  15. A note on the laboratory culture of benthic foraminifera collected from nearshore region off Goa, India

    Digital Repository Service at National Institute of Oceanography (India)

    Nigam, R.; Khare, N.; Koli, N.Y.

    these culture dish under the microscope one must be careful thatthe microscope light does not overheat the water and the cover should be removed from time to time to allow aeration. The sea water of the dishes was changed alternative- ly and food (diatoms... to be utilized for various experiments under phase 2. How- ever, in phase 1 we changed half of the medium on alternate days and supplied food (diatoms) weekly. While changing the medium, care was taken to maintain the salinity by adjusting the loss due...

  16. Not Just Pulp Fiction: Science Fiction Integral to U.S. Culture and LC Collections.

    Science.gov (United States)

    Johnson, Eric A.; Stumbaugh, Colleen R. C.

    1996-01-01

    Traces the evolution of the science fiction genre and its representation at the Library of Congress, including original paperbacks, hardcovers, television, film, and sound recordings. Highlights include science fiction "classics", the Library of Congress collection development policy, library programs, and preservation activities…

  17. Pringsheim's living legacy: CCALA, CCAP, SAG and UTEX culture collections of algae

    Czech Academy of Sciences Publication Activity Database

    Day, J. G.; Lukavský, Jaromír; Friedl, T.; Brand, J. J.; Campbell, CH. N.; Lorenz, M.; Elster, Josef

    2004-01-01

    Roč. 79, 1-2 (2004), s. 27-37 ISSN 0029-5035 R&D Projects: GA AV ČR KSK6005114 Keywords : cyanobacteria * algae * Pringsheim * algal collections Subject RIV: EF - Botanics Impact factor: 0.594, year: 2004

  18. Collective motion of cells mediates segregation and pattern formation in co-cultures.

    Directory of Open Access Journals (Sweden)

    Elod Méhes

    Full Text Available Pattern formation by segregation of cell types is an important process during embryonic development. We show that an experimentally yet unexplored mechanism based on collective motility of segregating cells enhances the effects of known pattern formation mechanisms such as differential adhesion, mechanochemical interactions or cell migration directed by morphogens. To study in vitro cell segregation we use time-lapse videomicroscopy and quantitative analysis of the main features of the motion of individual cells or groups. Our observations have been extensive, typically involving the investigation of the development of patterns containing up to 200,000 cells. By either comparing keratocyte types with different collective motility characteristics or increasing cells' directional persistence by the inhibition of Rac1 GTP-ase we demonstrate that enhanced collective cell motility results in faster cell segregation leading to the formation of more extensive patterns. The growth of the characteristic scale of patterns generally follows an algebraic scaling law with exponent values up to 0.74 in the presence of collective motion, compared to significantly smaller exponents in case of diffusive motion.

  19. Diversity and characterization of culturable fungi from marine sediment collected from St. Helena Bay, South Africa

    CSIR Research Space (South Africa)

    Mouton, M

    2012-08-01

    Full Text Available origins. It has not been proven whether these fungi merely survive the harsh environmental conditions presented by the ocean sediment, as opposed to playing an active role in this ecological niche. During this study, marine sediment was collected from St...

  20. Recognising Opportunities : A Case Study on Fostering a Culture of Innovation Through Individual and Collective Ownership

    NARCIS (Netherlands)

    Beekhof, Lysanne; van Vuuren, Mark; Olckers, Chantal; van Zyl, Llewellyn; van der Vaart, Leoni

    2017-01-01

    Every innovation in organisations starts with recognising the opportunity to improve one’s way of working. Feeling psychological ownership for such innovative work behaviours can be identified for individuals (i.e. ‘this task is mine’) and collectives (i.e. ‘this task is ours’). Our question was how

  1. Using Pure Cultures to Define the Site Preference of Nitrous Oxide Produced by Microbial Nitrification and Denitrification

    Science.gov (United States)

    Sutka, R. L.; Breznak, J. A.; Ostrom, N. E.; Ostrom, P. H.; Gandhi, H.

    2004-12-01

    Defining the site preference of nitrous oxide (N2O) produced in pure culture studies is crucial to interpreting field data. We have previously demonstrated that the intramolecular distribution of nitrogen isotopes (isotopomers) can be used to differentiate N2O produced by nitrifier denitrification and nitrification in cultures of Nitrosomonas europaea. Here, we have expanded on our initial results and evaluated the isotopomeric composition of N2O produced during nitrification and nitrifier denitrification with cultures of Nitrosospira multiformis. In addition, we have analyzed N2O produced during methanotrophic nitrification, denitrification, and fungal denitrification. To evaluate N2O production during nitrification and nitrifier denitrification, we compared the site preference of N2O formed as a result of nitrite reduction and hydroxylamine oxidation with Nitrosomonas europaea and Nitrosospira multiformis. The average site preference of N2O produced by hydroxylamine oxidation was similar for Nitrosomonas europaea (33.0 ± 3.5 ‰ ) and Nitrosospira multiformis (33.1 ± 4.2 ‰ ). Nitrous oxide produced by nitrifier-denitrification by Nitrosomonas europaea and Nitrosospira multiformis had a similar site preference of - 1.4 ± 4.4 ‰ and - 1.1 ± 2.6 ‰ respectively. The results indicate that it is possible to differentiate between N2O produced by nitrite reduction and hydroxylamine oxidation by ammonia oxidizing bacteria. Methanotrophic nitrification was evaluated by analyzing the N2O produced during hydroxylamine oxidation in concentrated cell suspensions of two methane oxidizing bacteria. The site preference of N2O produced by the two methane oxidizers, Methylococcus capsulatus Bath and Methylosinus trichosporium was 31.8 ± 4.7 ‰ and 33.0 ± 4.5 ‰ respectively. The results indicate that a site preference of 33 ‰ is applicable for nitrification regardless of whether a methane oxidizer or ammonia oxidizer is involved in the reaction. To determine the site

  2. The maturing of microbial ecology.

    Science.gov (United States)

    Schmidt, Thomas M

    2006-09-01

    A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

  3. Detoxification Treatments of Free Gossypol in Cottonseed Meal by Microbial Treatment of Mixed Cultures and Biochemical Evaluation on Rabbits

    International Nuclear Information System (INIS)

    Atia, A.I.; Abdel- Rahim, G.A.

    2009-01-01

    Detoxification of ti-ee gossypol (FG) in cottonseed meal (CSM) by Saccharomyces cerevisiae and Aspergillus niger, as a mixed culture, was carried out in solid state fermentation (SSF). Experiments were adopted to optimize the fermentation conditions. Maximum detoxification efficiency (90.2%) occurred after 48 h of incubation at 30 degree C in a 250 ml conical flask containing 15 g of CSM supplemented with 1 % (w/w) (NH 4 ) 2 SO 4 at the optimal conditions including the initial moisture content 55% (w/w) and inoculum level at 5% (v/w). The detoxification of FG was a growth-associated process, which was highly correlated with the dry matter weight loss. Moreover, high activities of hydrolytic enzymes were also produced in solid state fermentation, which enhanced the nutritive value of the detoxified cottonseed powder. A total number of 48 white New Zealand male rabbits were used to biologically examine the feeding of treated (detoxified) CSM without any adverse effects. Hematological and biochemical relevant parameters of white New Zealand male rabbits as affected by feeding treated meal were in the normal physiological range without no obvious change. No significant changes in liver and kidney functions of the rabbits weight gain, feed conversion and efficiency did not significantly change among experimental groups. The study showed that the feeding of the detoxified CSM by S. cerevisiae and A. niger as a mixed culture in this research without any adverse effects on rabbits

  4. Removal of the pharmaceuticals ibuprofen and iohexol by four wetland plant species in hydroponic culture: plant uptake and microbial degradation.

    Science.gov (United States)

    Zhang, Yang; Lv, Tao; Carvalho, Pedro N; Arias, Carlos A; Chen, Zhanghe; Brix, Hans

    2016-02-01

    We aimed at assessing the effects of four wetland plant species commonly used in constructed wetland systems: Typha, Phragmites, Iris and Juncus for removing ibuprofen (IBU) and iohexol (IOH) from spiked culture solution and exploring the mechanisms responsible for the removal. IBU was nearly completely removed by all plant species during the 24-day experiment, whereas the IOH removal varied between 13 and 80 %. Typha and Phragmites were the most efficient in removing IBU and IOH, respectively, with first-order removal rate constants of 0.38 and 0.06 day(-1), respectively. The pharmaceuticals were taken up by the roots and translocated to the aerial tissues. However, at the end of the experiment, plant accumulation constituted only up to 1.1 and 5.7 % of the amount of IBU and IOH spiked initially. The data suggest that the plants mainly function by facilitating pharmaceutical degradation in the rhizosphere through release of root exudates.

  5. Microbial resistance and frequency of extended-spectrum beta-lactamase (ESBL in isolated from blood cultures

    Directory of Open Access Journals (Sweden)

    Ruan Carlos Gomes da Silva

    2014-12-01

    Full Text Available Introduction:The emergence and spread of isolated carriers of extended-spectrum beta-lactamase (ESBL have complicated the treatment of nosocomial infections, since its production is not easily identified by the sensitivity tests, routinely performed in clinical laboratories, leading to difficulties in the hospital control of resistant microorganisms and antibiotics misuse.Objective:The objective of this study was to analyze the resistance profile and the frequency of ESBL in Gram-negative bacteria isolated from blood cultures. A hundred bacterial samples from blood cultures of adult patients were analyzed, which were phenotypically identified by biochemical tests of carbohydrates fermentation and submitted to determination of the resistance profile by disc diffusion test and ESBL screening by disc approximation and disc replacement methods.Results:Among the bacterial samples tested, 30 were identified as Gram-negative bacteria, predominantly by Proteus mirabilis, Pantoea agglomerans, and Escherichia coli. Of these, 73.33% were positive for the detection of ESBL by phenotypic tests, and was found mainly in Pantoea agglomerans, Proteus mirabilis, and Enterobacter cloacae.Conclusion:The increase in the occurrence of ESBL in different Enterobacteriaceae shows the importance of the amplification of detection in other species than Escherichia coli or Klebsiella sp., so that the assistance to the patient is not restrained, since these resistant bacteria cannot be detected by the laboratories. Considering the frequency of ESBL in this study, we highlight the importance of its detection, aiming to its contribution to the development of improvements in the health care policies of hospitals.

  6. Effect of Feeding a Mixed Microbial Culture Fortified with Trace Minerals on the Performance and Carcass Characteristics of Late-fattening Hanwoo Steers: A Field Study

    Directory of Open Access Journals (Sweden)

    W. S. Kwak

    2015-11-01

    Full Text Available This study was conducted to determine the effects of feeding a trace minerals-fortified microbial culture (TMC on the performance and carcass characteristics of late-fattening Hanwoo steers. A mixture of microbes (0.6% [v/w] of Enterobacter sp., Bacillus sp., Lactobacillus sp., and Saccharomyces sp. was cultured with 99% feedstuff for ensiling and 0.4% trace minerals (zinc, selenium, copper, and cobalt. Sixteen late-fattening steers (mean age, 21.8 months were allocated to two diets: a control diet (concentrate mix and rice straw and a treated diet (control diet+3.3% TMC. At a mean age of 31.1 months, all the steers were slaughtered. The addition of TMC to the diet did not affect the average daily weight gain of the late fattening steers, compared with that of control steers. Moreover, consuming the TMC-supplemented diet did not affect cold carcass weight, yield traits such as back fat thickness, longissimus muscle area, yield index or yield grade, or quality traits such as meat color, fat color, texture, maturity, marbling score, or quality grade. However, consumption of a TMC-supplemented diet increased the concentrations of zinc, selenium, and sulfur (p<0.05 in the longissimus muscle. With respect to amino acids, animals consuming TMC showed increased (p<0.05 concentrations of lysine, leucine, and valine among essential amino acids and a decreased (p<0.05 concentration of proline among non-essential amino acids. In conclusion, the consumption of a TMC-supplemented diet during the late-fattening period elevated the concentrations of certain trace minerals and essential amino acids in the longissimus muscle, without any deleterious effects on performance and other carcass characteristics of Hanwoo steers.

  7. The CUPID (Cultural and Psychosocial Influences on Disability) Study: Methods of Data Collection and Characteristics of Study Sample

    Science.gov (United States)

    Coggon, David; Ntani, Georgia; Palmer, Keith T.; Felli, Vanda E.; Harari, Raul; Barrero, Lope H.; Felknor, Sarah A.; Gimeno, David; Cattrell, Anna; Serra, Consol; Bonzini, Matteo; Solidaki, Eleni; Merisalu, Eda; Habib, Rima R.; Sadeghian, Farideh; Kadir, Masood; Warnakulasuriya, Sudath S. P.; Matsudaira, Ko; Nyantumbu, Busisiwe; Sim, Malcolm R.; Harcombe, Helen; Cox, Ken; Marziale, Maria H.; Sarquis, Leila M.; Harari, Florencia; Freire, Rocio; Harari, Natalia; Monroy, Magda V.; Quintana, Leonardo A.; Rojas, Marianela; Salazar Vega, Eduardo J.; Harris, E. Clare; Vargas-Prada, Sergio; Martinez, J. Miguel; Delclos, George; Benavides, Fernando G.; Carugno, Michele; Ferrario, Marco M.; Pesatori, Angela C.; Chatzi, Leda; Bitsios, Panos; Kogevinas, Manolis; Oha, Kristel; Sirk, Tuuli; Sadeghian, Ali; Peiris-John, Roshini J.; Sathiakumar, Nalini; Wickremasinghe, A. Rajitha; Yoshimura, Noriko; Kielkowski, Danuta; Kelsall, Helen L.; Hoe, Victor C. W.; Urquhart, Donna M.; Derett, Sarah; McBride, David; Gray, Andrew

    2012-01-01

    Background The CUPID (Cultural and Psychosocial Influences on Disability) study was established to explore the hypothesis that common musculoskeletal disorders (MSDs) and associated disability are importantly influenced by culturally determined health beliefs and expectations. This paper describes the methods of data collection and various characteristics of the study sample. Methods/Principal Findings A standardised questionnaire covering musculoskeletal symptoms, disability and potential risk factors, was used to collect information from 47 samples of nurses, office workers, and other (mostly manual) workers in 18 countries from six continents. In addition, local investigators provided data on economic aspects of employment for each occupational group. Participation exceeded 80% in 33 of the 47 occupational groups, and after pre-specified exclusions, analysis was based on 12,426 subjects (92 to 1018 per occupational group). As expected, there was high usage of computer keyboards by office workers, while nurses had the highest prevalence of heavy manual lifting in all but one country. There was substantial heterogeneity between occupational groups in economic and psychosocial aspects of work; three- to five-fold variation in awareness of someone outside work with musculoskeletal pain; and more than ten-fold variation in the prevalence of adverse health beliefs about back and arm pain, and in awareness of terms such as “repetitive strain injury” (RSI). Conclusions/Significance The large differences in psychosocial risk factors (including knowledge and beliefs about MSDs) between occupational groups should allow the study hypothesis to be addressed effectively. PMID:22792189

  8. Declining trends in alcohol consumption among Swedish youth-does the theory of collectivity of drinking cultures apply?

    Science.gov (United States)

    Raninen, Jonas; Livingston, Michael; Leifman, Håkan

    2014-11-01

    To analyse trends in alcohol consumption among young people in Sweden between 2004 and 2012, to test whether the theory of collectivity of drinking cultures is valid for a population of young people and to investigate the impact of an increasing proportion of abstainers on the overall per capita trends. Data were drawn from an annual survey of a nationally representative sample of students in year 11 (17-18 years old). The data covered 9 years and the total sample comprised 36,141 students. Changes in the overall per capita consumption were tested using linear regression on log-transformed data, and changes in abstention rates were tested using logistic regression. The analyses were then continued by calculating average consumption in deciles. Alcohol consumption among year 11 students declined significantly among both boys and girls between 2004 and 2012. These changes were reflected at all levels of consumption, and the same results were found when abstainers were excluded from the analyses. The increasing proportion of abstainers had a minimal effect on the overall decline in consumption; rather, this was driven by a decline in consumption among the heaviest drinkers. The theory of collectivity of drinking cultures seems valid for understanding changes in alcohol consumption among Swedish year 11 students. No support was found for a polarization of alcohol consumption in this nationally representative sample. © The Author 2014. Medical Council on Alcohol and Oxford University Press. All rights reserved.

  9. The CUPID (Cultural and Psychosocial Influences on Disability study: methods of data collection and characteristics of study sample.

    Directory of Open Access Journals (Sweden)

    David Coggon

    Full Text Available The CUPID (Cultural and Psychosocial Influences on Disability study was established to explore the hypothesis that common musculoskeletal disorders (MSDs and associated disability are importantly influenced by culturally determined health beliefs and expectations. This paper describes the methods of data collection and various characteristics of the study sample.A standardised questionnaire covering musculoskeletal symptoms, disability and potential risk factors, was used to collect information from 47 samples of nurses, office workers, and other (mostly manual workers in 18 countries from six continents. In addition, local investigators provided data on economic aspects of employment for each occupational group. Participation exceeded 80% in 33 of the 47 occupational groups, and after pre-specified exclusions, analysis was based on 12,426 subjects (92 to 1018 per occupational group. As expected, there was high usage of computer keyboards by office workers, while nurses had the highest prevalence of heavy manual lifting in all but one country. There was substantial heterogeneity between occupational groups in economic and psychosocial aspects of work; three- to five-fold variation in awareness of someone outside work with musculoskeletal pain; and more than ten-fold variation in the prevalence of adverse health beliefs about back and arm pain, and in awareness of terms such as "repetitive strain injury" (RSI.The large differences in psychosocial risk factors (including knowledge and beliefs about MSDs between occupational groups should allow the study hypothesis to be addressed effectively.

  10. Biorremediación de los efluentes de cultivo del camarón Litopenaeus vannamei (Boone, 1931 utilizando tapetes microbianos en un sistema de recirculación Bioremediacion of effluents ones of the culture of Litopenaeus vannamei (Boone, 1931 using microbial mats in a recirculating system

    Directory of Open Access Journals (Sweden)

    Carlos Lezama-Cervantes

    2010-01-01

    Full Text Available Se desarrolló un sistema de recirculación (SR integrando el cultivo del camarón con tapetes microbianos buscando mitigar los impactos ambientales de los subproductos del cultivo del camarón y avanzar hacia la biorremediación del agua de cultivo. Los consorcios microbianos obtenidos de ambientes naturales (TaM estuvieron constituidos por bacterias (55,6%, cianófitas (18,4%, diatomeas (9%, nemátodos (5,6% y clorófitas (1,4%, entre los grupos taxonómicos principales. La remoción de nutrientes y sólidos se evaluó en un SR (2 ciclos/hora conteniendo (n = 3 60 y 120 ind m-2 de Litopenaeus vannamei. Los resultados demostraron que los TaM redujeron los niveles de nitrógeno amoniacal por encima del 71% diariamente; la demanda bioquímica de oxígeno (DBO5 se redujo más de 68% y los sólidos suspendidos (SST hasta en 62% al compararse con los sistemas control (p 0,05. El agua bio-remediada tiene un efecto positivo en el cultivo de Litopenaeus vannamei, y promueve el crecimiento y sobrevivencia en presencia de TaM en el SR.We developed a recirculating system integrating shrimp culture with microbial mats aiming to mitigate the environmental impacts of by-products from shrimp culture and to advance toward the bioremediation of the shrimp culture water. The microbial consortia collected from natural environments (TaM was constituted by bacteria (55.6%, Cyanophyte (18.4%, diatoms (9%, nematods (5.6% and Chlorophyte algae (1.4% among the major taxonomic groups. The removal of nutrients and solids by these mats was assessed in a recirculating system (2 cycles/hour (n = 3 containing 60 and 120 ind m-2 of Litopenaeus vannamei. Results showed that the microbial mat reduces daily up to 71% of ammonia nitrogen, decreases around 68% of the biochemical oxygen demand (DBO5 and up to 62% of suspended solids (SST when comparing to the control systems (p 0.05. The Bioremediated culture water had a positive effect on the culture of Litopenaeus vannamei, and

  11. Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches.

    Science.gov (United States)

    Nishiyama, Minako; Yamamoto, Shuichi; Kurosawa, Norio

    2013-08-01

    Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.

