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Sample records for environmental molecular microbiology

  1. Environmental microbiology

    SciTech Connect

    Mitchell, R.

    1992-01-01

    This book covers issues ranging from global climate changes to biocontrol of plant diseases. Many of its contributions stress how new technologies in areas such as molecular biology and environmental engineering expand understanding and applications of basic concepts in environmental microbiology. Articles in the book are in three basic subject areas: effects of environmental contamination on the role of microbes in geochemical cycling of the major elements, pathogens in the environment, and microbial activities in environmental management.

  2. [Environmental microbiological control].

    PubMed

    Martín Salas, Carmen; Tordoya Titichoca, Igberto J; Ezpeleta Baquedano, Carmen

    2016-07-01

    The environmental microbiological control is necessary to prevent infections associated with certain procedures that are performed at the hospital. In this review the procedures for control of water and dialysis fluids, and air in operating rooms and immunocompromised units are addressed. The dialysis quality management guidelines define the highest levels of chemical, microbiological and endotoxin in purified water and dialysis fluids based on the recommendations of scientific societies. The microbiological control of water and dialysis fluids should include detection of microorganisms and endotoxin levels. Regarding the microbiological air sampling of operating rooms and immunocompromised units the types of clean rooms in which is recommended to perform microbiological air monitoring; the sample collection methods; culture media; incubation conditions; the most common microorganisms, and permissible levels depending on the type of surgery are described. PMID:27474243

  3. INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY

    EPA Science Inventory

    Environmental microbiology is the study of those microorganisms which exist in natural or artificial environments. The origin of scientific research in this field rests in the observations of Antony van Leewenhoeck that were published in 1677(4). Van Leewenhoeck used a microsco...

  4. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.

    PubMed

    Székely, Anna J; Breitbart, Mya

    2016-03-01

    Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics. PMID:26850442

  5. Microbiological Detection Systems for Molecular Analysis of Environmental Water and Soil Samples

    EPA Science Inventory

    Multiple detection systems are being targeted to track various species and genotypes of pathogens found in environmental samples with the overreaching goal of developing analytical separation and detection techniques for Salmonella enterica Serovars Typhi, Cryptosporidium parvum,...

  6. Manual of Environmental Microbiology - Literature Review.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The field of environmental microbiology has made tremendous strides since the original microscopic observations of Antony van Leeuwenhock in 1677. The Manual of Environmental Microbiology, 3rd edition embraces these technological advances and is perhaps the most comprehensive and informative book s...

  7. Applied and Environmental Microbiology Gordon Research Conference

    SciTech Connect

    Wall, Judy D.

    2003-11-19

    The main objective of the Gordon Research Conference on Applied and Environmental Microbiology was to present and discuss new, fundamental research findings on microorganisms, their activities in the environment, their ecosystem-level effects, and their environmental or commercial applications. To accomplish this goal, knowledge of microbial diversity, interactions and population dynamics was required. The genomic basis of microbial processes, the cycling of naturally occurring and hazardous substances, and methodologies to assess the functional relationships of microorganisms in their habitats were essential for understanding the ecological consequences of microbial activities and the formulation of generalizing principles. In the last decade, molecular technology has revealed that microbial diversity is far more extensive than the limited view obtained from culturing procedures. Great advances in environmental microbiology have resulted from the development and application of molecular approaches to ecology and molecular evolution. A further surprise resulting from the application of these new tools is the blurring of the distinction between pathogenic traits versus those considered non-pathogenic. This year's conference addressed the issues of biodiversity, its development, and the impact of stress on gene selection and expression. In addition microbial metabolic versatility with toxins such as heavy metals, antibiotics, and organic pollutants were discussed. The nine session topics were (1) biodiversity and the bacterial species, (2) mechanisms of biodiversification, (3) biofilms in health and environment, (4) a genomic view of microbial response to stress, (5) microbial use of toxic metals, (6) microbial mineral formation and dissolution, (7) power and limitations of antimicrobials, (8) biodegradation of organic pollutants, and (9) astrobiology. The Conference had an international profile: the Conference Vice-Chair, Dr. Gerard Muyzer, was from The Nether lands