  12. Induction of peroxisomal beta-oxidation by a microbial catabolite of cholic acid in rat liver and cultured rat hepatocytes.

    Science.gov (United States)

    Nishimaki-Mogami, T; Takahashi, A; Toyoda, K; Hayashi, Y

    1993-01-01

    The capability of (4R)-4-(2,3,4,6,6a beta,7,8,9,9a alpha,9b beta-decahydro-6a beta-methyl-3-oxo-1H-cyclopental[f]quinolin-7 beta-yl)valeric acid (DCQVA), a catabolite of cholic acid produced by enterobacteria, to induce peroxisome proliferation in vivo and in vitro was studied. Rats given 0.3% DCQVA in the diet for 2 weeks showed marked increases in peroxisomal beta-oxidation, mitochondrial 2,4-dienoyl-CoA reductase and microsomal laurate omega-oxidation activities in the liver compared with control rats given the diet without DCQVA. Cultured rat hepatocytes treated with DCQVA for 72 h also exhibited greatly enhanced beta-oxidation activity. The increased activity was concentration-dependent and the effective concentrations were comparable with those of clofibric acid that produced the same degree of induction in the assay. The results demonstrate that DCQVA is a potent peroxisome proliferator that occurs naturally in rat intestine. PMID:8216219

  13. Approaches for Reverse Line Blot-Based Detection of Microbial Pathogens in Ixodes ricinus Ticks Collected in Austria and Impact of the Chosen Method.

    Science.gov (United States)

    Schötta, Anna-Margarita; Wijnveld, Michiel; Stockinger, Hannes; Stanek, Gerold

    2017-07-01

    observation of significant coinfections of certain microorganisms in field-collected ticks is an initial step to an improved understanding of microbial interactions in ticks. In addition, we show that variations in molecular detection methods, such as in primer pairs and target genes, can considerably influence the final results. For instance, detection of certain genospecies of borreliae may be better or worse by one method or the other, a fact of great importance for future screening studies. Copyright © 2017 American Society for Microbiology.

  14. In vitro culture of oocytes and granulosa cells collected from normal, obese, emaciated and metabolically stressed ewes.

    Science.gov (United States)

    Tripathi, S K; Farman, M; Nandi, S; Mondal, S; Gupta, Psp; Kumar, V Girish

    2016-07-01

    The present study was undertaken to investigate the oocyte morphology, its fertilizing capacity and granulosa cell functions in ewes (obese, normal, metabolic stressed and emaciated). Ewes (Ovis aries) of approximately 3 years of age (Bellary breed) from a local village were screened, chosen and categorized into a) normal b) obese but not metabolically stressed, c) Emaciated but not metabolically stressed d) Metabolically stressed based on body condition scoring and blood markers. Oocytes and granulosa cells were collected from ovaries of the ewes of all categories after slaughter and were classified into good (oocytes with more than three layers of cumulus cells and homogenous ooplasm), fair (oocytes one or two layers of cumulus cells and homogenous ooplasm) and poor (denuded oocytes or with dark ooplasm). The good and fair quality oocytes were in vitro matured and cultured with fresh semen present and the fertilization, cleavage and blastocyst development were observed. The granulosa cells were cultured for evaluation of metabolic activity by use of the MTT assay, and cell viability, cell number as well as estrogen and progesterone production were assessed. It was observed that the good and fair quality oocytes had greater metabolic activity when collected from normal and obese ewes compared with those from emaciated and metabolically stressed ewes. No significant difference was observed in oocyte quality and maturation amongst the oocytes collected from normal and obese ewes. The cleavage and blastocyst production rates were different for the various body condition classifications and when ranked were: normal>obese>metabolically stressed>emaciated. Lesser metabolic activity was observed in granulosa cells obtained from ovaries of emaciated ewes. However, no changes were observed in viability and cell number of granulosa cells obtained from ewes with the different body condition categories. Estrogen and progesterone production from cultured granulosa cells were

  15. Using Co-Design to Develop a Collective Leadership Intervention for Healthcare Teams to Improve Safety Culture

    Directory of Open Access Journals (Sweden)

    Marie E. Ward

    2018-06-01

    Full Text Available While co-design methods are becoming more popular in healthcare; there is a gap within the peer-reviewed literature on how to do co-design in practice. This paper addresses this gap by delineating the approach taken in the co-design of a collective leadership intervention to improve healthcare team performance and patient safety culture. Over the course of six workshops healthcare staff, patient representatives and advocates, and health systems researchers collaboratively co-designed the intervention. The inputs to the process, exercises and activities that took place during the workshops and the outputs of the workshops are described. The co-design method, while challenging at times, had many benefits including grounding the intervention in the real-world experiences of healthcare teams. Implications of the method for health systems research are discussed.

  16. Collective efficacy versus self-efficacy in coping responses to stressors and control: a cross-cultural study.

    Science.gov (United States)

    Schaubroeck, J; Lam, S S; Xie, J L

    2000-08-01

    This study examined how cultural differences and efficacy perceptions influence the role of job control in coping with job demands. Perceiving higher control mitigated the effects of demands on psychological health symptoms and turnover intentions only among American bank tellers reporting high job self-efficacy. Among American tellers reporting low job self-efficacy, perceived control exacerbated the effects of demands. However, in a matched Hong Kong sample, collective efficacy interacted in the same way with control and demands as job self-efficacy had in the American sample. These differences appear to be explained by the individual attributes of idiocentrism and allocentrism that are linked to the societal norms of individualism and collectivism, respectively.

  17. Microbial community analysis of ambient temperature anaerobic digesters

    Energy Technology Data Exchange (ETDEWEB)

    Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

    2010-07-01

    This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

  18. Collective Intellectual Property in Michoacán: Negotiating Economic and Cultural Agendas in the Artisanal Field

    Directory of Open Access Journals (Sweden)

    Lucero Ibarra Rojas

    2016-09-01

    Full Text Available The state of Michoacán, México, has almost 50 collective trademarks registered for artisanal products, which were created by initiative of different state institutions. This article aims to understand the different influences that are mediated by law when collective forms of intellectual property are incorporated and negotiated by different institutions with different aims within the realm of the state. By looking closely at the experience in Michoacán, I argue that two economic/cultural agendas can be identified. On the one hand, there is the federal agenda that aims for a national and international projection of a Mexican product, focused on the successfully industrialized national products closely linked with México's imagery for a foreign audience. On the other hand, there are the expectations of Michoacán's local government, which are strongly related with a pluralist discourse and with the different policy approaches it inspires. Between the two, the country’s cultural agenda becomes shaped by economic concerns that are, in turn, defined by the worldviews of state institution's agents. El estado de Michoacán, México, tiene casi 50 marcas colectivas de productos artesanales, que fueron registradas por iniciativa de diferentes instituciones estatales. Este artículo busca comprender las variadas influencias que son mediadas por el derecho cuando se incorporan formas colectivas de propiedad intelectual, mediante la negociación de diferentes instituciones con diferentes objetivos dentro del ámbito estatal. A través de la experiencia de Michoacán, sostengo que se pueden identificar dos agendas económicas/culturales. Por un lado, se encuentra la agenda federal que busca una proyección nacional e internacional de un producto identificable como mexicano, enfocándose en los productos nacionales que han tenido una industrialización exitosa. Por otro lado, se encuentran las expectativas del gobierno local de Michoacán, que se

  19. Culture of the entrepreneur: collective entrepreneurial action and profile of the entrepreneur Cultura empreendedora: empreendedorismo coletivo e perfil empreendedor

    Directory of Open Access Journals (Sweden)

    Carla Maria Schmidt

    2008-03-01

    Full Text Available The culture of the entrepreneur is fundamental because it represents the essence of entrepreneurial action which may be exemplified in many ways. An analysis was made of the contribution of this culture to the formation of a local productive arrangement for sustainable tourism in Nova Russia, Blumenau, S.C.. Data were obtained from the ten owner managers involved by means of a participative survey as well as meetings, visits, presentations and structured interviews. An entrepreneurial culture was identified; however it is still weak, in spite of collective entrepreneurial actions undertaken. The entrepreneurial profiles of those investigated were in an incipient stage hindering the arrangement at this time. More extensive development of the profiles would encourage progress of the arrangement and stimulate collective and timely innovations in view of continuing market developments.A cultura empreendedora é fundamental, pois representa a essência do empreendedorismo, e pode manifestar-se de várias formas. Dessa forma, o objetivo geral desta pesquisa foi analisar a contribuição dessa cultura para a formação do Arranjo Produtivo Local (APL de turismo sustentável na Nova Rússia em Blumenau - SC. O estudo foi realizado mediante pesquisa participante com os dez proprietários-dirigentes do aglomerado turístico da Nova Rússia. Os dados foram obtidos de reuniões, visitas, palestras e entrevistas estruturadas. Como principal resultado, identificou-se que existe cultura empreendedora na região, porém bem fragilizada, pois, apesar de existirem ações de empreendedorismo coletivo na Nova Rússia, o perfil empreendedor dos investigados ainda apresenta um nível bastante baixo de desenvolvimento, o que compromete o início do APL neste momento. Caso a cultura empreendedora estivesse mais caracterizada, teria influência muita positiva sobre a formação do APL, pois os empreendedores se tornariam inovadores diante das constantes evoluções do

  20. Iron oxyhydroxide mineralization on microbial extracellular polysaccharides

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Clara S.; Fakra, Sirine C.; Edwards, David C.; Emerson, David; Banfield, Jillian F.

    2010-06-22

    Iron biominerals can form in neutral pH microaerophilic environments where microbes both catalyze iron oxidation and create polymers that localize mineral precipitation. In order to classify the microbial polymers that influence FeOOH mineralogy, we studied the organic and mineral components of biominerals using scanning transmission X-ray microscopy (STXM), micro X-ray fluorescence ({mu}XRF) microscopy, and high-resolution transmission electron microscopy (HRTEM). We focused on iron microbial mat samples from a creek and abandoned mine; these samples are dominated by iron oxyhydroxide-coated structures with sheath, stalk, and filament morphologies. In addition, we characterized the mineralized products of an iron-oxidizing, stalk-forming bacterial culture isolated from the mine. In both natural and cultured samples, microbial polymers were found to be acidic polysaccharides with carboxyl functional groups, strongly spatially correlated with iron oxyhydroxide distribution patterns. Organic fibrils collect FeOOH and control its recrystallization, in some cases resulting in oriented crystals with high aspect ratios. The impact of polymers is particularly pronounced as the materials age. Synthesis experiments designed to mimic the biomineralization processes show that the polysaccharide carboxyl groups bind dissolved iron strongly but release it as mineralization proceeds. Our results suggest that carboxyl groups of acidic polysaccharides are produced by different microorganisms to create a wide range of iron oxyhydroxide biomineral structures. The intimate and potentially long-term association controls the crystal growth, phase, and reactivity of iron oxyhydroxide nanoparticles in natural systems.

  1. cultural

    Directory of Open Access Journals (Sweden)

    Irene Kreutz

    2006-01-01

    Full Text Available Es un estudio cualitativo que adoptó como referencial teorico-motodológico la antropología y la etnografía. Presenta las experiencias vivenciadas por mujeres de una comunidad en el proceso salud-enfermedad, con el objetivo de comprender los determinantes sócio-culturales e históricos de las prácticas de prevención y tratamiento adoptados por el grupo cultural por medio de la entrevista semi-estructurada. Los temas que emergieron fueron: la relación entre la alimentación y lo proceso salud-enfermedad, las relaciones con el sistema de salud oficial y el proceso salud-enfermedad y lo sobrenatural. Los dados revelaron que los moradores de la comunidad investigada tienen un modo particular de explicar sus procedimientos terapéuticos. Consideramos que es papel de los profesionales de la salud en sus prácticas, la adopción de abordajes o enfoques que consideren al individuo en su dimensión sócio-cultural e histórica, considerando la enorme diversidad cultural en nuestro país.

  2. Nutrient and physical profile data from four Microbial Exchanges and Coupling in Coastal Atlantic Systems (MECCAS) cruises collected aboard the R/V Gyre at the mouth of the Chesapeake Bay and northern Atlantic Ocean from February 17, 1985 to September 7, 1986 (NODC Accession 8800324)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Microbial Exchanges and Coupling in Coastal Atlantic Systems (MECCAS) cruise data collected aboard the R/V Gyre at the mouth of the Chesapeake Bay and northern...

  3. Microbial incorporation of nitrogen in stream detritus

    Science.gov (United States)

    Diane M. Sanzone; Jennifer L. Tank; Judy L. Meyer; Patrick J. Mulholland; Stuart E.G. Findlay

    2001-01-01

    We adapted the chloroform fumigation method to determine microbial nitrogen (N) and microbial incorporation of 15N on three common substrates [leaves, wood and fine benthic organic matter (FBOM)] in three forest streams. We compared microbial N and 15 content of samples collected during a 6-week15N-NH...

  4. Plant pathogen culture collections: it takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology.

    Science.gov (United States)

    Kang, Seogchan; Blair, Jaime E; Geiser, David M; Khang, Chang-Hyun; Park, Sook-Young; Gahegan, Mark; O'Donnell, Kerry; Luster, Douglas G; Kim, Seong H; Ivors, Kelly L; Lee, Yong-Hwan; Lee, Yin-Won; Grünwald, Niklaus J; Martin, Frank M; Coffey, Michael D; Veeraraghavan, Narayanan; Makalowska, Izabela

    2006-09-01

    ABSTRACT Plant pathogen culture collections are essential resources in our fight against plant disease and for connecting discoveries of the present with established knowledge of the past. However, available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections. As novel and reemerging plant pathogens threaten agriculture, their timely identification and monitoring depends on rapid access to cultures representing the known diversity of plant pathogens along with genotypic, phenotypic, and epidemiological data associated with them. Archiving such data in a format that can be easily accessed and searched is essential for rapid assessment of potential risk and can help track the change and movement of pathogens. The underexplored pathogen diversity in nature further underscores the importance of cataloguing pathogen cultures. Realizing the potential of pathogen genomics as a foundation for developing effective disease control also hinges on how effectively we use the sequenced isolate as a reference to understand the genetic and phenotypic diversity within a pathogen species. In this letter, we propose a number of measures for improving pathogen culture collections.

  5. Collective Cultural Memory as a TV Guide: “Living” History and Nostalgia on the Digital Television Platform

    Directory of Open Access Journals (Sweden)

    Hagedoorn Berber

    2017-12-01

    circulation of “living history” on the digital thematic channel – collective cultural memory hence functioning as a TV guide.

  6. Microbial bio-based plastics from olive-mill wastewater: Generation and properties of polyhydroxyalkanoates from mixed cultures in a two-stage pilot scale system.

    Science.gov (United States)

    Ntaikou, I; Valencia Peroni, C; Kourmentza, C; Ilieva, V I; Morelli, A; Chiellini, E; Lyberatos, G

    2014-10-20

    The operational efficiency of a two stage pilot scale system for polyhydroxyalkanoates (PHAs) production from three phase olive oil mill wastewater (OMW) was investigated in this study. A mixed anaerobic, acidogenic culture derived from a municipal wastewater treatment plant, was used in the first stage, aiming to the acidification of OMW. The effluent of the first bioreactor that was operated in continuous mode, was collected in a sedimentation tank in which partial removal of the suspended solids was taking place, and was then forwarded to an aerobic reactor, operated in sequential batch mode under nutrient limitation. In the second stage an enriched culture of Pseudomonas sp. was used as initial inoculum for the production of PHAs from the acidified waste. Clarification of the acidified waste, using aluminium sulphate which causes flocculation and precipitation of solids, was also performed, and its effect on the composition of the acidified waste as well as on the yields and properties of PHAs was investigated. It was shown that clarification had no significant qualitative or quantitative effect on the primary carbon sources, i.e. short chain fatty acids and residual sugars, but only on the values of total suspended solids and total chemical oxygen demand of the acidified waste. The type and thermal characteristics of the produced PHAs were also similar for both types of feed. However the clarification of the waste seemed to have a positive impact on final PHAs yield, measured as gPHAs/100g of VSS, which reached up to 25%. Analysis of the final products via nuclear magnetic resonance spectroscopy revealed the existence of 3-hydroxybutyrate (3HB) and 3-hydroxyoctanoate (HO) units, leading to the conclusion that the polymer could be either a blend of P3HB and P3HO homopolymers or/and the 3HB-co-3HO co-polymer, an unusual polymer occurring in nature with advanced properties. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Crafts and Craft Education as Expressions of Cultural Heritage: Individual Experiences and Collective Values among an International Group of Women University Students

    Science.gov (United States)

    Kokko, Sirpa; Dillon, Patrick

    2011-01-01

    This paper explores relationships between crafts, craft education and cultural heritage as reflected in the individual experiences and collective values of fifteen female university students of different nationalities. The students (all trainee teachers) were following a course in crafts and craft education as part of an International Study…

  8. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  9. Utilization of Alternate Chirality Enantiomers in Microbial Communities

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2010-01-01

    Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

  10. Hydrogen production from microbial strains

    Science.gov (United States)

    Harwood, Caroline S; Rey, Federico E

    2012-09-18

    The present invention is directed to a method of screening microbe strains capable of generating hydrogen. This method involves inoculating one or more microbes in a sample containing cell culture medium to form an inoculated culture medium. The inoculated culture medium is then incubated under hydrogen producing conditions. Once incubating causes the inoculated culture medium to produce hydrogen, microbes in the culture medium are identified as candidate microbe strains capable of generating hydrogen. Methods of producing hydrogen using one or more of the microbial strains identified as well as the hydrogen producing strains themselves are also disclosed.

  11. Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques

    DEFF Research Database (Denmark)

    Ryssel, Mia; Johansen, Pernille; Abu Al-Soud, Waleed

    2015-01-01

    ) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture...

  12. Effect of specimen collection techniques, transport media, and incubation of cultures on the detection rate of Helicobacter pylori

    NARCIS (Netherlands)

    van der Hulst, R. W.; Verheul, S. B.; Weel, J. F.; Gerrits, Y.; ten Kate, F. J.; Dankert, J.; Tytgat, G. N.

    1996-01-01

    Culture and histologic examination are considered "gold standard" methods for the detection of Helicobacter pylori, but discrepancies may occur with either method. Failure to detect Helicobacter pylori may be due to sampling error, inappropriate transport or culture media, or insufficient duration

  13. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Directory of Open Access Journals (Sweden)

    Peter Larsen

    Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  14. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Science.gov (United States)

    Larsen, Peter; Gilbert, Jack

    2013-01-01

    In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  15. Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

    Science.gov (United States)

    Davis, R.; Tebo, B. M.

    2013-12-01

    Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn

  16. Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses.

    Science.gov (United States)

    Ruark, Casey L; Koenning, Stephen R; Davis, Eric L; Opperman, Charles H; Lommel, Steven A; Mitchum, Melissa G; Sit, Tim L

    2017-01-01

    Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2), and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO). Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst) and Heterodera schachtii (beet cyst), but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation.

  17. Culture, corporation and collective action: The Department of Energy's American Indian consultation program on the Nevada Test Site in political ecological perspective

    Science.gov (United States)

    Halmo, David Brian

    In the western United States, Numic-speaking Indian peoples wield more power today than ever before. Following centuries of depopulation, land and resource loss, and directed change interventions aimed at assimilating them into mainstream society, they are revitalizing traditional culture and renewing their claims to lands and resources by demanding equal participation in national-level activities that affect land and resources that were once under their control. In 1994, representatives of Numic Indian tribes representing three ethnic groups involved in consultation with the U.S. Department of Energy on the Nevada Test Site (NTS) decided by consensus to "incorporate" themselves as the Consolidated Group of Tribes and Organizations (CGTO) to defend their common interests in and claims to NTS lands and resources. What caused 16 distinct, autonomous, sovereign American Indian tribal entities to incorporate themselves as a corporate organization? Using a political ecology perspective, this study examines the social, cultural and political processes operating at multiple levels of analysis and applies social and cultural theories of (1) ethnic cultural persistence, (2) the emergence and evolution of collective action groups for defending cultural interests in "common property," (3) the role of corporate and organizational structure and culture in the articulation of social relations between contending groups, and (4) the related shifts or changes in the distribution of structural power as a result of changing policy environments to a case study-based ethnographic analysis of an ongoing program of American Indian consultation.

  18. Collective action in culturally similar and dissimilar groups: An axperiment on parochialism, conditional cooperation, and their linkages

    NARCIS (Netherlands)

    Koopmans, R.; Rebers, S.

    2009-01-01

    This study examines the effects of ingroup favoritism and outgroup hostility ("parochialism"), as well as of conditionally cooperative strategies, in explaining contributions to experimental public goods games. The experimental conditions vary group composition along two culturally inheritable

  19. Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

    Science.gov (United States)

    Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

    2017-05-01

    Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

  20. Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses.

    Directory of Open Access Journals (Sweden)

    Casey L Ruark

    Full Text Available Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC and Missouri (MO. The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2, and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO. Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst and Heterodera schachtii (beet cyst, but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation.

  1. Viability and molecular authentication of Coccidioides spp. isolates from the Instituto de Medicina Tropical de São Paulo culture collection, Brazil

    OpenAIRE

    Cavalcanti,Sarah Desirée Barbosa; Vidal,Mônica Scarpelli Martinelli; Sousa,Maria da Glória Teixeira de; Del Negro,Gilda Maria Barbaro

    2013-01-01

    Coccidioidomycosis is an emerging fungal disease in Brazil; adequate maintenance and authentication of Coccidioides isolates are essential for research into genetic diversity of the environmental organisms, as well as for understanding the human disease. Seventeen Coccidioides isolates maintained under mineral oil since 1975 in the Instituto de Medicina Tropical de São Paulo (IMTSP) culture collection, Brazil, were evaluated with respect to their viability, morphological characteristics and g...

  2. Multilevel participation within on-line collections of local memories as a practice of cultural citizenship : the value of local cultural heritage for societ

    NARCIS (Netherlands)

    de Kreek, M.

    2011-01-01

    Collecting local memories on-line is a growing practice with participatory elements on different levels. Three levels of participation – micro, meso and macro – are introduced by describing an exemplary case: the Memory of East in Amsterdam. These levels of this particular case can be grounded in

  3. Microbial glycoproteomics

    DEFF Research Database (Denmark)

    Halim, Adnan; Anonsen, Jan Haug

    2017-01-01

    Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins...... and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation....

  4. Sappinia sp. (Amoebozoa: Thecamoebida) and Rosculus sp. (SAR: Cercozoa) Isolated From King Penguin Guano Collected in the Subantarctic (South Georgia, Salisbury Plain) and their Coexistence in Culture.

    Science.gov (United States)

    Tyml, Tomáš; Dyková, Iva

    2018-01-16

    Two amoeboid organisms of the genera Sappinia Dangeard, 1896 and Rosculus Hawes, 1963 were identified in a sample containing king penguin guano. This sample, collected in the Subantarctic, enlarges the list of fecal habitats known for the presence of coprophilic amoebae. The two organisms were co-isolated and subcultured for over 6 mo, with continuous efforts being invested to separate each one from the mixed culture. In the mixed culture, Rosculus cells were fast growing, tolerated changes in culturing conditions, formed cysts, and evidently were attracted by Sappinia trophozoites. The separation of the Rosculus strain was accomplished, whereas the Sappinia strain remained intermixed with inseparable Rosculus cells. Sappinia cell populations were sensitive to changes in culturing conditions; they improved with reduction of Rosculus cells in the mixed culture. Thick-walled cysts, reportedly formed by Sappinia species, were not seen. The ultrastructure of both organisms was congruent with the currently accepted generic characteristics; however, some details were remarkable at the species level. Combined with the results of phylogenetic analyses, our findings indicate that the ultrastructure of the glycocalyx and the presence/absence of the Golgi apparatus in differential diagnoses of Sappinia species require a critical re-evaluation. © 2018 The Author(s) Journal of Eukaryotic Microbiology © 2018 International Society of Protistologists.

  5. Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

    Science.gov (United States)

    Ben Said, Sami; Or, Dani

    2017-01-01

    potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.

  6. Biilliards, rhythms, collectives - Billiards at a Danish activity center as a culturally specific form of active ageing

    DEFF Research Database (Denmark)

    Lassen, Aske Juul

    2014-01-01

    Through an ethnographic study of older men playing billiards at an activity centre and a document study of how the concept of activity has changed during the last 60 years, this article argues that active ageing policies overlook that activities are culturally significant forms of practise situated...

  7. Microbial conversion of sulfur dioxide in flue gas to sulfide using bulk drug industry wastewater as an organic source by mixed cultures of sulfate reducing bacteria

    International Nuclear Information System (INIS)

    Rao, A. Gangagni; Ravichandra, P.; Joseph, Johny; Jetty, Annapurna; Sarma, P.N.

    2007-01-01

    Mixed cultures of sulfate reducing bacteria (SRB) were isolated from anaerobic cultures and enriched with SRB media. Studies on batch and continuous reactors for the removal of SO 2 with bulk drug industry wastewater as an organic source using isolated mixed cultures of SRB revealed that isolation and enrichment methodology adopted in the present study were apt to suppress the undesirable growth of anaerobic bacteria other than SRB. Studies on anaerobic reactors showed that process was sustainable at COD/S ratio of 2.2 and above with optimum sulfur loading rate (SLR) of 5.46 kg S/(m 3 day), organic loading rate (OLR) of 12.63 kg COD/(m 3 day) and at hydraulic residence time (HRT) of 8 h. Free sulfide (FS) concentration in the range of 300-390 mg FS/l was found to be inhibitory to mixed cultures of SRB used in the present studies

  8. A differential centrifugation protocol and validation criterion for enhancing mass spectrometry (MALDI-TOF) results in microbial identification using blood culture growth bottles.

    Science.gov (United States)

    March-Rosselló, G A; Muñoz-Moreno, M F; García-Loygorri-Jordán de Urriés, M C; Bratos-Pérez, M A

    2013-05-01

    Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) is a widely used tool in clinical microbiology for rapidly identifying microorganisms. This technique can be applied directly on positive blood cultures without the need for its culturing, thereby, reducing the time required for microbiological diagnosis. The present study proposes an innovative identification protocol applied to positive blood culture bottles using MALDI-TOF. We have processed 100 positive blood culture bottles, of which 36 of 37 Gram-negative bacteria (97.3 %) were correctly identified directly with 100 % of Enterobacteriaceae and other Gram-negative rods and 87.5 % of non-fermenting Gram-negative rods. We also correctly identified directly 62 of 63 of Gram-positive bacteria (98.4 %) with 100 % of Streptococcus, Enterococcus, and Gram-positive bacilli and 98 % of Staphylococcus. Applying the differential centrifugation protocol at the moment the automatic blood culture incubation system gives a positive reading together with the proposed validation criterion offers 98 % sensitivity (95 % confidence interval: 95.2-100 %). The MALDI-TOF system, thus, provides a rapid and reliable system for identifying microorganisms from blood culture growth bottles.

  9. Collective leadership and safety cultures (Co-Lead): protocol for a mixed-methods pilot evaluation of the impact of a co-designed collective leadership intervention on team performance and safety culture in a hospital group in Ireland.

    Science.gov (United States)

    McAuliffe, Eilish; De Brún, Aoife; Ward, Marie; O'Shea, Marie; Cunningham, Una; O'Donovan, Róisín; McGinley, Sinead; Fitzsimons, John; Corrigan, Siobhán; McDonald, Nick

    2017-11-03

    There is accumulating evidence implicating the role of leadership in system failures that have resulted in a range of errors in healthcare, from misdiagnoses to failures to recognise and respond to patient deterioration. This has led to concerns about traditional hierarchical leadership structures and created an interest in the development of collective ways of working that distribute leadership roles and responsibilities across team members. Such collective leadership approaches have been associated with improved team performance and staff engagement. This research seeks to improve our understanding of collective leadership by addressing two specific issues: (1) Does collective leadership emerge organically (and in what forms) in a newly networked structure? and (2) Is it possible to design and implement collective leadership interventions that enable teams to collectively improve team performance and patient safety? The first phase will include a social network analysis, using an online survey and semistructured interviews at three time points over 12 months, to document the frequency of contact and collaboration between senior hospital management staff in a recently configured hospital group. This study will explore how the network of 11 hospitals is operating and will assess whether collective leadership emerges organically. Second, collective leadership interventions will be co-designed during a series of workshops with healthcare staff, researchers and patient representatives, and then implemented and evaluated with four healthcare teams within the hospital network. A mixed-methods evaluation will explore the impact of the intervention on team effectiveness and team performance indicators to assess whether the intervention is suitable for wider roll-out and evaluation across the hospital group. Favourable ethical opinion has been received from the University College Dublin Research Ethics Committee (HREC-LS-16-116397/LS-16-20). Results will be disseminated

  10. Insect Cell Culture

    NARCIS (Netherlands)

    Oers, van M.M.; Lynn, D.E.

    2010-01-01

    Insect cell cultures are widely used in studies on insect cell physiology, developmental biology and microbial pathology. In particular, insect cell culture is an indispensable tool for the study of insect viruses. The first continuously growing insect cell cultures were established from

  11. Microbial and chemical transformation studies of the bioactive marine sesquiterpenes (S)-(+)-curcuphenol and -curcudiol isolated from a deep reef collection of the Jamaican sponge Didiscus oxeata.

    Science.gov (United States)

    El Sayed, Khalid A; Yousaf, Muhammad; Hamann, Mark T; Avery, Mitchell A; Kelly, Michelle; Wipf, Peter

    2002-11-01

    Microbial and chemical transformation studies of the marine sesquiterpene phenols (S)-(+)-curcuphenol (1) and (S)-(+)-curcudiol (2), isolated from the Jamaican sponge Didiscus oxeata, were accomplished. Preparative-scale fermentation of 1 with Kluyveromyces marxianus var. lactis (ATCC 2628) has resulted in the isolation of six new metabolites: (S)-(+)-15-hydroxycurcuphenol (3), (S)-(+)-12-hydroxycurcuphenol (4), (S)-(+)-12,15-dihydroxycurcuphenol (5), (S)-(+)-15-hydroxycurcuphenol-12-al (6), (S)-(+)-12-carboxy-10,11-dihydrocurcuphenol (7), and (S)-(+)-12-hydroxy-10,11-dihydrocurcuphenol (8). Fourteen-days incubation of 1 with Aspergillus alliaceus (NRRL 315) afforded the new compounds (S)-(+)-10beta-hydroxycurcudiol (9), (S)-(+)-curcudiol-10-one (10), and (S)-(+)-4-[1-(2-hydroxy-4-methyl)phenyl)]pentanoic acid (11). Rhizopus arrhizus (ATCC 11145) and Rhodotorula glutinus (ATCC 15125) afforded (S)-curcuphenol-1alpha-D-glucopyranoside (12) and (S)-curcudiol-1alpha-D-glucopyranoside (13) when incubated for 6 and 8 days with 1 and 2, respectively. The absolute configuration of C(10) and C(11) of metabolites 7-9 was established by optical rotation computations. Reaction of 1 with NaNO(2) and HCl afforded (S)-(+)-4-nitrocurcuphenol (14) and (S)-(+)-2-nitrocurcuphenol (15) in a 2:1 ratio. Acylation of 1 and 2 with isonicotinoyl chloride afforded the expected esters (S)-(+)-curcuphenol-1-O-isonicotinate (16) and (S)-(+)-curcudiol-1-O-isonicotinate (17), respectively. Curcuphenol (1) shows potent antimicrobial activity against Candida albicans, Cryptococcus neoformans, methicillin-resistant Staphylococcus aureus, and S. aureus with MIC and MFC/MBC ranges of 7.5-25 and 12.5-50 microg/mL, respectively. Compounds 1 and 3 also display in vitro antimalarial activity against Palsmodium falciparium (D6 clone) with MIC values of 3600 and 3800 ng/mL, respectively (selectivity index >1.3). Both compounds were also active against P. falciparium (W2 clone) with MIC values of 1800 (S

  12. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  13. A fermented meat model system for studies of microbial aroma formation

    DEFF Research Database (Denmark)

    Tjener, Karsten; Stahnke, Louise Heller; Andersen, L.

    2003-01-01

    A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starte......H, microbial growth and volatile profiles was similar to sausage production. Based on these findings, the model system was considered valid for studies of aroma formation of meat cultures for fermented sausage.......A fermented meat model system was developed, by which microbial formation of volatiles could be examined The model was evaluated against dry, fermented sausages with respect to microbial growth, pH and volatile profiles. Fast and slowly acidified sausages and models were produced using the starter...... cultures Pediococcus pentosaceus and Staphylococcus xylosus. Volatiles were collected and analysed by dynamic headspace sampling and GC MS. The analysis was primarily focused on volatiles arising from amino acid degradation and a total of 24 compounds, of which 19 were quantified, were used...

  14. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  15. Cultural commons and cultural evolution

    OpenAIRE

    Bravo, Giangiacomo

    2010-01-01

    Culture evolves following a process that is akin to biological evolution, although with some significant differences. At the same time culture has often a collective good value for human groups. This paper studies culture in an evolutionary perspective, with a focus on the implications of group definition for the coexistence of different cultures. A model of cultural evolution is presented where agents interacts in an artificial environment. The belonging to a specific memetic group is a majo...

  16. The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate.

    Science.gov (United States)

    Batista, Nádia Nara; Ramos, Cíntia Lacerda; Dias, Disney Ribeiro; Pinheiro, Ana Carla Marques; Schwan, Rosane Freitas

    2016-02-01

    Theobroma cacao seeds are the main raw material for chocolate production. During their fermentation, a succession of microorganisms are responsible for the physicochemical changes occurring in the pulp and inside the beans. The aim of this study was to investigate the effects of yeast inoculation (Saccharomyces cerevisiae UFLA CA11, Pichia kluivery CCMA0237, and Hanseniaspora uvarum CCMA0236) on the profile of the volatile compounds and microbial communities in cocoa fermentation. The resulting chocolate was also evaluated by temporal dominance of sensations (TDS) analyses. The dominant microorganisms during spontaneous fermentation were S. cerevisiae, H. uvarum, H. guilliermondii, Lactobacillus fermentum, Pediococcus sp., and Acetobacter pasteurianus. Similarly, S. cerevisiae, P. kluyveri, Candida sp., Pediococcus sp., and A. pasteurianus were the predominant microorganisms assessed by Denaturing Gradient Gel Electrophoresis (DGGE) in inoculated fermentation. Sixty-seven volatile compounds were detected and quantified by gas chromatography/mass spectrometry (GC/MS) at the end of fermentation and chocolates. The main group of volatile compound found after the inoculated and spontaneous fermentations was esters (41 and 39 %, respectively). In the chocolates, the main group was acids (73 and 44 % from the inoculated and spontaneous fermentations, respectively). The TDS analyses showed a dominance of bitter and cocoa attributes in both chocolates. However, in the inoculated chocolate, lingering fruity notes were more intense, while the chocolate produced by spontaneous fermentation was more astringent. Thus, the inoculation of yeast influenced the microbial profile, which likely affected the volatile compounds that affect sensory characteristics, resulting in chocolate with dominant bitter, cocoa, and fruity attributes.

  17. Viability and molecular authentication of Coccidioides spp. isolates from the Instituto de Medicina Tropical de São Paulo culture collection, Brazil.

    Science.gov (United States)

    Cavalcanti, Sarah Desirée Barbosa; Vidal, Mônica Scarpelli Martinelli; Sousa, Maria da Glória Teixeira de; Del Negro, Gilda Maria Barbaro

    2013-01-01

    Coccidioidomycosis is an emerging fungal disease in Brazil; adequate maintenance and authentication of Coccidioides isolates are essential for research into genetic diversity of the environmental organisms, as well as for understanding the human disease. Seventeen Coccidioides isolates maintained under mineral oil since 1975 in the Instituto de Medicina Tropical de São Paulo (IMTSP) culture collection, Brazil, were evaluated with respect to their viability, morphological characteristics and genetic features in order to authenticate these fungal cultures. Only five isolates were viable after almost 30 years, showing typical morphological characteristics, and sequencing analysis using Coi-F and Coi-R primers revealed 99% identity with Coccidioides genera. These five isolates were then preserved in liquid nitrogen and sterile water, and remained viable after two years of storage under these conditions, maintaining the same features.

  18. Viability and molecular authentication of Coccidioides spp. isolates from the Instituto de Medicina Tropical de São Paulo culture collection, Brazil

    Directory of Open Access Journals (Sweden)

    Sarah Desirée Barbosa Cavalcanti

    2013-02-01

    Full Text Available Coccidioidomycosis is an emerging fungal disease in Brazil; adequate maintenance and authentication of Coccidioides isolates are essential for research into genetic diversity of the environmental organisms, as well as for understanding the human disease. Seventeen Coccidioides isolates maintained under mineral oil since 1975 in the Instituto de Medicina Tropical de São Paulo (IMTSP culture collection, Brazil, were evaluated with respect to their viability, morphological characteristics and genetic features in order to authenticate these fungal cultures. Only five isolates were viable after almost 30 years, showing typical morphological characteristics, and sequencing analysis using Coi-F and Coi-R primers revealed 99% identity with Coccidioides genera. These five isolates were then preserved in liquid nitrogen and sterile water, and remained viable after two years of storage under these conditions, maintaining the same features.

  19. Microbial effects on colloidal agglomeration

    International Nuclear Information System (INIS)

    Hersman, L.

    1995-11-01

    Colloidal particles are known to enhance the transport of radioactive metals through soil and rock systems. This study was performed to determine if a soil microorganism, isolated from the surface samples collected at Yucca Mountain, NV, could affect the colloidal properties of day particles. The agglomeration of a Wyoming bentonite clay in a sterile uninoculated microbial growth medium was compared to the agglomeration in the medium inoculated with a Pseudomonas sp. In a second experiment, microorganisms were cultured in the succinate medium for 50 h and removed by centrifugation. The agglomeration of the clay in this spent was compared to sterile uninoculated medium. In both experiments, the agglomeration of the clay was greater than that of the sterile, uninoculated control. Based on these results, which indicate that this microorganism enhanced the agglomeration of the bentonite clay, it is possible to say that in the presence of microorganisms colloidal movement through a rock matrix could be reduced because of an overall increase in the size of colloidal particle agglomerates. 32 refs

  20. Genes Required for Survival in Microgravity Revealed by Genome-Wide Yeast Deletion Collections Cultured during Spaceflight

    Directory of Open Access Journals (Sweden)

    Corey Nislow

    2015-01-01

    Full Text Available Spaceflight is a unique environment with profound effects on biological systems including tissue redistribution and musculoskeletal stresses. However, the more subtle biological effects of spaceflight on cells and organisms are difficult to measure in a systematic, unbiased manner. Here we test the utility of the molecularly barcoded yeast deletion collection to provide a quantitative assessment of the effects of microgravity on a model organism. We developed robust hardware to screen, in parallel, the complete collection of ~4800 homozygous and ~5900 heterozygous (including ~1100 single-copy deletions of essential genes yeast deletion strains, each carrying unique DNA that acts as strain identifiers. We compared strain fitness for the homozygous and heterozygous yeast deletion collections grown in spaceflight and ground, as well as plus and minus hyperosmolar sodium chloride, providing a second additive stressor. The genome-wide sensitivity profiles obtained from these treatments were then queried for their similarity to a compendium of drugs whose effects on the yeast collection have been previously reported. We found that the effects of spaceflight have high concordance with the effects of DNA-damaging agents and changes in redox state, suggesting mechanisms by which spaceflight may negatively affect cell fitness.

  1. A New Kind of English: Cultural Variance, Citizenship and DiY Politics amongst the Exodus Collective in England

    Science.gov (United States)

    Blackstone, Lee Robert

    2005-01-01

    This article addresses the construction of citizenship in contemporary England as a boundary between "proper" and "improper" English behavior. Through an ethnographic study of the Exodus Collective, a Rastafarian-anarchist community that was located north of London, I show that constructing citizenship also constructs…

  2. Enabling School Structure, Collective Responsibility, and a Culture of Academic Optimism: Toward a Robust Model of School Performance in Taiwan

    Science.gov (United States)

    Wu, Jason H.; Hoy, Wayne K.; Tarter, C. John

    2013-01-01

    Purpose: The purpose of this research is twofold: to test a theory of academic optimism in Taiwan elementary schools and to expand the theory by adding new variables, collective responsibility and enabling school structure, to the model. Design/methodology/approach: Structural equation modeling was used to test, refine, and expand an…

  3. [Blood cultures in the paediatric emergency department. Guidelines and recommendations on their indications, collection, processing and interpretation].