  8. Quality in the molecular microbiology laboratory.

    PubMed

    Wallace, Paul S; MacKay, William G

    2013-01-01

    In the clinical microbiology laboratory advances in nucleic acid detection, quantification, and sequence analysis have led to considerable improvements in the diagnosis, management, and monitoring of infectious diseases. Molecular diagnostic methods are routinely used to make clinical decisions based on when and how to treat a patient as well as monitor the effectiveness of a therapeutic regime and identify any potential drug resistant strains that may impact on the long term patient treatment program. Therefore, confidence in the reliability of the result provided by the laboratory service to the clinician is essential for patient treatment. Hence, suitable quality assurance and quality control measures are important to ensure that the laboratory methods and service meet the necessary regulatory requirements both at the national and international level. In essence, the modern clinical microbiology laboratory ensures the appropriateness of its services through a quality management system that monitors all aspects of the laboratory service pre- and post-analytical-from patient sample receipt to reporting of results, from checking and upholding staff competency within the laboratory to identifying areas for quality improvements within the service offered. For most European based clinical microbiology laboratories this means following the common International Standard Organization (ISO9001) framework and ISO15189 which sets out the quality management requirements for the medical laboratory (BS EN ISO 15189 (2003) Medical laboratories-particular requirements for quality and competence. British Standards Institute, Bristol, UK). In the United States clinical laboratories performing human diagnostic tests are regulated by the Centers for Medicare and Medicaid Services (CMS) following the requirements within the Clinical Laboratory Improvement Amendments document 1988 (CLIA-88). This chapter focuses on the key quality assurance and quality control requirements within the

  9. Sampling and Data Analysis for Environmental Microbiology

    SciTech Connect

    Murray, Christopher J.

    2001-06-01

    A brief review of the literature indicates the importance of statistical analysis in applied and environmental microbiology. Sampling designs are particularly important for successful studies, and it is highly recommended that researchers review their sampling design before heading to the laboratory or the field. Most statisticians have numerous stories of scientists who approached them after their study was complete only to have to tell them that the data they gathered could not be used to test the hypothesis they wanted to address. Once the data are gathered, a large and complex body of statistical techniques are available for analysis of the data. Those methods include both numerical and graphical techniques for exploratory characterization of the data. Hypothesis testing and analysis of variance (ANOVA) are techniques that can be used to compare the mean and variance of two or more groups of samples. Regression can be used to examine the relationships between sets of variables and is often used to examine the dependence of microbiological populations on microbiological parameters. Multivariate statistics provides several methods that can be used for interpretation of datasets with a large number of variables and to partition samples into similar groups, a task that is very common in taxonomy, but also has applications in other fields of microbiology. Geostatistics and other techniques have been used to examine the spatial distribution of microorganisms. The objectives of this chapter are to provide a brief survey of some of the statistical techniques that can be used for sample design and data analysis of microbiological data in environmental studies, and to provide some examples of their use from the literature.

  10. 2009 Applied and Environmental Microbiology GRC

    SciTech Connect

    Nicole Dubilier

    2009-07-12

    The topic of the 2009 Gordon Conference on Applied and Environmental Microbiology is: From Single Cells to the Environment. The Conference will present and discuss cutting-edge research on applied and environmental microbiology with a focus on understanding interactions between microorganisms and the environment at levels ranging from single cells to complex communities. The Conference will feature a wide range of topics such as single cell techniques (including genomics, imaging, and NanoSIMS), microbial diversity at scales ranging from clonal to global, environmental 'meta-omics', biodegradation and bioremediation, metal - microbe interactions, animal microbiomes and symbioses. The Conference will bring together investigators who are at the forefront of their field, and will provide opportunities for junior scientists and graduate students to present their work in poster format and exchange ideas with leaders in the field. Some poster presenters will be selected for short talks. The collegial atmosphere of this Conference, with extensive discussion sessions as well as opportunities for informal gatherings in the afternoons and evenings, provides an ideal setting for scientists from different disciplines to exchange ideas, brainstorm and discuss cross-disciplinary collaborations.

  11. 76 FR 63615 - Environmental Science Center Microbiology Laboratory; Notice of Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-13

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY Environmental Science Center Microbiology Laboratory; Notice of Public Meeting AGENCY... discussions which will be held at the EPA Environmental Science Center Microbiology Laboratory. DATES:...