    Science.gov (United States)

    Hernández-Bou, S; Álvarez Álvarez, C; Campo Fernández, M N; García Herrero, M A; Gené Giralt, A; Giménez Pérez, M; Piñeiro Pérez, R; Gómez Cortés, B; Velasco, R; Menasalvas Ruiz, A I; García García, J J; Rodrigo Gonzalo de Liria, C

    2016-05-01

    Blood culture (BC) is the gold standard when a bacteraemia is suspected, and is one of the most requested microbiological tests in paediatrics. Some changes have occurred in recent years: the introduction of new vaccines, the increasing number of patients with central vascular catheters, as well as the introduction of continuous monitoring BC systems. These changes have led to the review and update of different factors related to this technique in order to optimise its use. A practice guideline is presented with recommendations on BC, established by the Spanish Society of Paediatric Emergency Care and the Spanish Society for Paediatric Infectious Diseases. After reviewing the available scientific evidence, several recommendations for each of the following aspects are presented: BC indications in the Emergency Department, how to obtain, transport and process cultures, special situations (indications and interpretation of results in immunosuppressed patients and/or central vascular catheter carriers, indications for anaerobic BC), differentiation between bacteraemia and contamination when a BC shows bacterial growth and actions to take with a positive BC in patients with fever of unknown origin. Copyright © 2015 Asociación Española de Pediatría. Published by Elsevier España, S.L.U. All rights reserved.

  4. Microbial effects

    International Nuclear Information System (INIS)

    Sharpe, V.J.

    1985-10-01

    The long term safety and integrity of radioactive waste disposal sites proposed for use by Ontario Hydro may be affected by the release of radioactive gases. Microbes mediate the primary pathways of waste degradation and hence an assessment of their potential to produce gaseous end products from the breakdown of low level waste was performed. Due to a number of unknown variables, assumptions were made regarding environmental and waste conditions that controlled microbial activity; however, it was concluded that 14 C and 3 H would be produced, albeit over a long time scale of about 1500 years for 14 C in the worst case situation

  5. Microbial content of abattoir wastewater and its contaminated soil in ...

    African Journals Online (AJOL)

    Microbial content of wastewater in two abattoirs and the impact on microbial population of receiving soil was studied in Agege and Ojo Local Government Areas in Lagos State, Nigeria. Wastewater samples were collected from each of the abattoirs over three months period and examined for microbial content. Soil samples ...

  6. A simple method for rapid microbial identification from positive monomicrobial blood culture bottles through matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Lin, Jung-Fu; Ge, Mao-Cheng; Liu, Tsui-Ping; Chang, Shih-Cheng; Lu, Jang-Jih

    2017-06-30

    Rapid identification of microbes in the bloodstream is crucial in managing septicemia because of its high disease severity, and direct identification from positive blood culture bottles through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can shorten the turnaround time. Therefore, we developed a simple method for rapid microbiological identification from positive blood cultures by using MALDI-TOF MS. We modified previously developed methods to propose a faster, simpler and more economical method, which includes centrifugation and hemolysis. Specifically, our method comprises two-stage centrifugation with gravitational acceleration (g) at 600g and 3000g, followed by the addition of a lysis buffer and another 3000g centrifugation. In total, 324 monomicrobial bacterial cultures were identified. The success rate of species identification was 81.8%, which is comparable with other complex methods. The identification success rate was the highest for Gram-negative aerobes (85%), followed by Gram-positive aerobes (78.2%) and anaerobes (67%). The proposed method requires less than 10 min, costs less than US$0.2 per usage, and facilitates batch processing. We conclude that this method is feasible for clinical use in microbiology laboratories, and can serve as a reference for treatments or further complementary diagnostic testing. Copyright © 2017. Published by Elsevier B.V.

  7. Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

    Science.gov (United States)

    Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

    2013-01-01

    The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the

  8. Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

    1995-01-05

    Two chronosequence of unsaturated buried loess sediments ranging in age from <10,000 years to >1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was {approx}250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: {approx}1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be

  9. The Microbial Fecal Indicator Paradigm: Tools in the Toolbox Applications in Recreational Waters

    Science.gov (United States)

    Summary of ORD’s recent research to develop tools for assessing microbial water quality in recreational waters. Methods discussed include the development of health associations between microbial fecal indicators and the development of culture, and molecular methods for fec...

  10. Environmental controls on microbial communities in continental serpentinite fluids

    Directory of Open Access Journals (Sweden)

    Melitza eCrespo-Medina

    2014-11-01

    Full Text Available Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate and formate, with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

  11. Microbial keratitis in West and East Malaysia

    OpenAIRE

    Vanitha Ratnalingam; Thiageswari Umapathy; Kala Sumugam; Hanida Hanafi; Shamala Retnasabapathy

    2017-01-01

    AIM: To evaluate the epidemiological and etiological factors of microbial keratitis seen in tertiary hospitals in West and East Malaysia.METHODS: A total of 207 patients were enrolled. Patients referred for microbial keratitis to Sungai Buloh Hospital and Kuala Lumpur Hospital in West Malaysia and Queen Elizabeth Hospital and Kuching General Hospital in East Malaysia were recruited. Risk factors were documented. Corneal scrapings for microscopy and culture were performed.RESULTS: The most com...

  12. Optimization of culture medium for anaerobic production of rhamnolipid by recombinant Pseudomonas stutzeri Rhl for microbial enhanced oil recovery.

    Science.gov (United States)

    Zhao, F; Mandlaa, M; Hao, J; Liang, X; Shi, R; Han, S; Zhang, Y

    2014-08-01

    Response surface methodology was employed to enhance the anaerobic production of rhamnolipid by recombinant Pseudomonas stutzeri Rhl. Glycerol is a promising carbon source used to anaerobically produce rhamnolipid. In a Plackett-Burman design, glycerol, KH2 PO4 and yeast extract were significant factors. The proposed optimized medium contained the following: 46·55 g l(-1) glycerol; 3 g l(-1) NaNO3 ; 5·25 g l(-1) K2 HPO4 ·3H2 O; 5·71 g l(-1) KH2 PO4 ; 0·40 g l(-1) MgSO4 ·7H2 O; 0·13 g l(-1) CaCl2 ; 1·0 g l(-1) KCl; 1·0 g l(-1) NaCl; and 2·69 g l(-1) yeast extract. Using this optimized medium, we obtained an anaerobic yield of rhamnolipid of 3·12 ± 0·11 g l(-1) with a 0·85-fold increase. Core flooding test results also revealed that Ps. stutzeri Rhl grown in an optimized medium enhanced the oil recovery efficiency by 15·7%, which was 6·6% higher than in the initial medium. Results suggested that the optimized medium is a promising nutrient source that could effectively mobilize oil by enhancing the in situ production of rhamnolipid. The ex situ application of rhamnolipid for microbial enhanced oil recovery (MEOR) is costly and complex in terms of rhamnolipid production, purification and transportation. Compared with ex situ applications, the in situ production of rhamnolipid in anaerobic oil reservoir is more advantageous for MEOR. This study is the first to report the anaerobic production optimization of rhamnolipid. Results showed that the optimized medium enhanced not only the anaerobic production of rhamnolipid but also crude oil recovery. © 2014 The Society for Applied Microbiology.

  13. Comparison of microbial fermentation of high- and low-forage diets in Rusitec, single-flow continuous-culture fermenters and sheep rumen.

    Science.gov (United States)

    Carro, M D; Ranilla, M J; Martín-García, A I; Molina-Alcaide, E

    2009-04-01

    Eight Rusitec and eight single-flow continuous-culture fermenters (SFCCF) were used to compare the ruminal fermentation of two diets composed of alfalfa hay and concentrate in proportions of 80 : 20 (F80) and 20 : 80 (F20). Results were validated with those obtained previously in sheep fed the same diets. Rusitec fermenters were fed once daily and SFCCF twice, but liquid dilution rates were similar in both types of fermenters. Mean values of pH over the 12 h postfeeding were higher (P 0.05) were found in any in vitro system. A more precise control of pH in both types of fermenters and a reduction of concentrate retention time in Rusitec could probably improve the simulation of in vivo fermentation.

  14. Genetically engineering Synechocystis sp. Pasteur Culture Collection 6803 for the sustainable production of the plant secondary metabolite p-coumaric acid.

    Science.gov (United States)

    Xue, Yong; Zhang, Yan; Cheng, Dan; Daddy, Soumana; He, Qingfang

    2014-07-01

    p-Coumaric acid is the precursor of phenylpropanoids, which are plant secondary metabolites that are beneficial to human health. Tyrosine ammonia lyase catalyzes the production of p-coumaric acid from tyrosine. Because of their photosynthetic ability and biosynthetic versatility, cyanobacteria are promising candidates for the production of certain plant metabolites, including phenylpropanoids. Here, we produced p-coumaric acid in a strain of transgenic cyanobacterium Synechocystis sp. Pasteur Culture Collection 6803 (hereafter Synechocystis 6803). Whereas a strain of Synechocystis 6803 genetically engineered to express sam8, a tyrosine ammonia lyase gene from the actinomycete Saccharothrix espanaensis, accumulated little or no p-coumaric acid, a strain that both expressed sam8 and lacked slr1573, a native hypothetical gene shown here to encode a laccase that oxidizes polyphenols, produced ∼82.6 mg/L p-coumaric acid, which was readily purified from the growth medium.

  15. Reassessing the ichthyotoxin profile of cultured Prymnesium parvum (golden algae) and comparing it to samples collected from recent freshwater bloom and fish kill events in North America.

    Science.gov (United States)

    Henrikson, Jon C; Gharfeh, Majed S; Easton, Anne C; Easton, James D; Glenn, Karen L; Shadfan, Miriam; Mooberry, Susan L; Hambright, K David; Cichewicz, Robert H

    2010-06-15

    Within the last two decades, Prymnesium parvum (golden algae) has rapidly spread into inland waterways across the southern portion of North America and this organism has now appeared in more northerly distributed watersheds. In its wake, golden algae blooms have left an alarming trail of ecological devastation, namely massive fish kills, which are threatening the economic and recreational value of freshwater systems throughout the United States. To further understand the nature of this emerging crisis, our group investigated the chemical nature of the toxin(s) produced by P. parvum. We approached the problem using a two-pronged strategy that included analyzing both laboratory-grown golden algae and field-collected samples of P. parvum. Our results demonstrate that there is a striking difference in the toxin profiles for these two systems. An assemblage of potently ichthyotoxic fatty acids consisting primarily of stearidonic acid was identified in P. parvum cultures. While the concentration of the fatty acids alone was sufficient to account for the rapid-onset ichthyotoxic properties of cultured P. parvum, we also detected a second type of highly labile ichthyotoxic substance(s) in laboratory-grown golden algae that remains uncharacterized. In contrast, the amounts of stearidonic acid and its related congeners present in samples from recent bloom and fish kill sites fell well below the limits necessary to induce acute toxicity in fish. However, a highly labile ichthyotoxic substance, which is similar to the one found in laboratory-grown P. parvum cultures, was also detected. We propose that the uncharacterized labile metabolite produced by P. parvum is responsible for golden algae's devastating fish killing effects. Moreover, we have determined that the biologically-relevant ichthyotoxins produced by P. parvum are not the prymnesins as is widely believed. Our results suggest that further intensive efforts will be required to chemically define P. parvum

  16. Exploring social norms around cohabitation: The life course, individualization, and culture: Introduction to Special Collection: "Focus on Partnerships: Discourses on cohabitation and marriage throughout Europe and Australia"

    Directory of Open Access Journals (Sweden)

    Brienna Perelli-Harris

    2015-10-01

    Full Text Available Background: Explanations of the increase in cohabitation often rely on the concept of ideational change and shifting social norms. While researchers have investigated cohabitation and the role of social norms from a quantitative perspective, few studies have examined how people discuss the normative context of cohabitation, especially in cross-national comparison. Objective: This article introduces a Special Collection that uses focus group research to compare social norms relating to cohabitation and marriage in 8 countries in Europe. The Introduction explicates the concept of social norms, describes the focus group project, reflects on the method's advantages and limitations, and summarizes the theoretical and methodological contributions of the project. Methods: Collaborators conducted 7−8 focus groups in each country using a standardized questionnaire. They coded each discussion, analyzed the results, and produced a country-specific chapter on a particular theme. They also collaborated on an overview paper that synthesized the overall findings of the project. Results: The articles provide insights into the meanings of partnership formation in each country. In addition, their findings contribute to three main theoretical themes: 1 life courses, sequencing, and intersections; 2 individualization, freedom, and commitment; and 3 culture, religion, and the persistence of the past. Conclusions: This Special Collection contributes to and challenges current explanations of family change by pointing out how social norms shape partnership behavior. The project informs quantitative research by emphasizing the need for a culturally informed interpretation of demographic behavior. We urge researchers to recognize the multiple meanings of cohabitation within each context and across countries.

  17. Microbial Safari.

    Science.gov (United States)

    Wagner, Stephen C.; Stewart, Robert S., Jr.

    2000-01-01

    Introduces an investigative microbiology laboratory activity emphasizing critical thinking and experimental design in which students isolate and characterize a bacterium from a specific habitat. Explains the procedures of the laboratory including safety, sample collection, and isolation. (YDS)

  18. The microbial community of the cystic fibrosis airway is disrupted in early life.

    Directory of Open Access Journals (Sweden)

    Julie Renwick

    Full Text Available Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.Bronchoalveolar lavage (BAL fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13 and BAL from children without CF (n = 9 were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test and Principle coordinate analysis (p = 0.01; Adonis test. Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.

  19. The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

    Science.gov (United States)

    Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

    2004-01-01

    An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

  20. Developmental stages of fish blood flukes, Cardicola forsteri and Cardicola opisthorchis (Trematoda: Aporocotylidae), in their polychaete intermediate hosts collected at Pacific bluefin tuna culture sites in Japan.

    Science.gov (United States)

    Ogawa, Kazuo; Shirakashi, Sho; Tani, Kazuki; Shin, Sang Phil; Ishimaru, Katsuya; Honryo, Tomoki; Sugihara, Yukitaka; Uchida, Hiro'omi

    2017-02-01

    Farming of Pacific bluefin tuna (PBT), Thunnus orientalis, is a rapidly growing industry in Japan. Aporocotylid blood flukes of the genus Cardicola comprising C. orientalis, C. opisthorchis and C. forsteri are parasites of economic importance for PBT farming. Recently, terebellid polychaetes have been identified as the intermediate hosts for all these parasites. We collected infected polychaetes, Terebella sp., the intermediate host of C. opisthorchis, from ropes and floats attached to tuna cages in Tsushima, Nagasaki Prefecture, Japan. Also, Neoamphitrite vigintipes (formerly as Amphitrite sp. sensu Shirakashi et al., 2016), the intermediate host of C. forsteri, were collected from culture cages in Kushimoto, Wakayama Prefecture, Japan. The terebellid intermediate hosts harbored the sporocysts and cercariae in their body cavity. Developmental stages of these blood flukes were molecularly identified using species specific PCR primers. In this paper, we describe the cercaria and sporocyst stages of C. opisthorchis and C. forsteri and compare their morphological characteristics among three Cardicola blood flukes infecting PBT. We also discuss phylogenetic relations of the six genera of the terebellid intermediate hosts (Artacama, Lanassa, Longicarpus, Terebella, Nicolea and Neoamphitrite) of blood flukes infecting marine fishes, based on their morphological characters. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. [Engineering issues of microbial ecology in space agriculture].

    Science.gov (United States)

    Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

    2005-03-01

    Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define

  2. Microbial micropatches within microbial hotspots

    Science.gov (United States)

    Smith, Renee J.; Tobe, Shanan S.; Paterson, James S.; Seymour, Justin R.; Oliver, Rod L.; Mitchell, James G.

    2018-01-01

    The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur. PMID:29787564

  3. [Preservation of high risk fungal cultures of Histoplasma and Cryptococcus].

    Science.gov (United States)

    Fernández Andreu, C Carlos Manuel; Díaz Suárez, Luis Alberto; Ilnait Zaragozi, María Teresa; Aragonés López, Carlos; Martínez Machín, Gerardo; Perurena Lancha, Mayda R

    2012-01-01

    culture collections are responsible for providing the microbial resources for development of biological sciences. Storage in distilled water is one of the easiest and least expensive method for long-term fungal preservation. to evaluate the usefulness of this preservation method in fungal culture of Histoplasma and Cryptococcus. the preservation condition of the highest biological risk species from Histoplasma y Cryptococcus genera, included in the fungal culture collection of "Pedro Kouri" Institute of Tropical Medicine in Havana, was evaluated in this study. One hundred and two strains stored in distilled water, 92% of which had been preserved for more than 10 years, were analyzed. the percentages of recovered strains from H. capsulatum, C. neoformans and C. gattii were 64.3%; 79.1% and 100% respectively. This method of preservation proved to be satisfactory for fungal culture in labs with limited financial resources. A web-based database with interesting information about the collection was made. The importance of strict compliance with the biosafety measures in these collections, particularly with high risk pathogens. preservation of fungal cultures in distilled water is a very useful method for laboratories with limited resources. Culture collections should be assumed as an essential activity in order to solve increasing challenges in the development of biomedical sciences.

  4. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    Energy Technology Data Exchange (ETDEWEB)

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  5. Genome engineering for microbial natural product discovery.

    Science.gov (United States)

    Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

    2018-03-03

    The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

  6. study of oral and gingival microbial flora in institutionalized mentally

    African Journals Online (AJOL)

    boaz

    from the mouth and gingiva of 138 institutionalized mentally retarded patients of Sari to culture in specific media to ... Key words: Oral and gingival microbial flora, Mental retardation, D%, Sari ... staphylococcus aureus and, in case of negative.

  7. Microbial Flocculant for Nature Soda

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Peiyong; Zhang, Tong; Chen, Cuixian

    2004-03-31

    Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

  8. Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

    Science.gov (United States)

    Hyde, A.; Joye, S. B.; Teske, A.

    2017-12-01

    Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

  9. Arginine vasopressin increases cellular free calcium concentration and adenosine 3',5'-monophosphate production in rat renal papillary collecting tubule cells in culture

    International Nuclear Information System (INIS)

    Ishikawa, S.; Okada, K.; Saito, T.

    1988-01-01

    The role of calcium (Ca) in the cellular action of arginine vasopressin (AVP) was examined in rat renal papillary collecting tubule cells in culture. AVP increased both the cellular free Ca concentration ([Ca2+]i) using fura-2, and cAMP production in a dose-dependent manner. AVP-induced cellular Ca mobilization was totally blocked by the antagonist to the antidiuretic action of AVP, and somewhat weakened by the antagonist to the vascular action of AVP. 1-Deamino-8-D-AVP (dDAVP). an antidiuretic analog of AVP, also increased [Ca2+] significantly. Cellular Ca mobilization was not obtained with cAMP, forskolin (a diterpene activator of adenylate cyclase), or phorbol-12-myristate-13-acetate. The early phase of [Ca2+]i depended on the intracellular Ca pool, since an AVP-induced rise in [Ca2+]i was obtained in cells pretreated with Ca-free medium containing 1 mM EGTA, verapamil, or cobalt, which blocked cellular Ca uptake. Also, AVP increased 45 Ca2+ influx during the initial 10 min, which initiated the sustained phase of cellular Ca mobilization. However, cellular cAMP production induced by AVP during the 10-min observation period was diminished in the cells pretreated with Ca-free medium, verapamil, or cobalt, but was still significantly higher than the basal level. This was also diminished by a high Ca concentration in medium. These results indicate that 1) AVP concomitantly regulates cellular free Ca as well as its second messenger cAMP production; 2) AVP-induced elevation of cellular free Ca is dependent on both the cellular Ca pool and extracellular Ca; and 3) there is an optimal level of extracellular Ca to modulate the AVP action in renal papillary collecting tubule cells

  10. The Microbial DNA Index System (MiDIS): A tool for microbial pathogen source identification

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2010-08-09

    The microbial DNA Index System (MiDIS) is a concept for a microbial forensic database and investigative decision support system that can be used to help investigators identify the sources of microbial agents that have been used in a criminal or terrorist incident. The heart of the proposed system is a rigorous method for calculating source probabilities by using certain fundamental sampling distributions associated with the propagation and mutation of microbes on disease transmission networks. This formalism has a close relationship to mitochondrial and Y-chromosomal human DNA forensics, and the proposed decision support system is somewhat analogous to the CODIS and SWGDAM mtDNA databases. The MiDIS concept does not involve the use of opportunistic collections of microbial isolates and phylogenetic tree building as a basis for inference. A staged approach can be used to build MiDIS as an enduring capability, beginning with a pilot demonstration program that must meet user expectations for performance and validation before evolving into a continuing effort. Because MiDIS requires input from a a broad array of expertise including outbreak surveillance, field microbial isolate collection, microbial genome sequencing, disease transmission networks, and laboratory mutation rate studies, it will be necessary to assemble a national multi-laboratory team to develop such a system. The MiDIS effort would lend direction and focus to the national microbial genetics research program for microbial forensics, and would provide an appropriate forensic framework for interfacing to future national and international disease surveillance efforts.