  12. ENVIRONMENTAL BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciTech Connect

    J.R. Paterek

    2002-03-01

    The overall program objective is to develop and evaluate environmental benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is one or more environmental benign, a.k.a. ''green'' products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter has been to evaluate a number of real world pipeline sources for microbial communities or consortia that form biofilms under laboratory simulations of pipelines. The microorganisms will be identified using classical and molecular microbiological tools and there activities under pipeline simulating conditions will be studied. The quarter saw the collection of the first samples from the industry for isolation of the microorganisms, as well as the design and construction of the laboratory-scale pipeline simulators. Methods development for MIC and biofilm microbial isolations and identification, and laboratory design and construction of pipeline simulators were the only activities. At this stage of the study (first quarter), only preliminary results are available.

  13. Application of phenotypic microarrays to environmental microbiology

    SciTech Connect

    Borglin, sharon; Joyner, Dominique; DeAngelis, Kristen; Khudyakov, Jane; D'haeseleer, Patrik; Joachimiak, Marcin; Hazen, Terry C; Fagan, Lisa Anne

    2012-01-01

    Environmental organisms are extremely diverse and only a small fraction has been successfully cultured in the laboratory. Culture in micro wells provides a method for rapid screening of a wide variety of growth conditions and commercially available plates contain a large number of substrates, nutrient sources, and inhibitors, which can provide an assessment of the phenotype of an organism. This review describes applications of phenotype arrays to anaerobic and thermophilic microorganisms, use of the plates in stress response studies, in development of culture media for newly discovered strains, and for assessment of phenotype of environmental communities. Also discussed are considerations and challenges in data interpretation and visualization, including data normalization, statistics, and curve fitting.

  14. Environmental microbiology as related to planetary quarantine

    NASA Technical Reports Server (NTRS)

    Pflug, I. J.

    1971-01-01

    The experiments carried out to determine the effects of temperature and relative humidity on the survival rate of Bacillus subtillis var. niger spores are reported. The experiments were conducted in environmental chambers at temperatures of 75 and 90 C. Data are also included on the survival characteristics of the spores suspended in sucrose solutions at 90 C with water activities of 0.99, 0.9, and 0.85

  15. Microbiology

    ERIC Educational Resources Information Center

    Spooner, D.

    1973-01-01

    Describes various types of training programs carried out in the study of microbiology. Indicates that the need for new energy sources and the expansion of medical schools and food industry may lead to an increasing demand for qualified microbiologists. (CC)

  16. Microbiology

    ERIC Educational Resources Information Center

    Anderson, Lucia

    1976-01-01

    Presents classroom activities for teaching microbiology at the elementary and secondary levels. Activities demonstrate the existence of the microbial world, types of microbes, and their growth needs and effects in nature. (MLH)

  17. Environmental microbiology as related to planetary quarantine

    NASA Technical Reports Server (NTRS)

    Pflug, I. J.

    1972-01-01

    The experimental design of a study to evaluate the effect of different cleaning methods and storage conditions on the dry heat resistance of Bacillus subtilis var. niger spores is described and the results for the first evaluation are reported. Specifically, the synergistic effect which occurs when spores are subjected simultaneously to dry heat and gamma radiation so as to be able to specify thermoradiation sterilization cycles was investigated. Attempts were made to understand the underlying mechanism(s) that lead to spore death from this combination of stresses. Data cover: (1) the survival of spores on surfaces at various temperatures in a precisely controlled environmental system, (2) the rate of destruction of these spores at ambient temperature when subjected to gamma radiation, and (3) the rate of destruction of spores when they are subjected to combined gamma radiation and thermal stresses.

  18. Dictionary of microbiology and molecular biology. 2nd ed

    SciTech Connect

    Singleton, P.; Sainsbury, D.

    1988-01-01

    A newly revised edition of the standard reference for microbiology and molecular biology. Includes a multitude of new terms and designations which, although widely used in the literature, are seldom defined outside the book or paper in which they first appeared. Also accounts for the changes in the meanings of older terms brought about by advances in knowledge. Definition of all terms reflects their actual usage in current journals and texts, and also given (where appropriate) are former meanings, alternative meanings, and synonyms. Includes terms from such fields as mycology, protozoology, virology, etc.

  19. Applications of MALDI-TOF MS in environmental microbiology.

    PubMed

    Santos, Inês C; Hildenbrand, Zacariah L; Schug, Kevin A

    2016-05-10

    Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is an emerging technique for microbial identification, characterization, and typing. The single colony method can be used for obtaining a protein fingerprint or profile unique to each microorganism. This technique has been mainly used in the clinical field, but it also has significant potential in the environmental field. The applications of MALDI-TOF MS in environmental microbiology are discussed in this review. An overview on the use of MALDI-TOF MS for environmental proteomics and metabolomics is given as well as its use for bacterial strain typing and bioremediation research. A more detailed review on the use of this technique for the identification, differentiation, and categorization of environmental microorganisms is given. Some of the parameters that can influence the results and reproducibility of MALDI-TOF MS are also discussed. PMID:27072574

  20. Advances and applications of molecular cloning in clinical microbiology.

    PubMed

    Sharma, Kamal; Mishra, Ajay Kumar; Mehraj, Vikram; Duraisamy, Ganesh Selvaraj

    2014-10-01

    Molecular cloning is based on isolation of a DNA sequence of interest to obtain multiple copies of it in vitro. Application of this technique has become an increasingly important tool in clinical microbiology due to its simplicity, cost effectiveness, rapidity, and reliability. This review entails the recent advances in molecular cloning and its application in the clinical microbiology in the context of polymicrobial infections, recombinant antigens, recombinant vaccines, diagnostic probes, antimicrobial peptides, and recombinant cytokines. Culture-based methods in polymicrobial infection have many limitation, which has been overcome by cloning techniques and provide gold standard technique. Recombinant antigens produced by cloning technique are now being used for screening of HIV, HCV, HBV, CMV, Treponema pallidum, and other clinical infectious agents. Recombinant vaccines for hepatitis B, cholera, influenza A, and other diseases also use recombinant antigens which have replaced the use of live vaccines and thus reduce the risk for adverse effects. Gene probes developed by gene cloning have many applications including in early diagnosis of hereditary diseases, forensic investigations, and routine diagnosis. Industrial application of this technology produces new antibiotics in the form of antimicrobial peptides and recombinant cytokines that can be used as therapeutic agents. PMID:25023463

  1. Prospects for microbiological solutions to environmental pollution with plastics.

    PubMed

    Krueger, Martin C; Harms, Hauke; Schlosser, Dietmar

    2015-11-01

    Synthetic polymers, commonly named plastics, are among the most widespread anthropogenic pollutants of marine, limnic and terrestrial ecosystems. Disruptive effects of plastics are known to threaten wildlife and exert effects on natural food webs, but signs for and knowledge on plastic biodegradation are limited. Microorganisms are the most promising candidates for an eventual bioremediation of environmental plastics. Laboratory studies have reported various effects of microorganisms on many types of polymers, usually by enzymatic hydrolysis or oxidation. However, most common plastics have proved to be highly recalcitrant even under conditions known to favour microbial degradation. Knowledge on environmental degradation is yet scarcer. With this review, we provide a comprehensive overview of the current knowledge on microbiological degradation of several of the most common plastic types. Furthermore, we illustrate the analytical challenges concerning the evaluation of plastic biodegradation as well as constraints likely standing against the evolution of effective biodegradation pathways. PMID:26318446

  2. Applied and Environmental Microbiology [agenda and attendee list

    SciTech Connect

    1999-07-03

    Conference sessions were held on the following topics: Microbes, metals and metabolism; Biological weapons, facts and fiction; Antimicrobials in food safety and human health; Microbial DNA chips; Global processes, microorganisms and molecular ecology; Microbes, art and artifacts; Functional genomics of environmental strains; and Biodegradation and biotransformation breakthroughs. There was also a special lecture titled ''The hand is quicker than a sneeze as a disseminator of disease.''

  3. ENVIRONMENTAL MONITORING FOR PUBLIC ACCESS AND COMMUNITY TRACKING (EMPACT) PROGRAM MICROBIOLOGICAL MONITORING OF RECREATIONAL WATER

    EPA Science Inventory

    Current Environmental Protection Agency (EPA) recommended microbiological monitoring practices for bathing beach water quality were suggested in 1968, as a part of the fecal coliform guideline developed by the Federal Water Pollution Control Administration. The guideline stated ...

  4. Planned Environmental Microbiology Aspects of Future Lunar and Mars Missions

    NASA Technical Reports Server (NTRS)

    Ott, C. Mark; Castro, Victoria A.; Pierson, Duane L.