  11. 11 Soil Microbial Biomass

    African Journals Online (AJOL)

    186–198. Insam H. (1990). Are the soil microbial biomass and basal respiration governed by the climatic regime? Soil. Biol. Biochem. 22: 525–532. Insam H. D. and Domsch K. H. (1989). Influence of microclimate on soil microbial biomass. Soil Biol. Biochem. 21: 211–21. Jenkinson D. S. (1988). Determination of microbial.

  12. Molecular microbial ecology manual

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

    2004-01-01

    The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

  13. Microbial Rechargeable Battery

    NARCIS (Netherlands)

    Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

    2016-01-01

    Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

  14. Childhood microbial keratitis

    Directory of Open Access Journals (Sweden)

    Abdullah G Al Otaibi

    2012-01-01

    Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

  15. Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.

    Science.gov (United States)

    Medina, Daniel; Walke, Jenifer B; Gajewski, Zachary; Becker, Matthew H; Swartwout, Meredith C; Belden, Lisa K

    2017-01-01

    One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads ( Anaxyrus americanus ) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting

  16. Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material.

    Science.gov (United States)

    Triest, David; De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

    2016-09-01

    Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium -like clade was adopted. The few species of the Fusarium -like clade were moved to new, re-installed or existing genera or provisionally retained as " Fusarium ." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium -like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium -like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium -like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides . The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium -like clade and were also found morphologically distinct from other members of the Fusarium -like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium -like clade.

  17. The Potential of Popular Culture for the Creation of Left Populism in Serbia: The Case of the Hip-Hop Collective “The Bombs of the Nineties”

    Directory of Open Access Journals (Sweden)

    Jovana Papović

    2016-12-01

    Full Text Available The focus of this article is to highlight the potential of popular culture to become an agent of leftist populist politics in contemporary Serbia. The authors observe the hip-hop collective “The Bombs of the Nineties”, whose music tackles topics from recent history, and who subvert the fashion style of the 1990s “Dizel” subculture, which is often connected to Serbian nationalism and war profiteering. The paper analyses the relationships “The Bombs of the Nineties” create between their practices, class warfare and leftist discourses, aiming to show the potentials and threats those relationships introduce. Following Ernesto Laclau’s understanding of populism as a “hegemonic political articulation of demands”, we assume that “The Bombs of the Nineties” could represent a solid populist political agent in that they attempt to reveal and draw attention to the “unfulfilled demands” of disempowered Serbian youth. On the other hand, the counter-intuitive merge of ideologies they operate, and the limited impact of their strategies on the official politics could be an obstacle to the expansion of their message.

  18. Microbial consortia of gorgonian corals from the Aleutian islands.

    Science.gov (United States)

    Gray, Michael A; Stone, Robert P; McLaughlin, Molly R; Kellogg, Christina A

    2011-04-01

    Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae. FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

  19. Interval scanning photomicrography of microbial cell populations.

    Science.gov (United States)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  20. Microbial contamination of the Tzu-Chi Cord Blood Bank from 2005 to 2006.

    Science.gov (United States)

    Chen, Shu-Huey; Zheng, Ya-Jun; Yang, Shang-Hsien; Yang, Kuo-Liang; Shyr, Ming-Hwang; Ho, Yu-Huai

    2008-01-01

    In total, 4502 units of cord blood (CB) were collected during a 2-year period from 2005 to 2006 by the Buddhist Tzu-Chi Stem Cells Center. The aim of this study was to analyze the incidence of microbial contamination and type of organism present in the cord blood. The clinical impact of microbial contamination on hematopoietic progenitor cell (HPC) grafts used for HPC transplantation is also discussed. First and second specimens were obtained for microbial assessment. These were collected in laboratory after cord blood collection and after cord blood unit manipulation, respectively. The samples were cultured and the results reviewed. The overall incidence of microbiological contamination was 1.8% (82/4502). Three CB units were contaminated with two different organisms. Infectious organisms comprised 9.4% (8/85) of total isolated microbes. These infectious microorganisms were beta-Streptococci group B, Candida tropicalis and Staphylococcus aureus which were isolated in 6, 1 and 1 of CB units respectively. Escherichia coli, Bacteroides fragilis, Lactobacillus spp., Enterococcus, beta-Streptococcus Group B, Bacteroides valgatus, Corynebacterium spp., Klebsiella pneumonia and Peptococcus spp. were the most frequently encountered microorganisms. A higher contamination rate of the CB units was noted after vaginal delivery (2.16%) compared to caesarian section (0.85%) (p bank, we use a closed system but an in utero method. Similar to other studies, most of microorganisms reported here as contaminants are non-pathogenic.

  1. Dynamics of culturable soil microbial communities during ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-10-20

    Oct 20, 2008 ... 1Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology,. Faculty of Science and Agriculture, University of ..... manual of Microbiology. WH Freeman and Co, USA.

  2. PHA Production in Aerobic Mixed Microbial Cultures

    NARCIS (Netherlands)

    Johnson, K.

    2010-01-01

    Polyhydroxyalkanoate (PHA) is a common intracellular energy and carbon storage material in bacteria, which is considered as a bioplastic due to its plastic like properties. PHAs are versatile materials which are biodegradable and made from renewable resources. Commercial production of PHAs is

  3. Raman Spectroscopy of Microbial Pigments

    Science.gov (United States)

    Edwards, Howell G. M.; Oren, Aharon

    2014-01-01

    Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions. PMID:24682303

  4. Onshore Wind Speed Modulates Microbial Aerosols along an Urban Waterfront

    Directory of Open Access Journals (Sweden)

    M. Elias Dueker

    2017-11-01

    Full Text Available Wind blowing over aquatic and terrestrial surfaces produces aerosols, which include microbial aerosols. We studied the effect of onshore wind speeds on aerosol concentrations as well as total and culturable microbial aerosols (bacterial and viral at an urban waterfront (New York, NY, United States of America. We used two distinct methods to characterize microbial aerosol responses to wind speed: A culture-based exposure-plate method measuring viable bacterial deposition near-shore (CFU accumulation rate; and a culture-independent aerosol sampler-based method measuring total bacterial and viral aerosols (cells m−3 air. While ambient coarse (>2 µm and fine (0.3–2 µm aerosol particle number concentrations (regulated indicators of air quality decreased with increasing onshore wind speeds, total and depositing culturable bacterial aerosols and total viral aerosols increased. Taxonomic identification of the 16S rDNA of bacterial aerosol isolates suggested both terrestrial and aquatic sources. Wind appears to increase microbial aerosol number concentrations in the near-shore environment by onshore transport at low wind speeds (<4 m s−1, and increased local production and transport of new microbial aerosols from adjacent water surfaces at higher wind speeds (>4 m s−1. This study demonstrates a wind-modulated microbial connection between water and air in the coastal urban environment, with implications for public health management and urban microbial ecology.

  5. Unique Phylogenetic Lineage Found in the Fusarium-like Clade after Re-examining BCCM/IHEM Fungal Culture Collection Material

    Science.gov (United States)

    De Cremer, Koen; Piérard, Denis; Hendrickx, Marijke

    2016-01-01

    Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade. PMID:27790062

  6. Bioaccumulation of perfluorinated carboxylates and sulfonates and polychlorinated biphenyls in laboratory-cultured Hexagenia spp., Lumbriculus variegatus and Pimephales promelas from field-collected sediments

    Energy Technology Data Exchange (ETDEWEB)

    Prosser, R.S., E-mail: prosserr@uoguelph.ca [School of Environmental Sciences, University of Guelph, Guelph, Ontario (Canada); Mahon, K. [Aquatic Toxicology Unit, Ontario Ministry of the Environment and Climate Change, Toronto, Ontario (Canada); Sibley, P.K. [School of Environmental Sciences, University of Guelph, Guelph, Ontario (Canada); Poirier, D.; Watson-Leung, T. [Aquatic Toxicology Unit, Ontario Ministry of the Environment and Climate Change, Toronto, Ontario (Canada)

    2016-02-01

    Polychlorinated biphenyls (PCBs) and perfluorinated carboxylates and sulfonates (PFASs) are persistent pollutants in sediment that can potentially bioaccumulate in aquatic organisms. The current study investigates variation in the accumulation of PCBs and PFASs in laboratory-cultured Hexagenia spp., Lumbriculus variegatus and Pimephales promelas from contaminated field-collected sediment using 28-day tests. BSAF{sup lipid} (lipid-normalized biota-sediment accumulation factor) values for total concentration of PCBs were greater in Hexagenia spp. relative to L. variegatus and P. promelas. The distribution of congeners contributing to the total concentration of PCBs in tissue varied among the three species. Trichlorobiphenyl congeners composed the greatest proportion of the total concentration of PCBs in L. variegatus while tetra- and pentabiphenyl congeners dominated in Hexagenia spp. and P. promelas. Perfluorooctane sulfonate (PFOS) was present in all three species at concentrations greater than all other PFASs analyzed. Hexagenia spp. also produced the greatest BSAF{sup lipid} and BSAF{sup ww} (non-lipid-normalized biota-sediment accumulation factor) values for PFOS relative to the other two species. However, this was not the case for all PFASs. The trend of BSAF values and number of carbon atoms in the perfluoroalkyl chain of perfluorinated carboxylates varied among the three species but was similar for perfluorinated sulfonates. Differences in the dominant pathways of exposure (e.g., water, sediment ingestion) likely explain a large proportion of the variation in accumulation observed across the three species. - Highlights: • BSAF values for total PCBs and PFOS greatest in Hexagenia spp. • BSAF values for other PFASs not consistently greatest in Hexagenia spp. • Trends in BSAF values for PFASs varied as a function of carbon chain length among species. • Differences in exposure pathways likely explain variation in accumulation across species.

  7. Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

    Science.gov (United States)

    Fortney, N. W.; Roden, E. E.; Boyd, E. S.; Converse, B. J.

    2014-12-01

    Previous work on dissimilatory iron reduction (DIR) in Yellowstone National Park (YNP) has focused on high temperature, low pH environments where soluble Fe(III) is utilized as an electron acceptor for respiration. Much less attention has been paid to DIR in lower temperature, circumneutral pH environments, where solid phase Fe(III) oxides are the dominant forms of Fe(III). This study explored the potential for DIR in the warm (ca. 40-50°C), circumneutral pH Chocolate Pots hot springs (CP) in YNP. Most probable number (MPN) enumerations and enrichment culture studies confirmed the presence of endogenous microbial communities that reduced native CP Fe(III) oxides. Enrichment cultures demonstrated sustained DIR coupled to acetate and lactate oxidation through repeated transfers over ca. 450 days. Pyrosequencing of 16S rRNA genes indicated that the dominant organisms in the enrichments were closely affiliated with the well known Fe(III) reducer Geobacter metallireducens. Additional taxa included relatives of sulfate reducing bacterial genera Desulfohalobium and Thermodesulfovibrio; however, amendment of enrichments with molybdate, an inhibitor of sulfate reduction, suggested that sulfate reduction was not a primary metabolic pathway involved in DIR in the cultures. A metagenomic analysis of enrichment cultures is underway in anticipation of identifying genes involved in DIR in the less well-characterized dominant organisms. Current studies are aimed at interrogating the in situ microbial community at CP. Core samples were collected along the flow path (Fig. 1) and subdivided into 1 cm depth intervals for geochemical and microbiological analysis. The presence of significant quantities of Fe(II) in the solids indicated that DIR is active in situ. A parallel study investigated in vitro microbial DIR in sediments collected from three of the coring sites. DNA was extracted from samples from both studies for 16S rRNA gene and metagenomic sequencing in order to obtain a

  8. Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

    NARCIS (Netherlands)

    Justé, A.; Thomma, B.P.H.J.; Lievens, B.

    2008-01-01

    In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids.

  9. Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

    Science.gov (United States)

    Hager, K. W.; Fullerton, H.; Moyer, C. L.

    2015-12-01

    Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

  10. Antibacterial activity of marine culturable bacteria collected from a global sampling of ocean surface waters and surface swabs of marine organisms

    DEFF Research Database (Denmark)

    Gram, Lone; Melchiorsen, Jette; Bruhn, Jesper Bartholin

    2010-01-01

    ). Total cell counts at the seawater surface were 5 × 105 to 106 cells/ml, of which 0.1–0.2% were culturable on dilute marine agar (20°C). Three percent of the colonies cultured from seawater inhibited Vibrio anguillarum, whereas a significantly higher proportion (13%) of colonies from inert or biotic...

  11. Conditioning biomass for microbial growth

    Science.gov (United States)

    Bodie, Elizabeth A; England, George

    2015-03-31

    The present invention relates to methods for improving the yield of microbial processes that use lignocellulose biomass as a nutrient source. The methods comprise conditioning a composition comprising lignocellulose biomass with an enzyme composition that comprises a phenol oxidizing enzyme. The conditioned composition can support a higher rate of growth of microorganisms in a process. In one embodiment, a laccase composition is used to condition lignocellulose biomass derived from non-woody plants, such as corn and sugar cane. The invention also encompasses methods for culturing microorganisms that are sensitive to inhibitory compounds in lignocellulose biomass. The invention further provides methods of making a product by culturing the production microorganisms in conditioned lignocellulose biomass.

  12. Microbial extremophiles from the 2008 Schirmacher Oasis Expedition: preliminary results

    Science.gov (United States)

    Hoover, Richard B.; Pikuta, Elena V.; Townsend, Alisa; Anthony, Joshua; Guisler, Melissa; McDaniel, Jasmine; Bej, Asim; Storrie-Lombardi, Michael

    2008-08-01

    Among the most interesting targets for Astrobiology research are the polar ice caps and the permafrost of Mars and the ice and liquid water bodies that may lie beneath the frozen crusts of comets, the icy moons of Jupiter (Europa, Io and Ganymede) and Saturn (Titan and Enceladus). The permanently ice-covered lakes of Antarctica, such as Lake Vostok and Lake Untersee, provide some of the best terrestrial analogues for these targets. The 2008 International Tawani Schirmacher Oasis/Lake Untersee Expeditions have been organized to conduct studies of novel microbial extremophiles and investigate the biodiversity of the glaciers and ice-covered lakes of Dronning Maud Land, East Antarctica. This paper describes the preliminary analysis of the anaerobic microbial extremophiles isolated from samples collected during the 2008 International Schirmacher Oasis Antarctica Reconnaissance Expedition. These samples showed great diversity of psychrophlic and psychrotolerant bacteria. Six new anaerobic strains have been isolated in pure cultures and partially characterized. Two of them (strains ARHSd-7G and ARHSd-9G) were isolated from a small tidal pool near the colony of African Penguins Spheniscus demersus. Strain ARHSd-7G was isolated on mineral anaerobic medium with 3 % NaCl, pH 7 and D-glucose, it has motile, vibrion shape cells, and is Gram variable. Strain ARHSd-9G grew on anaerobic, alkaline medium with pH 9 and 1 % NaCl at 3°C. The substrate was D-glucose supplemented with yeast extract (0.05 %). Cells of strain ARHSd-9G had morphology of straight or slightly curved elongated rods and demonstrated unusual optical effects under dark-field visible light microscopy. The cells were spore-forming and Gram positive. From the mat sample collected near Lake Zub, the new strain LZ-3 was isolated in pure culture at 3°C. Strain LZ-3 was anaerobic and grew on 0.5 % NaCl mineral medium with Dglucose as a substrate. The gram positive cells were spore-forming. They exhibited a

  13. Microbial Load of Some Medicinal Plants Sold in Some Local ...

    African Journals Online (AJOL)

    Microbial Load of Some Medicinal Plants Sold in Some Local Markets in Abeokuta, Nigeria. I MacDonald, S Omonigho, J Erhabor, H Efijuemue. Abstract. Purpose: To evaluate the microbial load on 17 randomly selected plant samples from 60 ethnobotanically collected medicinal plants from five local markets in Abeokuta, ...

  14. Microbial control of the dark end of the biological pump

    NARCIS (Netherlands)

    Herndl, G.J.; Reinthaler, T.

    2013-01-01

    A fraction of the carbon captured by phytoplankton in the sunlit surface ocean sinks to depth as dead organic matter and faecal material. The microbial breakdown of this material in the subsurface ocean generates carbon dioxide. Collectively, this microbially mediated flux of carbon from the

  15. Microbial safety of foods

    International Nuclear Information System (INIS)

    Bandekar, J.R.

    2013-01-01

    Despite advances in hygiene, consumer knowledge and food treatment and processing, food-borne diseases have become one of the most widespread public health problems in the world to-day. About two thirds of all outbreaks are traced to microbial contaminated food - one of the most hazardous being Clostridium botulinum, E. coli 0157: H7 and Salmonella. The pathogens can be introduced in the food products anywhere in the food chain and hence it is of prime important to have microbial vigilance in the entire food chain. WHO estimates that food-borne and water-borne diarrhoeal diseases taken together kill about 2.2 million people annually. The infants, children, elderly and immune-compromised people are particularly susceptible to food-borne diseases. Unsafe food causes many acute and life-long diseases, ranging from diarrhoeal diseases to various forms of cancer. A number of factors such as emergence of new food-borne pathogens, development of drug resistance in the pathogens, changing life style, global trade of food etc. are responsible for the continued persistence of food-borne diseases. Due to consumer demand, a number of Ready-To-Eat (RTE) minimally processed foods are increasingly marketed. However, there is increased risk of food-borne diseases with these products. The food-borne disease outbreaks due to E. coli O157:H7, Listeria monocytogenes, Salmonella and Campylobacter are responsible for recall of many foods resulting in heavy losses to food industry. The development of multi drug resistant pathogens due to indiscriminate use of antibiotics is also a major problem. Food Technology Division of Bhabha Atomic Research Centre has been working on food-borne bacterial pathogens particularly Salmonella, Campylobacter, Vibrio and Aeromonas species, their prevalence in export quality seafood as well in foods sold in retail market such as poultry, fish, sprouts and salads. These pathogens from Indian foods have been characterized for the presence of virulence genes

  16. Characterization of indigenous oil field microorganisms for microbially enhanced oil recovery (MEOR)

    Energy Technology Data Exchange (ETDEWEB)

    Sitte, J.; Krueger, M. [Bundesanstalt fuer Geowissenschaften und Rohstoffe (BGR), Hannover (Germany); Biegel, E.; Herold, A. [BASF SE, Ludwigshafen (Germany); Alkan, H. [Wintershall Holding GmbH, Kassel (Germany)

    2013-08-01

    Microbial activities and their resulting metabolites became a focus of attention for enhanced oil recovery (MEOR, microbial enhanced oil recovery) in the recent years. In order to develop a strategy for a MEOR application in a German oil field operated by Wintershall experiments were performed to investigate different sampling strategies and the microbial communities found in these samples. The objectives of this study were (1) to characterize the indigenous microbial communities, (2) to investigate the dependency of microbial activity/diversity on the different sampling strategies, and (3) to study the influence of the in situ pressure on bacterial growth and metabolite production. Fluids were sampled at the well head (surface) and in situ in approx. 785 m depth to collect uncontaminated production water directly from the reservoir horizon and under the in situ pressure of 31 bar (subsurface). In the lab the pressure was either released quickly or slowly to assess the sensitivity of microorganisms to rapid pressure changes. Quantitative PCR resulted in higher microbial cell numbers in the subsurface than in the surface sample. Biogenic CO{sub 2} and CH{sub 4} formation rates were determined under atmospheric and high pressure conditions in the original fluids, with highest rates found in the surface fluid. Interestingly, no methane was formed in the native fluid samples. While nitrate reduction was exclusively detected in the surface samples, sulfide formation also occurred in the subsurface fluids. Increased CO{sub 2} formation was measured after addition of a variety of substrates in the surface fluids, while only fructose and glucose showed a stimulating effect on CO{sub 2} production for the subsurface sample. Stable enrichment cultures were obtained in complex medium inoculated with the subsurface fluid, both under atmospheric and in situ pressure. Growth experiments with constant or changing pressure, and subsequent DGGE analysis of bacterial 16S rRNA genes

  17. The establishment of an in vitro gene bank in Dianthus spiculifolius Schur and D. glacialis ssp. gelidus (Schott Nym. et Kotschy Tutin: I. The initiation of a tissue collection and the characterization of the cultures in minimal growth conditions

    Directory of Open Access Journals (Sweden)

    Mihaela Holobiuc

    2009-12-01

    Full Text Available In the last decades the plants have to cope with the warming of the climate. As a consequence of this process more than half of the plant species could become vulnerable or threatened until 2080. Romania has a high plant diversity, with endemic and endangered plant species, the measures of biodiversity conservation being necessary. The integrated approach of biodiversity conservation involves both in situ and ex situ strategies. Among ex situ methods of conservation, besides the traditional ones (including field and botanic collection and seed banks, in vitro tissues techniques offer a viable alternative. The germplasm collections can efficiently preserve the species (of economic, scientific and conservative importance, in the same time being a source of plant material for international exchanges and for reintroduction in the native habitats.The "in vitro gene banking" term refers to in vitro tissues cultures from many accessions of a target species and involves the collection of plant material from field or from native habitats, the elaboration of sterilization, micropropagation and maintaining protocols. These collections have to be maintained in optimal conditions, morphologically and genetically characterized. The aim of our work was to characterize the response of the plant material to the minimal in vitro growth protocol for medium-term cultures achievement as a prerequisite condition for an active gene bank establishment in two rare Caryophyllaceae taxa: Dianthus spiculifolius and D. glacialis ssp. gelidus. Among different factors previously tested for medium-term preservation in Dianthus genus, mannitol proved to be more efficient for minimal cultures achievement. In vitro, the cultures were evaluated concerning their growth, regenerability and enzyme activity (POX, SOD, CAT as a response to the preservation conditions in the incipient phase of the initiation of the in vitro collection. The two species considered in this study showed a

  18. Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

    Directory of Open Access Journals (Sweden)

    Regina eLamendella

    2014-04-01

    Full Text Available One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252 well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.

  19. Overview: Microbial amendment of remediated soils for effective recycling

    Directory of Open Access Journals (Sweden)

    Kim Soo-Bin

    2017-01-01

    Full Text Available In recent years, various methods are being considered with appropriate amendments, not with conventional reclamation to recycle deteriorated soils after remediation as agricultural addition, backfilling and construction materials etc. Among these amendments, microbial amendments with effective microorganism(EMs are known to improve soil qualities such as fertility, strength and toxicity to be recycled into possible utilizations. This study indicates the possibility of recycling the remediated soils by using these EMs most efficiently. Soil samples will be collected from contaminated sites with either heavy metals or petroleum and will be remediated by bench-scale soil washing and thermal desorption. And then the remediated soils will be treated with easily obtainable inocula, substrates (culture media near our life and they are compared with commercial EM products in terms of the cost and efficiency. Also, after treating with a number of mixing ratios, soil properties of (1 fresh, (2 contaminated, (3 remediated (4 amended soils will be evaluated based on soil quality indicators depending on demands and the optimal mixing ratios which are effective than commercial EM products will be determined. The ratio derived from pre-tests could be applied on the remediated soils with pilot-scale in order to assess suitability for recycling and characterize correlation between soil properties and microbial amendments regarding contaminants and remediation, and furthermore for modelling. In conclusion, application of the established models on recycling remediated soils may help to dispose the remediated soils in future, including environmental and ecological values as well as economical values.

  20. Farm Deployable Microbial Bioreactor for Fuel Ethanol Production

    Energy Technology Data Exchange (ETDEWEB)

    Okeke, Benedict [Auburn Univ., Montgomery AL (United States)

    2016-03-30

    Research was conducted to develop a farm and field deployable microbial bioreactor for bioethanol production from biomass. Experiments were conducted to select the most efficient microorganisms for conversion of plant fiber to sugars for fermentation to ethanol. Mixtures of biomass and surface soil samples were collected from selected sites in Alabama black belt counties (Macon, Sumter, Choctaw, Dallas, Montgomery, Lowndes) and other areas within the state of Alabama. Experiments were conducted to determine the effects of culture parameters on key biomass saccharifying enzymes (cellulase, beta-glucosidase, xylanase and beta-xylosidase). A wide-scale sampling of locally-grown fruits in Central Alabama was embarked to isolate potential xylose fermenting microorganisms. Yeast isolates were evaluated for xylose fermentation. Selected microorganisms were characterized by DNA based methods. Factors affecting enzyme production and biomass saccharification were examined and optimized in the laboratory. Methods of biomass pretreatment were compared. Co-production of amylolytic enzymes with celluloytic-xylanolytic enzymes was evaluated; and co-saccharification of a combination of biomass, and starch-rich materials was examined. Simultaneous saccharification and fermentation with and without pre-saccharifcation was studied. Whole culture broth and filtered culture broth simultaneous saccahrifcation and fermentation were compared. A bioreactor system was designed and constructed to employ laboratory results for scale up of biomass saccharification.

  1. Microbial Profiling Of Cyanobacteria From VIT Lake

    Directory of Open Access Journals (Sweden)

    Swati Singh

    2015-08-01

    Full Text Available The application of molecular biological methods to study the diversity and ecology of micro-organisms in natural environments has been practice in mid-1980. The aim of our research is to access the diversity composition and functioning of complex microbial community found in VIT Lake. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA or RNA level which is useful for constructing genetically modified microbes by recombinant DNA technology for reputed use in the environment. In this research first we will isolate cyanobacteria in lab using conventional methods like broth culture and spread plate method then we will analyze their morphology using various staining methods and DNA and protein composition using electrophoresis method. The applications of community profiling approaches will advance our understanding of the functional role of microbial diversity in VIT Lake controls on microbial community composition.

  2. Effect of Multi-Microbial Probiotic Formulation Bokashi on Pro- and Anti-Inflammatory Cytokines Profile in the Serum, Colostrum and Milk of Sows, and in a Culture of Polymorphonuclear Cells Isolated from Colostrum.

    Science.gov (United States)

    Laskowska, Ewa; Jarosz, Łukasz; Grądzki, Zbigniew

    2018-01-05

    The use of probiotics in sows during pregnancy and lactation and their impact on the quality of colostrum and milk, as well as the health conditions of their offspring during the rearing period, are currently gaining the attention of researchers. The aim of the study was to determine the effect of Bokashi formulation on the concentrations of pro- and anti-inflammatory cytokines in the serum of sows during pregnancy, in their colostrum and milk, and in a culture of Con-A-stimulated polymorphonuclear cells (PMNs) isolated from the colostrum. The study was conducted on 60 sows aged 2-4 years. EM Bokashi were added to the sows' feed. The material for the study consisted of peripheral blood, colostrum, and milk. Blood samples were collected from the sows on days 60 and 114 of gestation. Colostrum and milk samples were collected from all sows at 0, 24, 48, 72, 96, 120, 144, and 168 h after parturition. The results indicate that the use of Bokashi as feed additives resulted in increased concentrations of pro-inflammatory cytokines TNF-α and IL-6, which increase the protective capacity of the colostrum by stimulating cellular immune mechanisms protecting the sow and neonates against infection. At the same time, the increased concentrations of cytokines IL-4, IL-10, TGF-β, and of immunoglobulins in the colostrum and milk from sows in the experimental group demonstrate the immunoregulatory effect of Bokashi on Th2 cells and may lead to increased expression of regulatory T cells and polarization of the immune response from Th1 to Th2.

  3. Cultural Understanding Through Cross-Cultural Analysis.

    Science.gov (United States)

    Briere, Jean-Francois

    1986-01-01

    A college course used an explicit intercultural approach and collective research activities to compare French and American cultures and to examine the reasons for cultural attitudes and culture conflict. Class assignments dealt with contrastive analyses of American and French institutions like advertising, cinema, feminism, etc. (MSE)

  4. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

  5. Microbial accumulation of uranium

    International Nuclear Information System (INIS)

    Zhang Wei; Dong Faqin; Dai Qunwei

    2005-01-01

    The mechanism of microbial accumulation of uranium and the effects of some factors (including pH, initial uranium concentration, pretreatment of bacteria, and so on) on microbial accumulation of uranium are discussed briefly. The research direction and application prospect are presented. (authors)

  6. MICROBIAL FUEL CELL

    DEFF Research Database (Denmark)

    2008-01-01

    A novel microbial fuel cell construction for the generation of electrical energy. The microbial fuel cell comprises: (i) an anode electrode, (ii) a cathode chamber, said cathode chamber comprising an in let through which an influent enters the cathode chamber, an outlet through which an effluent...

  7. Microbial control of pollution

    Energy Technology Data Exchange (ETDEWEB)

    Fry, J C; Gadd, G M; Herbert, R A; Jones, C W; Watson-Craik, I A [eds.

    1992-01-01

    12 papers are presented on the microbial control of pollution. Topics covered include: bioremediation of oil spills; microbial control of heavy metal pollution; pollution control using microorganisms and magnetic separation; degradation of cyanide and nitriles; nitrogen removal from water and waste; and land reclamation and restoration.

  8. Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

    International Nuclear Information System (INIS)

    Kieft, T.L.; Murphy, E.M.; Haldeman, D.L.; Amy, P.S.; Bjornstad, B.N.; McDonald, E.V.; Ringelberg, D.B.; White, D.C.; Stair, J.; Griffiths, R.P.; Gsell, T.C.; Holben, W.E.; Boone, D.R.

    1995-01-01

    Two chronosequence of unsaturated buried loess sediments ranging in age from and lt;10,000 years to and gt;1 million years were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession were inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Samples were collected by coring at two sites 40 km apart in the Palouse region of eastern Washington State near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the elevation of the Winona site is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was(approx)250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age:(approx)1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Sediments of equivalent age had equal quantities of microorganisms, but differing community types. Differences in community make-up between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the ages of the microbial communities can be constrained by porewater and sediment ages. In the shallower sediments ( and lt;9 m at Washtucna, and lt;12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the

  9. Heavy metal levels, physicochemical properties and microbial ...

    African Journals Online (AJOL)

    Journal of Applied Sciences and Environmental Management ... out to assess the microbial, physicochemical and heavy metal characteristics of soil samples from five different waste collection sites within the University of Benin, Benin City and evaluated using standard analytical and classical microbiological methods.

  10. Distributional records of Antarctic fungi based on strains preserved in the Culture Collection of Fungi from Extreme Environments (CCFEE Mycological Section associated with the Italian National Antarctic Museum (MNA

    Directory of Open Access Journals (Sweden)

    Laura Selbmann

    2015-07-01

    Full Text Available This dataset includes information regarding fungal strains collected during several Antarctic expeditions: the Italian National Antarctic Research program (PNRA expeditions “X” (1994/1995, “XII” (1996/1997, “XVII” (2001/2002, “XIX” (2003/2004, “XXVI” (2010/2011, the Czech “IPY Expedition” (2007–2009 and a number of strains donated by E. Imre Friedmann (Florida State University in 2001, isolated from samples collected during the U.S.A. Antarctic Expeditions of 1980-1982. Samples, consisting of colonized rocks, mosses, lichens, sediments and soils, were collected in Southern and Northern Victoria Land of the continental Antarctica and in the Antarctic Peninsula. A total of 259 different strains were isolated, belonging to 32 genera and 38 species, out of which 12 represented new taxa. These strains are preserved in the Antarctic section of the Culture Collection of Fungi from Extreme Environments (CCFEE, which represents one of the collections associated with the Italian National Antarctic Museum (MNA, Section of Genoa, Italy, located at the Laboratory of Systematic Botany and Mycology, Department of Ecological and Biological Sciences (DEB, Tuscia University (Viterbo, Italy. The CCFEE hosts a total of 486 Antarctic fungal strains from worldwide extreme environments. Distributional records are reported here for 259 of these strains. The holotypes of the 12 new species included in this dataset are maintained at CCFEE and in other international collections: CBS-KNAW Fungal Biodiversity Centre (Utrecht, Netherlands; DBVPG, Industrial Yeasts Collection (University of Perugia, Italy; DSMZ, German Collection of Microorganisms and Cell Cultures (Brunswick, Germany; IMI, International Mycological Institute (London, U.K..

  11. Blood culture

    Science.gov (United States)

    ... There, it is placed in a special dish (culture). It is then watched to see if bacteria or other disease-causing germs grow. A gram stain may also ... any time the skin is broken) Alternative Names ... Charnot-Katsikas A. Specimen collection and handling for diagnosis of infectious diseases. In: McPherson RA, Pincus MR, eds. Henry's Clinical ...

  12. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  13. Microbial syntrophy: interaction for the common good.

    Science.gov (United States)

    Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

    2013-05-01

    Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  14. Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient.

    Science.gov (United States)

    Bartlewicz, Jacek; Lievens, Bart; Honnay, Olivier; Jacquemyn, Hans

    2016-03-30

    Microbes are common inhabitants of floral nectar and are capable of influencing plant-pollinator interactions. All studies so far investigated microbial communities in floral nectar in plant populations that were located in natural environments, but nothing is known about these communities in nectar of plants inhabiting urban environments. However, at least some microbes are vectored into floral nectar by pollinators, and because urbanization can have a profound impact on pollinator communities and plant-pollinator interactions, it can be expected that it affects nectar microbes as well. To test this hypothesis, we related microbial diversity in floral nectar to the degree of urbanization in the late-flowering plant Linaria vulgaris. Floral nectar was collected from twenty populations along an urbanization gradient and culturable bacteria and yeasts were isolated and identified by partially sequencing the genes coding for small and large ribosome subunits, respectively. A total of seven yeast and 13 bacterial operational taxonomic units (OTUs) were found at 3 and 1% sequence dissimilarity cut-offs, respectively. In agreement with previous studies, Metschnikowia reukaufii and M. gruessi were the main yeast constituents of nectar yeast communities, whereas Acinetobacter nectaris and Rosenbergiella epipactidis were the most frequently found bacterial species. Microbial incidence was high and did not change along the investigated urbanization gradient. However, microbial communities showed a nested subset structure, indicating that species-poor communities were a subset of species-rich communities. The level of urbanization was putatively identified as an important driver of nestedness, suggesting that environmental changes related to urbanization may impact microbial communities in floral nectar of plants growing in urban environments.

  15. An assessment of microbial communities associated with surface mining-disturbed overburden.

    Science.gov (United States)

    Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

    2014-03-01

    To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

  16. Comparative study of predatory responses in blue mussels (Mytilus edulis L.) produced in suspended long line cultures or collected from natural bottom mussel beds

    DEFF Research Database (Denmark)

    Christensen, Helle Torp; Dolmer, Per; Petersen, Jens Kjerulf

    2011-01-01

    Blue mussels (Mytilus edulis L.) are a valuable resource for commercial shellfish production and may also have uses as a tool in habitat improvement, because mussel beds can increase habitat diversity and complexity. A prerequisite for both commercial mussel production and habitat improvement...... originated from suspended cultures had a higher length increment and lower mortality when compared to bottom mussels. It is concluded that suspended mussels potentially are an alternative resource to bottom culture and can be used in habitat improvement of mussel beds, but that the use of suspended mussels...

  17. Microbial Biofilm as a Smart Material

    DEFF Research Database (Denmark)

    Garde, Christian; Welch, Martin; Ferkinghoff-Borg, Jesper

    2015-01-01

    Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ......, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes...

  18. Microbial ecosystem constructed in water for successful organic hydroponics

    OpenAIRE

    Makoto Shinohara; Hiromi Ohmori; Yoichi Uehara

    2008-01-01

    Conventional hydroponics systems generally use only chemical fertilisers, not organic ones, since there are no microbial ecosystems present in such systems to mineralise organic compounds to inorganic nutrients. Addition of organic compounds to the hydroponic solution generally has phytotoxic effects and causes poor plant growth. We developed a novel hydroponic culture method using organic fertiliser. A microbial ecosystem was constructed in hydroponic solution by regulating the amounts of or...

  19. Electricity production and microbial characterization of thermophilic microbial fuel cells.

    Science.gov (United States)

    Dai, Kun; Wen, Jun-Li; Zhang, Fang; Ma, Xi-Wen; Cui, Xiang-Yu; Zhang, Qi; Zhao, Ting-Jia; Zeng, Raymond J

    2017-11-01

    Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m 2 , and the columbic efficiency in this work was 20.5±6.0%. The Firmicutes bacteria, related to the uncultured bacterium clone A55_D21_H_B_C01 with a similarity of 99%, accounted for 90.9% of all bacteria in the TMFC biofilm. This unknown bacterium has the potential to become a new thermophilic exoelectrogenic bacterium that is yet to be cultured. The development of TMFC-involved biotechnologies will be beneficial for the production of valuable chemicals and generation of energy in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. School Libraries Addressing the Needs of ELL Students: Enhancing Language Acquisition, Confidence, and Cultural Fluency in ELL Students by Developing a Targeted Collection and Enriching Your Makerspace

    Science.gov (United States)

    Murphy, Peggy Henderson

    2018-01-01

    English Language Learner (ELL) students are sometimes a small constituency. Many resources already in the library can be used to enhance their language acquisition, confidence, and cultural fluency--resources such as graphic novels, hi-lo books, and makerspace materials. This article discusses enhancing language acquisition, confidence, and…

  1. Cultured Trash, Not Trash Culture

    Directory of Open Access Journals (Sweden)

    Taufiqurrohman Taufiqurrohman

    2017-09-01

    Full Text Available As civilized creature, human actually can manage trash as well as possible although it is often stereotyped as a vain thing. This article gives the proof that trash can be cultured as well so that a society can take benefits from the existence of it. This article parses ways of orderly managing it at schools, in this case two schools in Jepara. The results say that trash can be cultured by having an organization to manage the Trash Bank at schools and to train students to classify and recycle trash then take advantage of it by selling the collected and the recycled trash. It makes trash have good transformation of values, repelling against the prior stereotype. Finally, by taking example from Trash Bank management at schools, human can have so cultured trash that they would not be trapped by trash culture.

  2. Microbial activity of trench leachates from shallow-land, low-level radioactive waste disposal sites

    International Nuclear Information System (INIS)

    Francis, A.J.; Dobbs, S.; Nine, B.J.

    1980-01-01

    Trench leachate samples collected anoxically from shallow-land, low-level radioactive waste disposal sites were analyzed for total aerobic and anaerobic populations, sulfate reducers, denitrifiers, and methanogens. Among the several aerobic and anaerobic bacteria isolated, only Bacillus sp., Pseudomonas sp., Citrobacter sp., and Clostridium sp. were identified. Mixed bacterial cultures isolated from the trench leachates were able to grow anaerobically in trench leachates, which indicates that the radionuclides and organic chemicals present were not toxic to these bacteria. Changes in concentrations of several of the organic constituents of the waste leachate samples were observed due to anaerobic microbial activity. Growth of a mixed culture of trench-water bacteria in media containing a mixture of radionuclides, 60 Co, 85 Sr, and 134 137 Cs, was not affected at total activity concentrations of 2.6 x 10 2 and 2.7 x 10 3 pCi/ml

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

    OpenAIRE

    Gonzalez-Toril , E.; Amils , R.; J. Delmas , Robert; Petit , Jean-Robert; Komarek , 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...

  4. Production of hydrogen by microbial fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Roychowdhury, S.; Cox, D.; Levandowsky, M.

    1988-01-01

    Production of hydrogen by defined and undefined bacterial cultures was studied, using pure sugars (glucose and maltose) or natural sources rich in either pure sugars or polysaccharides. The latter included sugar cane juice, corn pulp (enzymatically treated or untreated), and enzymatically treated paper. Mixed microbial flora from sewage and landfill sediments, as well as pure and mixed cultures of known coliform bacteria produced mixtures of hydrogen and carbon dioxide at 37/sup 0/C and 55/sup 0/C, with hydrogen concentrations as high as 87%. In the case of the pure glucose substrate, an average yield of 0.7 mol hydrogen per mol glucose was obtained.