    2006-01-01

    With the establishment of the Constellation Program, NASA has initiated efforts designed similar to the Apollo Program to return to the moon and subsequently travel to Mars. Early lunar sorties will take 4 crewmembers to the moon for 4 to 7 days. Later missions will increase in duration up to 6 months as a lunar habitat is constructed. These missions and vehicle designs are the forerunners of further missions destined for human exploration of Mars. Throughout the planning and design process, lessons learned from the International Space Station (ISS) and past programs will be implemented toward future exploration goals. The standards and requirements for these missions will vary depending on life support systems, mission duration, crew activities, and payloads. From a microbiological perspective, preventative measures will remain the primary techniques to mitigate microbial risk. Thus, most of the effort will focus on stringent preflight monitoring requirements and engineering controls designed into the vehicle, such as HEPA air filters. Due to volume constraints in the CEV, in-flight monitoring will be limited for short-duration missions to the measurement of biocide concentration for water potability. Once long-duration habitation begins on the lunar surface, a more extensive environmental monitoring plan will be initiated. However, limited in-flight volume constraints and the inability to return samples to Earth will increase the need for crew capabilities in determining the nature of contamination problems and method of remediation. In addition, limited shelf life of current monitoring hardware consumables and limited capabilities to dispose of biohazardous trash will drive flight hardware toward non-culture based methodologies, such as hardware that rapidly distinguishes biotic versus abiotic surface contamination. As missions progress to Mars, environmental systems will depend heavily on regeneration of air and water and biological waste remediation and

  5. Introduction of Molecular Methods into a Food Microbiology Curriculum

    ERIC Educational Resources Information Center

    Pleitner, Aaron M.; Hammons, Susan R.; McKenzie, Emily; Cho, Young-Hee; Oliver, Haley F.

    2014-01-01

    Maintaining current, relevant curriculum in undergraduate Food Microbiology courses is essential for training future experts in food quality and safety. Having an understanding of the fundamental techniques (for example, polymerase chain reaction [PCR]) that are used in the food industry and regulatory agencies is critical for students entering…

  6. Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

    PubMed Central

    Cazanave, Charles; Greenwood-Quaintance, Kerryl E.; Hanssen, Arlen D.; Karau, Melissa J.; Schmidt, Suzannah M.; Gomez Urena, Eric O.; Mandrekar, Jayawant N.; Osmon, Douglas R.; Lough, Lindsay E.; Pritt, Bobbi S.; Steckelberg, James M.

    2013-01-01

    We previously showed that culture of samples obtained by prosthesis vortexing and sonication was more sensitive than tissue culture for prosthetic joint infection (PJI) diagnosis. Despite improved sensitivity, culture-negative cases remained; furthermore, culture has a long turnaround time. We designed a genus-/group-specific rapid PCR assay panel targeting PJI bacteria and applied it to samples obtained by vortexing and sonicating explanted hip and knee prostheses, and we compared the results to those with sonicate fluid and periprosthetic tissue culture obtained at revision or resection arthroplasty. We studied 434 subjects with knee (n = 272) or hip (n = 162) prostheses; using a standardized definition, 144 had PJI. Sensitivities of tissue culture, of sonicate fluid culture, and of PCR were 70.1, 72.9, and 77.1%, respectively. Specificities were 97.9, 98.3, and 97.9%, respectively. Sonicate fluid PCR was more sensitive than tissue culture (P = 0.04). PCR of prosthesis sonication samples is more sensitive than tissue culture for the microbiologic diagnosis of prosthetic hip and knee infection and provides same-day PJI diagnosis with definition of microbiology. The high assay specificity suggests that typical PJI bacteria may not cause aseptic implant failure. PMID:23658273

  7. Microbiological diagnosis and molecular typing of Legionella strains during an outbreak of legionellosis in Southern Germany.