  5. Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete.

    Science.gov (United States)

    Zhang, Jiaguang; Zhou, Aijuan; Liu, Yuanzhen; Zhao, Bowei; Luan, Yunbo; Wang, Sufang; Yue, Xiuping; Li, Zhu

    2017-11-06

    Current studies have employed various pure-cultures for improving concrete durability based on microbially induced carbonate precipitation (MICP). However, there have been very few reports concerned with microbial consortia, which could perform more complex tasks and be more robust in their resistance to environmental fluctuations. In this study, we constructed three microbial consortia that are capable of MICP under aerobic (AE), anaerobic (AN) and facultative anaerobic (FA) conditions. The results showed that AE consortia showed more positive effects on inorganic carbon conversion than AN and FA consortia. Pyrosequencing analysis showed that clear distinctions appeared in the community structure between different microbial consortia systems. Further investigation on microbial community networks revealed that the species in the three microbial consortia built thorough energetic and metabolic interaction networks regarding MICP, nitrate-reduction, bacterial endospores and fermentation communities. Crack-healing experiments showed that the selected cracks of the three consortia-based concrete specimens were almost completely healed in 28 days, which was consistent with the studies using pure cultures. Although the economic advantage might not be clear yet, this study highlights the potential implementation of microbial consortia on crack healing in concrete.

  6. Shotgun microbial profiling of fossil remains

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Ermini, Luca; Jónsson, Hákon

    2014-01-01

    the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach...... to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial...... community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using...

  7. Smoking cessation alters subgingival microbial recolonization.

    Science.gov (United States)

    Fullmer, S C; Preshaw, P M; Heasman, P A; Kumar, P S

    2009-06-01

    Smoking cessation improves the clinical manifestations of periodontitis; however, its effect on the subgingival biofilm, the primary etiological agent of periodontitis, is unclear. The purpose of this study was to investigate, longitudinally, if smoking cessation altered the composition of the subgingival microbial community, by means of a quantitative, cultivation-independent assay for bacterial profiling. Subgingival plaque was collected at baseline, and 3, 6, and 12 months post-treatment from smokers who received root planing and smoking cessation counseling. The plaque was analyzed by terminal restriction fragment length polymorphism (t-RFLP). Microbial profiles differed significantly between smokers and quitters at 6 and 12 months following smoking cessation. The microbial community in smokers was similar to baseline, while quitters demonstrated significantly divergent profiles. Changes in bacterial levels contributed to this shift. These findings reveal a critical role for smoking cessation in altering the subgingival biofilm and suggest a mechanism for improved periodontal health associated with smoking cessation.

  8. Assessment of Microbial Contamination of Surfaces and Medical Equipment in Wards of the Panjom Azar Hospital of Gorgan in 2014

    Directory of Open Access Journals (Sweden)

    Roghaye Noroozi

    2014-06-01

    Full Text Available Methods: In this cross-sectional study, different wards of panjom Azar educational hospital including ICU, dialysis and surgery room were investigated. Samples were collected randomly, for three months from July to September 2014, from beds, oxygen masks, oxygen manometer, patient table, covers of the patient's medical records, nurse's desk, border walls and water tap.  Samples were then cultured on blood agar and EMB agar. In order to determine the bacteria type, specific culture media with specific biochemical tests and diagnostic disks were used. Results: Results showed that from 216 samples collected from the levels, the 190 cases (88% had microbial contamination. Most of the recognized bacteria were Staphylococcus saprophyticus, Staphylococcus epidermidis, Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli, Enterobacter and klebsiela. Results of microbial culture of equipments and levels were positive in case of bacterial contamination and maximum contamination was observed in the dialysis ward of the hospital. Conclusion: Due to the relatively high detected contamination, contamination control of levels and patient care equipments could considered as an effective action in reducing nosocomial infections. Thus, using appropriate disinfectant equipment, monitoring the disinfectants preparation, continuous monitoring and detection of common microorganisms are the most important ways for infection control in hospitals.

  9. Evolution of microbial pathogens

    National Research Council Canada - National Science Library

    DiRita, Victor J; Seifert, H. Steven

    2006-01-01

    ... A. Hogan vvi ■ CONTENTS 8. Evolution of Pathogens in Soil Rachel Muir and Man-Wah Tan / 131 9. Experimental Models of Symbiotic Host-Microbial Relationships: Understanding the Underpinnings of ...

  10. Synthetic Electric Microbial Biosensors

    Science.gov (United States)

    2017-06-10

    domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

  11. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  12. Microbial Diversity in Soil Treatment Systems for Wastewater

    Science.gov (United States)

    Van Cuyk, S.; Spear, J.; Siegrist, R.; Pace, N.

    2002-05-01

    There is an increasing awareness and concern over land based wastewater system performance with respect to the removal of bacteria and virus. The goal of this work is to describe and identify the organismal composition of the microbiota in the applied wastewater effluent, the rich biomat that develops at the infiltrative surface, and in the soil percolate in order to aid in the understanding of bacterial and virus purification in soil treatment systems. The traditional reliance on pure culture techniques to describe microbiota is circumvented by the employment of a molecular approach. Microbial community characterization is underway based on cloning and sequencing of 16S rRNA genes for phylogenetic analyses, to determine the nature and quantity of microbiota that constitute these ecosystems. Knowledge of the organisms naturally present can influence the design and treatment capacity of these widely used land based systems. Laboratory, intermediate and field scale systems are currently under study. Since human pathogens are known to exist in sewage effluents, their removal in wastewater infiltration systems and within the underlying soil are in need of a more fundamental understanding. The relationship between design parameters and environmental conditions, including a microbial characterization, is essential for the prevention of contamination in groundwater sources. Preliminary results indicate the presence of uncultured organisms and phylogenetic kinds that had not been detected in these systems using other methods. Acinetobacter johnsonii and Acrobacter cryaerophilus were the two dominant species found in septic tank effluent, comprising 20% and 11% of the library respectively. In soil samples collected from the infiltrative surface of a column dosed with STE, there was no dominant bacterial species present. Percolate samples collected from the outflow of the column showed that a tuber borchii symbiont, a common soil microorganism, dominated the bacterial

  13. Specialized microbial databases for inductive exploration of microbial genome sequences

    Directory of Open Access Journals (Sweden)

    Cabau Cédric

    2005-02-01

    Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

  14. Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens?

    Directory of Open Access Journals (Sweden)

    Luis A. Ramírez-Camejo

    2017-01-01

    Full Text Available Drosophila melanogaster has become a model system to study interactions between innate immunity and microbial pathogens, yet many aspects regarding its microbial community and interactions with pathogens remain unclear. In this study wild D. melanogaster were collected from tropical fruits in Puerto Rico to test how the microbiota is distributed and to compare the culturable diversity of fungi and bacteria. Additionally, we investigated whether flies are potential vectors of human and plant pathogens. Eighteen species of fungi and twelve species of bacteria were isolated from wild flies. The most abundant microorganisms identified were the yeast Candida inconspicua and the bacterium Klebsiella sp. The yeast Issatchenkia hanoiensis was significantly more common internally than externally in flies. Species richness was higher in fungi than in bacteria, but diversity was lower in fungi than in bacteria. The microbial composition of flies was similar internally and externally. We identified a variety of opportunistic human and plant pathogens in flies such as Alcaligenes faecalis, Aspergillus flavus, A. fumigatus, A. niger, Fusarium equiseti/oxysporum, Geotrichum candidum, Klebsiella oxytoca, Microbacterium oxydans, and Stenotrophomonas maltophilia. Despite its utility as a model system, D. melanogaster can be a vector of microorganisms that represent a potential risk to plant and public health.

  15. Information and Corporate Cultures.

    Science.gov (United States)

    Drake, Miriam A.

    1984-01-01

    This paper defines "corporate culture" (set of values and beliefs shared by people working in an organization which represents employees' collective judgments about future) and discusses importance of corporate culture, nature of corporate cultures in business and academia, and role of information in shaping present and future corporate…

  16. Characterization of the photosynthetic conditions and pigment profiles of the colour strains of Hypnea musciformis from field-collected and in vitro cultured samples

    Directory of Open Access Journals (Sweden)

    Daniela R. P. Fernandes

    2012-08-01

    Full Text Available Hypnea musciformis (Wulfen JV Lamour. is a species of great economic interest as it produces Κ-carrageenan and has shown biological activities against HIV and HSV viruses. This species displays different colour strains in its natural habitat, which may have implications for the biotechnological potential of the species. The aim of this study was to characterize the photosynthetic apparatus and pigment profile of three colour strains of H. musciformis (green, brown and red in their natural habitat and in culture. Chlorophyll a fluorescence of photosystem II was measured with a pulse-amplitude modulated fluorometer and pigments were quantified by spectrofluorimetry (chlorophyll a and spectrophotometry (phycobiliproteins. In the natural habitat, we detected significant differences between the colour strains for the following photochemical parameters: the green strain had a higher effective quantum yield (ΦPSII than the red strain and a higher maximum relative electron transport rate (rETRmax than the brown and red strains. Saturation irradiances were 1000 µE.m-2.s-1 (green and 500 µE.m-2.s-1 (brown and red. Concerning in vitro culture, the green strain presented the lowest ΦPSII, rETRmax, and α rETR, while the brown strain presented the highest values for these same parameters. The chlorophyll a content of the cultured green strain was the lowest. The phycoerythrin contents of the three colour strains were unchanged by either natural of in vitro conditions: lower in green, intermediate in brown and higher in the red strain, ensuring the chromatic identity of the strains. Our results suggest that the green strain has a better performance when exposed to high irradiance, but a lower efficiency under low irradiance compared to the brown and red strains.

  17. Psychrophiles and astrobiology: microbial life of frozen worlds

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2003-01-01

    Most bodies of our Solar System are "Frozen Worlds" where the prevailing surface temperature remains at or below freezing. On Earth there are vast permanently frozen regions of permafrost, polar ice sheets, and glaciers and the deep oceans and deep-sea marine sediments have remained at 2 - 4°C for eons. Psychrophilic and psychrotrophic microbiota that inhabit these regimes provide analogs for microbial life that might inhabit ice sheets and permafrost of Mars, comets, or the ice/water interfaces or sediments deep beneath the icy crusts of Europa, Callisto, or Ganymede. Cryopreserved micro-organisms can remain viable (in a deep anabiotic state) for millions of years frozen in permafrost and ice. Psychrophilic and psychrotrophic (cold-loving) microbes can carry out metabolic processes in water films and brine, acidic, or alkaline chanels in permafrost or ice at temperatures far below 0°C. These microbes of the cryosphere help define the thermal and temporal limits of life on Earth and may provide clues to where and how to search for evidence of life elsewhere in the Cosmos. Astrobiologists at the NASA Marshall Space Flight Center have collected microbial extremophiles from the Pleistocene ice wedges and frozen thermokarst ponds from the Fox Permafrost Tunnel of Alaska. Microbes have also been isolated from samples of Magellanic Penguin guano from Patagonia; deep-sea marine muds near hydrothermal vents; snow and permafrost from Siberia, and deep ice cores, ice-bubble and cryoconite rocks of the Central Antarctic Ice Sheet. These samples have yielded microbial extremophiles representing a wide variety of anaerobic bacteria and archaea. These microbes have been isolated, cultured, characterized and analyzed by phylogenetic and genomic methods. Images were obtained by Phase Contrast, Environmental, Field Emission Scanning and Transmission Electron Microscopes to study the ultra-microstructure and elemental distribution in the composition of these micro-organisms. We

  18. Microbial Regulation in Gorgonian Corals

    Directory of Open Access Journals (Sweden)

    Laura D. Mydlarz

    2012-06-01

    Full Text Available Gorgonian corals possess many novel natural products that could potentially mediate coral-bacterial interactions. Since many bacteria use quorum sensing (QS signals to facilitate colonization of host organisms, regulation of prokaryotic cell-to-cell communication may represent an important bacterial control mechanism. In the present study, we examined extracts of twelve species of Caribbean gorgonian corals, for mechanisms that regulate microbial colonization, such as antibacterial activity and QS regulatory activity. Ethanol extracts of gorgonians collected from Puerto Rico and the Florida Keys showed a range of both antibacterial and QS activities using a specific Pseudomonas aeruginosa QS reporter, sensitive to long chain AHLs and a short chain N-acylhomoserine lactones (AHL biosensor, Chromobacterium violaceium. Overall, the gorgonian corals had higher antimicrobial activity against non-marine strains when compared to marine strains. Pseudopterogorgia americana, Pseusopterogorgia acerosa, and Pseudoplexuara flexuosa had the highest QS inhibitory effect. Interestingly, Pseudoplexuara porosa extracts stimulated QS activity with a striking 17-fold increase in signal. The stimulation of QS by P. porosa or other elements of the holobiont may encourage colonization or recruitment of specific microbial species. Overall, these results suggest the presence of novel stimulatory QS, inhibitory QS and bactericidal compounds in gorgonian corals. A better understanding of these compounds may reveal insight into coral-microbial ecology and whether a therapeutic potential exists.

  19. Difficult Past, Difficult Present?: How Collective Memory and Personal Experience Shape Beliefs on Politico-Cultural Identity in Post-Conflict Societies Today

    NARCIS (Netherlands)

    Leigh, James

    2013-01-01

    In essence, we are all products of our experience; thus the positions we adopt today are influenced by what we remember (and forget) about our past. This is true at both individual and collective levels. In societies traumatised by conflict, the act of recalling and dealing with the past is

  20. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

    DEFF Research Database (Denmark)

    Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte

    2016-01-01

    of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (mi...

  1. Deep subsurface microbial processes

    Science.gov (United States)

    Lovley, D.R.; Chapelle, F.H.

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  2. Methodological approaches for studying the microbial ecology of drinking water distribution systems

    OpenAIRE

    Douterelo, Isabel; Boxall, Joby B.; Deines, Peter; Sekar, Raju; Fish, Katherine E.; Biggs, Catherine A.

    2014-01-01

    The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for chara...

  3. Microbial conversion technologies

    Energy Technology Data Exchange (ETDEWEB)

    Lau, P. [National Research Council of Canada, Ottawa, ON (Canada). Bioconversion and Sustainable Development

    2006-07-01

    Microbes are a biomass and an valuable resource. This presentation discussed microbial conversion technologies along with background information on microbial cells, their characteristics and microbial diversity. Untapped opportunities for microbial conversion were identified. Metagenomic and genome mining approaches were also discussed, as they can provide access to uncultivated or unculturable microorganisms in communal populations and are an unlimited resource for biocatalysts, novel genes and metabolites. Genome mining was seen as an economical approach. The presentation also emphasized that the development of microbial biorefineries would require significant insights into the relevant microorganisms and that biocatalysts were the ultimate in sustainability. In addition, the presentation discussed the natural fibres initiative for biochemicals and biomaterials. Anticipated outputs were identified and work in progress of a new enzyme-retting cocktail to provide diversity and/or consistency in fibre characteristics for various applications were also presented. It was concluded that it is necessary to leverage understanding of biological processes to produce bioproducts in a clean and sustainable manner. tabs., figs.

  4. The Effect of Therapeutic Clowning on Handwashing Technique and Microbial Colonization in Preschool Children.

    Science.gov (United States)

    Arıkan, Duygu; Gürarslan Baş, Nazan; Kurudirek, Fatma; Baştopcu, Ayşe; Uslu, Hakan

    2018-05-15

    This study aimed to determine the effect of therapeutic clowning on handwashing technique and microbial colonization in preschool children. This randomized controlled trial was conducted using pre-test and post-test experimental and control groups. The study was conducted between March and June 2016 in two kindergartens in eastern Turkey. The study was completed with a total of 195 students, including 90 students in the experimental group and 105 students in the control group. A questionnaire was used for data collection. This questionnaire included sections about the subjects' descriptive characteristics and the results of the bacterial cultures of their hand swabs. For the collection of these swabs, the subjects were informed in advance, and samples were collected at predetermined times. The swabs were analyzed to determine the bacterial colonization of the subjects' hands. Clowns and video activities were used as intervention tools in the study. In the post-test, the microbial growth was ≤10 3 in 68.9% and >10 3 in 31.1% of the subjects in the experimental group. In contrast, the growth was ≤10 3 in 34.3% and >10 3 in 65.7% of the control group subjects. The difference in the post-test microbial growths of the two groups was statistically significant (p < .000). The hygienic handwashing technique taught in the therapeutic clowning and videos reduced the bacterial colonization on the preschool children's hands by 50%. Moreover, this method was effective in reducing the growth rate of coliform bacteria that indicate undesirable, poor hygiene of the hands. Considering these results, we recommend that pediatric healthcare professionals use entertaining methods such as those involving clowns to teach and guide children regarding hygienic handwashing techniques. © 2018 Sigma Theta Tau International.

  5. Microbial Life of North Pacific Oceanic Crust

    Science.gov (United States)

    Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

    2003-12-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep

  6. From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

    Science.gov (United States)

    Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

  7. Evaluation of microbial biofilm communities from an Alberta oil sands tailings pond.

    Science.gov (United States)

    Golby, Susanne; Ceri, Howard; Gieg, Lisa M; Chatterjee, Indranil; Marques, Lyriam L R; Turner, Raymond J

    2012-01-01

    Bitumen extraction from the oil sands of Alberta has resulted in millions of cubic meters of waste stored on-site in tailings ponds. Unique microbial ecology is expected in these ponds, which may be key to their bioremediation potential. We considered that direct culturing of microbes from a tailings sample as biofilms could lead to the recovery of microbial communities that provide good representation of the ecology of the tailings. Culturing of mixed species biofilms in vitro using the Calgary Biofilm Device (CBD) under aerobic, microaerobic, and anaerobic growth conditions was successful both with and without the addition of various growth nutrients. Denaturant gradient gel electrophoresis and 16S rRNA gene pyrotag sequencing revealed that unique mixed biofilm communities were recovered under each incubation condition, with the dominant species belonging to Pseudomonas, Thauera, Hydrogenophaga, Rhodoferax, and Acidovorax. This work used an approach that allowed organisms to grow as a biofilm directly from a sample collected of their environment, and the biofilms cultivated in vitro were representative of the endogenous environmental community. For the first time, representative environmental mixed species biofilms have been isolated and grown under laboratory conditions from an oil sands tailings pond environment and a description of their composition is provided.

  8. Microbial Forensics: A Scientific Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Keim, Paul

    2003-02-17

    Microorganisms have been used as weapons in criminal acts, most recently highlighted by the terrorist attack using anthrax in the fall of 2001. Although such ''biocrimes'' are few compared with other crimes, these acts raise questions about the ability to provide forensic evidence for criminal prosecution that can be used to identify the source of the microorganisms used as a weapon and, more importantly, the perpetrator of the crime. Microbiologists traditionally investigate the sources of microorganisms in epidemiological investigations, but rarely have been asked to assist in criminal investigations. A colloquium was convened by the American Academy of Microbiology in Burlington, Vermont, on June 7-9, 2002, in which 25 interdisciplinary, expert scientists representing evolutionary microbiology, ecology, genomics, genetics, bioinformatics, forensics, chemistry, and clinical microbiology, deliberated on issues in microbial forensics. The colloquium's purpose was to consider issues relating to microbial forensics, which included a detailed identification of a microorganism used in a bioattack and analysis of such a microorganism and related materials to identify its forensically meaningful source--the perpetrators of the bioattack. The colloquium examined the application of microbial forensics to assist in resolving biocrimes with a focus on what research and education are needed to facilitate the use of microbial forensics in criminal investigations and the subsequent prosecution of biocrimes, including acts of bioterrorism. First responders must consider forensic issues, such as proper collection of samples to allow for optimal laboratory testing, along with maintaining a chain of custody that will support eventual prosecution. Because a biocrime may not be immediately apparent, a linkage must be made between routine diagnosis, epidemiological investigation, and criminal investigation. There is a need for establishing standard operating

  9. Soil Microbial Activity in Conventional and Organic Agricultural Systems

    Directory of Open Access Journals (Sweden)

    Romero F.V. Carneiro

    2009-06-01

    Full Text Available The aim of this study was to evaluate microbial activity in soils under conventional and organic agricultural system management regimes. Soil samples were collected from plots under conventional management (CNV, organic management (ORG and native vegetation (AVN. Soil microbial activity and biomass was significantly greater in ORG compared with CNV. Soil bulk density decreased three years after adoption of organic system. Soil organic carbon (SOC was higher in the ORG than in the CNV. The soil under organic agricultural system presents higher microbial activity and biomass and lower bulk density than the conventional agricultural system.