    PubMed

    Essig, Andreas; von Baum, Heike; Gonser, Theodor; Haerter, Georg; Lück, Christian

    2016-02-01

    An explosive outbreak of Legionnaires' disease with 64 reported cases occurred in Ulm/Neu-Ulm in the South of Germany in December 2009/January 2010 caused by Legionella (L.) pneumophila serogroup 1, monoclonal (mAb) subtype Knoxville, sequence type (ST) 62. Here we present the clinical microbiological results from 51 patients who were diagnosed at the University hospital of Ulm, the results of the environmental investigations and of molecular typing of patients and environmental strains. All 50 patients from whom urine specimens were available were positive for L. pneumophila antigen when an enzyme-linked immunosorbent assay (EIA) was used following concentration of those urine samples that tested initially negative. The sensitivity of the BinaxNow rapid immunographic assay (ICA), after 15 min reading and after 60 min reading were 70% and 84%, respectively. Direct typing confirmed the monoclonal subtype Knoxville in 5 out of 8 concentrated urine samples. Real time PCR testing of respiratory tract specimens for L. pneumophila was positive in 15 out of 25 (60%) patients. Direct nested sequence based typing (nSBT) in some of these samples allowed partial confirmation of ST62. L. pneumophila serogroup 1, monoclonal subtype Knoxville ST62, defined as the epidemic strain was isolated from 8 out of 31 outbreak patients (26%) and from one cooling tower confirming it as the most likely source of the outbreak. While rapid detection of Legionella antigenuria was crucial for the recognition and management of the outbreak, culture and molecular typing of the strains from patients and environmental specimens was the clue for the rapid identification of the source of infection. PMID:26868659

  8. Adoption of Lean Principles in a High-Volume Molecular Diagnostic Microbiology Laboratory

    PubMed Central

    Mitchell, P. Shawn; Mandrekar, Jayawant N.

    2014-01-01

    Clinical laboratories are constantly facing challenges to do more with less, enhance quality, improve test turnaround time, and reduce operational expenses. Experience with adopting and applying lean concepts and tools used extensively in the manufacturing industry is described for a high-volume clinical molecular microbiology laboratory, illustrating how operational success and benefits can be achieved. PMID:24829247

  9. Adoption of lean principles in a high-volume molecular diagnostic microbiology laboratory.

    PubMed

    Mitchell, P Shawn; Mandrekar, Jayawant N; Yao, Joseph D C

    2014-07-01

    Clinical laboratories are constantly facing challenges to do more with less, enhance quality, improve test turnaround time, and reduce operational expenses. Experience with adopting and applying lean concepts and tools used extensively in the manufacturing industry is described for a high-volume clinical molecular microbiology laboratory, illustrating how operational success and benefits can be achieved. PMID:24829247

  10. Project environmental microbiology as related to planetary quarantine

    NASA Technical Reports Server (NTRS)

    Pflug, I. J.

    1974-01-01

    Microbiological analyses of soil particles allow for the following conclusions: (1) there is a considerable range in the values of aerobic, mesophilic microbial counts associated with different size soil fractions; (2) as soil particle size increases, there is an increase in the mean microbial concentration per particle; (3) plate counts of aerobic, mesophilic organisms in unheated soils yielded a mean concentration of about six organisms per particle for the smallest soil fraction; (4) aerobic, mesophilic counts for sonicated particles heated at 80 C for 20 minutes yielded mean values of about two organisms per particle for the smallest particles; (5) some actinomycetes associated with the soil fractions could survive dry heat treatment at 110 C for one hour; and (6) soil particles stored under ambient laboratory conditions for 2.5 years aerobic, mesophilic plate counts which were comparable or slightly greater than the counts for more recently collected soil.

  11. ENVIRONMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciTech Connect

    John J. Kilbane II; William Bogan

    2004-01-31

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter included the fractionation of extracts prepared from several varieties of pepper plants, and using several solvents, by high performance liquid chromatography (HPLC). A preliminary determination of antimicrobial activities of the new extracts and fractions using a growth inhibition assay, and evaluation of the extracts ability to inhibit biofilm formation was also performed. The analysis of multiple extracts of pepper plants and fractions of extracts of pepper plants obtained by HPLC illustrated that these extracts and fractions are extremely complex mixtures of chemicals. Gas chromatography-mass spectrometry was used to identify the chemical constituents of these extracts and fractions to the greatest degree possible. Analysis of the chemical composition of various extracts of pepper plants has illustrated the complexity of the chemical mixtures present, and while additional work will be performed to further characterize the extracts to identify bioactive compounds the focus of efforts should now shift to an evaluation of the ability of extracts to inhibit corrosion in mixed culture biofilms, and in pure cultures of bacterial types which are known or believed to be important in corrosion.