  10. Does iron inhibit cryptoendolithic microbial communities?

    Science.gov (United States)

    Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

    1988-01-01

    Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

  11. Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.

    Science.gov (United States)

    Kuehn, Joanna S; Gorden, Patrick J; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J; Wang, Chong; Phillips, Gregory J

    2013-01-01

    Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1-V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.

  12. Distribution of the dominant microbial communities in marine sediments containing high concentrations of gas hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Briggs, B.; Colwell, F.; Carini, P.; Torres, M. [Oregon State Univ., Corvallis, OR (United States); Hangsterfer, A.; Kastner, M. [California Univ., San Diego, CA (United States). Scripps Inst. of Oceanography; Brodie, E. [Lawrence Berkeley National Laboratory, Berkeley, CA (United States). Center for Environmental Biotechnology; Daly, R. [California Univ., Berkeley, CA (United States); Holland, M. [GeoTek, Daventry, Northants (United Kingdom); Long, P.; Schaef, H. [Pacific Northwest National Laboratory, Richland, WA (United States). Environmental Technology; Delwiche, M. [Idaho National Laboratory, Idaho Falls, ID (United States). Biotechnology; Winters, W. [United States Geological Survey, Woods Hole, MA (United States). Woods Hole Science Center; Riedel, M. [McGill Univ., Montreal, PQ (Canada). Dept. of Earth and Planetary Sciences

    2008-07-01

    Methane produced by microorganisms represents a large portion of the methane that occurs in marine sediments where gas hydrates are present. The diverse communities that populate these formations have been documented by cultures or through molecular traces. Previous studies have explored the biogeography of hydrate-bearing systems by comparing clone libraries developed from sediments where hydrates are abundant with those developed from sediments that lack hydrates. There is a distinct microbial community present in sediments that have methane hydrates. This paper presented an investigation into finer-scale biogeography, in order to determine how factors such as the presence or absence of hydrates, grain size, and the depositional environment in marine sediments may control the number, type and distribution of microbial communities in sediments. The purpose of the study was to understand the controls on the distribution and activity of all microbes that contribute to the conversion of organic matter to methane. To this aim, DNA was extracted from deep marine sediments cored from continental slope locations including offshore India and the Cascadia Margin. The data from the study was used to refine computational models that require biological rate terms that are consistent with sediment conditions in order to accurately describe the dynamics of this large methane reservoir. The paper discussed the materials and methods used for the study, including the sample site, sample collection and microbiological analysis. Results were presented in terms of DNA extractions; microbial diversity; and biofilm analyses. It was concluded that the findings from the study complemented previously reported studies which indicated the presence of diverse microbial communities in sediments containing methane hydrates. 9 refs., 5 figs.

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

    KAUST Repository

    Wang, Xin; Feng, Yujie; Wang, Heming; Qu, Youpeng; Yu, Yanling; Ren, Nanqi; Li, Nan; Wang, Elle; Lee, He; Logan, Bruce E.

    2009-01-01

    of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to singlechamber, air-cathode MFCs acclimated for power production using glucose. The MFC

  14. Smoking Impact on the Microbial Load of Clarias gariepinus ...

    African Journals Online (AJOL)

    Effects of different smoking methods on microbial load on freshly collected freshwater mud fish, Clarias gariepinus samples from Oyo State Fisheries Department, Ibadan in South-Western Nigeria was carried out. Seventy-two C. gariepinus (505 ± 0.45g and 25.5 ± 1.30cm) were collected and sorted into 4 groups. 10 fish ...

  15. An Inquiry-Based Laboratory Design for Microbial Ecology

    Science.gov (United States)

    Tessier, Jack T.; Penniman, Clayton A.

    2006-01-01

    There is a collective need to increase the use of inquiry-based instruction at the college level. This paper provides of an example of how inquiry was successfully used in the laboratory component of an undergraduate course in microbial ecology. Students were offered a collection of field and laboratory methods to choose from, and they developed a…

  16. Culture and Creativity

    DEFF Research Database (Denmark)

    Michelsen, Anders Ib

    INTRODUCTION The present publication deals with issues of imagination and creativity as a notion, philosophy – and social and cultural form, with point of departure in current debates on visual culture. Whereas these debates cover a large ground, spanning from media studies over design to cultural...... studies, they seldom reflect on the basic fact that visual culture in its present form indicates a huge collective creativity in some capacity, implicating the entire postwar era. From early focuses on the possible social and cultural roles of the image in the 1950s and 60s - e.g. in work of Roland...... and cognitive science. Thus visual culture points to an interesting inroad to - and a possible novel focus on - the image - pictorial representation - as an issue of cultural creativity. For one thing the current interest in visual culture goes along with a surge in concrete interest in culture and creativity...

  17. Examination of gutta-percha cones for microbial contamination during chemical use

    Directory of Open Access Journals (Sweden)

    Guven Kayaoglu

    2009-06-01

    Full Text Available OBJECTIVE: The aim of this study was to evaluate the degree of microbial contamination in packaged gutta-percha cones before and during use in clinical conditions. MATERIAL AND METHODS: Sealed packages of #15-40 gutta-percha cones were opened under aseptic laboratory conditions. Two gutta-percha cones from each size were randomly drawn and added to tubes containing glass beads and 750 µL of saline. The tubes were vortexed, serially diluted and samples of 250 µL were cultured on agar plates. The plates were incubated at 37ºC for 3 days and colonies were counted. The initially sampled packages were distributed to 12 final year dental students. The packages were collected at the end of the first and the third clinical practice days and sampled as described above. RESULTS: Baseline microbial counts did not exceed 3 CFU. At the end of the first and the third day, additional contamination was found in five and three of the packages, respectively. The ratio of contaminated packages at the first day and the third day was not significantly different (z-test; p > 0.05. The numbers of microorganisms cultured at the first day (8 ± 9.9 CFU and the third day (4.5 ± 8.3 CFU were not significantly different (Wilcoxon signed-rank test; p > 0.05. No significant correlation was found between the number of filled root canals and cultured microorganisms at either the first day (Spearman's rho; r = 0.481, p = 0.113 or the third day (r = -0.034, p = 0.917. CONCLUSIONS: Gutta-percha cones taken directly from manufacturer's sealed package harbored microorganisms. Clinical use of the packages has been found to be associated with additional contamination of the gutta-percha cones. The counts of cultured microorganisms did not correlate well with the number of filled root canals.

  18. Molecular ecology of microbial mats

    NARCIS (Netherlands)

    Bolhuis, H.; Cretoiu, M.S.; Stal, L.J.

    2014-01-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep

  19. Starting up microbial enhanced oil recovery.

    Science.gov (United States)

    Siegert, Michael; Sitte, Jana; Galushko, Alexander; Krüger, Martin

    2014-01-01

    This chapter gives the reader a practical introduction into microbial enhanced oil recovery (MEOR) including the microbial production of natural gas from oil. Decision makers who consider the use of one of these technologies are provided with the required scientific background as well as with practical advice for upgrading an existing laboratory in order to conduct microbiological experiments. We believe that the conversion of residual oil into natural gas (methane) and the in situ production of biosurfactants are the most promising approaches for MEOR and therefore focus on these topics. Moreover, we give an introduction to the microbiology of oilfields and demonstrate that in situ microorganisms as well as injected cultures can help displace unrecoverable oil in place (OIP). After an initial research phase, the enhanced oil recovery (EOR) manager must decide whether MEOR would be economical. MEOR generally improves oil production but the increment may not justify the investment. Therefore, we provide a brief economical assessment at the end of this chapter. We describe the necessary state-of-the-art scientific equipment to guide EOR managers towards an appropriate MEOR strategy. Because it is inevitable to characterize the microbial community of an oilfield that should be treated using MEOR techniques, we describe three complementary start-up approaches. These are: (i) culturing methods, (ii) the characterization of microbial communities and possible bio-geochemical pathways by using molecular biology methods, and (iii) interfacial tension measurements. In conclusion, we hope that this chapter will facilitate a decision on whether to launch MEOR activities. We also provide an update on relevant literature for experienced MEOR researchers and oilfield operators. Microbiologists will learn about basic principles of interface physics needed to study the impact of microorganisms living on oil droplets. Last but not least, students and technicians trying to understand

  20. Microbial populations in contaminant plumes

    Science.gov (United States)

    Haack, Sheridan K.; Bekins, Barbara A.

    Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation. La biodégradation efficace des polluants souterrains requiert deux éléments: des populations microbiennes possédant les aptitudes nécessaires à la dégradation, et des conditions géochimiques et hydrologiques souterraines favorables. Des contraintes pratiques sur la conception et l'interprétation des expériences à la fois en microbiologie et en hydrogéologie ont conduit à une connaissance limitée des interactions entre les

  1. Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

    Science.gov (United States)

    Crespo-Medina, Melitza; Twing, Katrina I; Kubo, Michael D Y; Hoehler, Tori M; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O

    2014-01-01

    Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

  2. Anaerobic microbial dehalogenation

    NARCIS (Netherlands)

    Smidt, H.; Vos, de W.M.

    2004-01-01

    The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the

  3. Diazotrophic microbial mats

    NARCIS (Netherlands)

    Severin, I.; Stal, L.J.; Seckbach, J.; Oren, A.

    2010-01-01

    Microbial mats have been the focus of scientific research for a few decades. These small-scale ecosystems are examples of versatile benthic communities of microorganisms, usually dominated by phototrophic bacteria (e.g., Krumbein et al., 1977; Jørgensen et al., 1983). They develop as vertically

  4. Microbial Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2006-10-01

    The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

  5. Microbial electrosynthesis of biochemicals

    NARCIS (Netherlands)

    Bajracharya, S.

    2016-01-01

    Microbial electrosynthesis (MES) is an electricity-driven production of chemicals from low-value waste using microorganisms as biocatalysts. MES from CO2 comprises conversion of CO2 to multi-carbon compounds employing microbes at the cathode which use electricity as an energy source. This thesis

  6. Limitations of ATP as a measure of microbial biomass

    African Journals Online (AJOL)

    limits the use of ATP as a measure of microbial biomass. S. AIr. J. Zool. 1982, 17: 93 - 95. Beraming van die totale .... only micro-organisms present in the experimental culture, but these were later succeeded by a large ... a value of 49: I by the last day of the experiment. Estimates of the total living biomass of the heterotro-.

  7. Microbial and heavy metal contamination of pineapple products ...

    African Journals Online (AJOL)

    SAM

    3Department of Social Sciences, University of Rwanda, P.O. Box 117 Butare, ... pineapple processing Enterprises (SMEs) over a storage duration of 12 months. .... The results were measured against ... analyzed for microbial contamination using International Organization ... All culture media used were manufactured by.

  8. Characterizing microbial diversity and damage in mural paintings.

    Science.gov (United States)

    Rosado, Tânia; Mirão, José; Candeias, António; Caldeira, Ana Teresa

    2015-02-01

    Mural paintings are some of the oldest and most important cultural expressions of mankind and play an important role for the understanding of societies and civilizations. These cultural assets have high economic and cultural value and therefore their degradation has social and economic impact. The present work presents a novel microanalytical approach to understand the damages caused by microbial communities in mural paintings. This comprises the characterization and identification of microbial diversity and evaluation of damage promoted by their biological activity. Culture-dependent methods and DNA-based approaches like denaturing gradient gel electrophoresis (DGGE) and pyrosequencing are important tools in the isolation and identification of the microbial communities allowing characterization of the biota involved in the biodeterioration phenomena. Raman microspectrometry, infrared spectrometry, and variable pressure scanning electron microscopy coupled with energy-dispersive X-ray spectrometry are also useful tools for evaluation of the presence of microbial contamination and detection of the alteration products resulting from metabolic activity of the microorganisms. This study shows that the degradation status of mural paintings can be correlated to the presence of metabolically active microorganisms.

  9. Current Microbial Pattern of Patients Presenting with Pre-Labour ...

    African Journals Online (AJOL)

    Current Microbial Pattern of Patients Presenting with Pre-Labour Rupture of Membranes (PROM) at Kenyatta National Hospital, Nairobi, Kenya. ... Subject: Fifty antenatal patients with premature Rapture of Membranes and 50 controls. Results: A total of 100 questionnaires and laboratory liquor microscopic culture and ...

  10. Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

    Directory of Open Access Journals (Sweden)

    Hui Wei

    2017-12-01

    Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

  11. Microbial metabolomics in open microscale platforms

    Science.gov (United States)

    Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

    2016-01-01

    The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393

  12. The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China.

    Science.gov (United States)

    Duan, Yulong; Wu, Fasi; Wang, Wanfu; He, Dongpeng; Gu, Ji-Dong; Feng, Huyuan; Chen, Tuo; Liu, Guangxiu; An, Lizhe

    2017-01-01

    In this study, a culture-independent Illumina MiSeq sequencing strategy was applied to investigate the microbial communities colonizing the ancient painted sculptures of the Maijishan Grottoes, a famous World Cultural Heritage site listed by UNESCO in China. Four mixed samples were collected from Cave 4-4 of the Maijishan Grottoes, the so-called Upper Seven Buddha Pavilion, which was built during the Northern Zhou Dynasty (557-581AD). The 16/18S rRNA gene-based sequences revealed a rich bacterial diversity and a relatively low fungal abundance, including the bacterial groups Actinobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes, Proteobacteria and Verrucomicrobia and the fungal groups Ascomycota, Basidiomycota and Chytridiomycota. Among them, the bacteria genera of Pseudonocardia and Rubrobacter and unclassified fungi in the order of Capnodiales were dominant. The relative abundance of Pseudonocardia in the painted layer samples was higher than that in the dust sample, while Cyanobacteria dominated in the dust sample. Many of them have been discovered at other cultural heritage sites and associated with the biodeterioration of cultural relics. The presence and activity of these pioneering microorganisms may lead to an unexpected deterioration of the painted sculptures that are preserved in this heritage site. Thus, proper management strategies and potential risk monitoring should be used in the Maijishan Grottoes to improve the conservation of these precious painted sculptures.

  13. Comparing the effect of echinacea and chlorhexidine mouthwash on the microbial flora of intubated patients admitted to the intensive care unit

    Directory of Open Access Journals (Sweden)

    Mehdi Safarabadi

    2017-01-01

    Full Text Available Background: Providing intubated patients admitted to the intensive care units with oral healthcare is one of the main tasks of nurses in order to prevent Ventilator-Associated Pneumonia (VAP. This study aimed at comparing the effects of two mouthwash solutions (echinacea and chlorhexidine on the oral microbial flora of patients hospitalized in the intensive care units. Materials and Methods: In this clinical trial, 70 patients aged between18 and 65 years undergoing tracheal intubation through the mouth in three hospitals in Arak, were selected using simple random sampling and were randomly divided into two groups: the intervention group and the control group. The oral health checklist was used to collect the data (before and after the intervention. The samples were obtained from the orally intubated patients and were then cultured in selective media. Afterwards, the aerobic microbial growth was investigated in all culture media. The data were analyzed using SPSS software. Results: The microbial flora in the echinacea group significantly decreased after the intervention (p < 0.0001 and it was also the case withmicrobial flora of the patients in the chlorhexidine group (p < 0.001. After 4 days, the oral microbial flora of the patients in the intervention group was lower than that of the patients in the control group (p < 0.001. Conclusions: The results showed that the echinacea solution was more effective in decreasing the oral microbial flora of patients in the intensive care unit. Given the benefits of the components of the herb Echinacea, it can be suggested as a viable alternative to chlorhexidine.

  14. Dynamic assessment of microbial ecology (DAME): A shiny app for analysis and visualization of microbial sequencing data

    Science.gov (United States)

    A new renaissance in knowledge about the role of commensal microbiota in health and disease is well underway facilitated by culture-independent sequencing technologies; however, microbial sequencing data poses new challenges (e.g., taxonomic hierarchy, overdispersion) not generally seen in more trad...

  15. Accuracy of the cytopathology, bacterioscopy, and vaginal flora culture.

    Science.gov (United States)

    Almeida, P Q; Pereira, M A P; Palomo, F S; Okazaki, C; Schimidt, M A; Speck, N M G; Ribalta, J C L

    2013-01-01

    An over-population of vaginal microorganisms causing inflammatory processes renders it difficult to properly assess the cytopathological exam that aims to screen precedent cervical lesions. On the contrary, the occurrence of the microbial flora saprophyte does not influence correct cythodiagnosis. To assess the composition of vaginal tract aerobic microorganisms of asymptomatic women in menacme and post-menopause, and to analyze the accuracy of cytopathologic, bacterioscopic exams, and culturing of the flora. The women were first submitted to a focused anamnestic interrogatory and then submitted to gynecological exam. A sample of the vaginal fluid was collected with a culture swab and a smear was made on two glass slides for stained bacterioscopic exam (GRAM). The collection of material was then compiled in a cytopathologic smear analysis. All women signed the free and informed consent letter and the project was approved by the Ethics Research Board of Hospital São Paulo - UNIFESP. Bacterioscopy and culture proved to be better than the cytopathologic exam in featuring the bacilli and cocci. The bacterioscopy provided a better detection of the presence of bacilli (p < 0.001); no statistical difference was seen between both exams with respect to the detected cocci. The beta-hemolytic Streptococcus group was of significance in post-menopausal women (p < 0.05). In this study, the bacterioscopic and culture exams of the vaginal fluid were more effective in assessing the vaginal flora and in the detection of bacilli, compared to the cytopathological exam.

  16. Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

    Directory of Open Access Journals (Sweden)

    Natalia Zeber-Lubecka

    Full Text Available Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities.To examine the effect of oral administration of Saccharomyces (S. boulardii and mode of delivery on the intestinal microbial community in preterm infants.Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18 or a placebo group (n = 21. Samples were collected before probiotic intake (day 0, and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform.A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants.While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

  17. Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants.

    Science.gov (United States)

    Zeber-Lubecka, Natalia; Kulecka, Maria; Ambrozkiewicz, Filip; Paziewska, Agnieszka; Lechowicz, Milosz; Konopka, Ewa; Majewska, Urszula; Borszewska-Kornacka, Maria; Mikula, Michal; Cukrowska, Bozena; Ostrowski, Jerzy

    2016-01-01

    Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.

  18. Charcoal Increases Microbial Activity in Eastern Sierra Nevada Forest Soils

    Directory of Open Access Journals (Sweden)

    Zachary W. Carter

    2018-02-01

    Full Text Available Fire is an important component of forests in the western United States. Not only are forests subjected to wildfires, but fire is also an important management tool to reduce fuels loads. Charcoal, a product of fire, can have major impacts on carbon (C and nitrogen (N cycling in forest soils, but it is unclear how these effects vary by dominant vegetation. In this study, soils collected from Jeffrey pine (JP or lodgepole pine (LP dominated areas and amended with charcoal derived from JP or LP were incubated to assess the importance of charcoal on microbial respiration and potential nitrification. In addition, polyphenol sorption was measured in unamended and charcoal-amended soils. In general, microbial respiration was highest at the 1% and 2.5% charcoal additions, but charcoal amendment had limited effects on potential nitrification rates throughout the incubation. Microbial respiration rates decreased but potential nitrification rates increased over time across most treatments. Increased microbial respiration may have been caused by priming of native organic matter rather than the decomposition of charcoal itself. Charcoal had a larger stimulatory effect on microbial respiration in LP soils than JP soils. Charcoal type had little effect on microbial processes, but polyphenol sorption was higher on LP-derived than JP-derived charcoal at higher amendment levels despite surface area being similar for both charcoal types. The results from our study suggest that the presence of charcoal can increase microbial activity in soils, but the exact mechanisms are still unclear.

  19. A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

    Science.gov (United States)

    Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

    2016-07-05

    Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

  20. Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

    Science.gov (United States)

    Wang, Yuanqi; Hatt, Janet K; Tsementzi, Despina; Rodriguez-R, Luis M; Ruiz-Pérez, Carlos A; Weigand, Michael R; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C; Konstantinidis, Konstantinos T

    2017-04-15

    A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (biosphere." How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species. IMPORTANCE A single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The