  12. ENVIRONMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciTech Connect

    J. Robert Paterek; Gemma Husmillo

    2002-07-01

    The overall program objective is to develop and evaluate environmental benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is one or more environmental benign, a.k.a. ''green'' products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Capsicum sp. extracts and pure compounds were screened for their antimicrobial activity against MIC causing bacteria. Studies on the ability of these compounds to dissociate biofilm from the substratum were conducted using microtiter plate assays. Tests using laboratory scale pipeline simulators continued. Preliminary results showed that the natural extracts possess strong antimicrobial activity being comparable to or even better than the pure compounds tested against strains of sulfate reducers. Their minimum inhibitory concentrations had been determined. It was also found that they possess bactericidal properties at minimal concentrations. Biofilm dissociation activity as assessed by microtiter plate assays demonstrated varying degrees of differences between the treated and untreated group with the superior performance of the extracts over pure compounds. Such is an indication of the possible benefits that could be obtained from these natural products. Confirmatory experiments are underway.

  13. ENVIRONMENTAL BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciTech Connect

    J.R. Paterek; G. Husmillo

    2002-11-01

    The overall program objective is to develop and evaluate environmental benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is one or more environmental benign, a.k.a. ''green'' products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter were monitoring the development of Desulfovibrio species biofilm using the continuous flow cell system, evaluation of pepper compounds by microtiter plate assay for mitigating and inhibiting biofilm formation, and testing the effective concentrations to verify the extent of corrosion on metal coupons. Biofilm formation of Desulfovibrio vulgaris and D. desulfuricans was monitored and documented over a 7-day period. The use of a continuous flow cell system proved to be efficient and non-destructive in studying biofilm growth. Live/Dead BacLight was an efficient stain to determine cell viability. The extracts showed 9-25% biofilm formation inhibition against the two organisms, and 18-19% activity in detaching the already formed biofilm. Preliminary data were obtained on the extent of corrosion of metal coupons when treated with pepper extracts as against the untreated ones. Confirmatory tests are underway. A presentation was prepared and give at the US DOE NETL meeting on gas and petroleum infrastructure. The presentation is include as an addition to this report.

  14. ENVIRONMENTAL BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciTech Connect

    J.R. Paterek; G. Husmillo; V. Trbovic

    2003-01-01

    The overall program objective is to develop and evaluate environmental benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is one or more environmental benign, a.k.a. ''green'' products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter were isolation and cultivation of MIC-causing microorganisms from corroded pipeline samples, optimizing parameters in the laboratory-scale corrosion test loop system and testing the effective concentrations of Capsicum sp. extracts to verify the extent of corrosion on metal coupons by batch culture method. A total of 22 strains from the group of heterotrophic, acid producing, denitrifying and sulfate reducing bacteria were isolated from the gas pipeline samples obtained from Northern Indiana Public Service Company in Trenton, Indiana. They were purified and will be sent out for identification. Bacterial strains of interest were used in antimicrobial screenings and test loop experiments. Parameters for the laboratory-scale test loop system such as gas and culture medium flow rate; temperature; inoculation period; and length of incubation were established. Batch culture corrosion study against Desulfovibrio vulgaris showed that one (S{sub 1}M) out of the four Capsicum sp. extracts tested was effective in controlling the corrosion rate in metal coupons by 33.33% when compared to the untreated group.

  15. Chemical and microbiological experimentation for development of environmental control and life support systems

    NASA Technical Reports Server (NTRS)

    Whitman, G. A.; Wilson, M. E.; Cole, H. E.; Traweek, M.

    1992-01-01

    Microbiological techniques are under study with a view to the identification of viable microorganisms in liquid cultures, improve the identification of stressed organisms, and determine the biocidal activity of iodine and other chemicals on isolates from recycled water. A quality-assurance program has been implemented to validate data employed in making decisions concerning engineering and human health and safety. Analytical laboratory refinements will strongly aid the development of environmental control and life-support systems.

  16. ENVIRONMENTALLY BENIGN MITIGATION OF MICROBIOLOGICALLY INFLUENCED CORROSION (MIC)

    SciTech Connect

    J. Robert Paterek; Gemma Husmillo; Amrutha Daram; Vesna Trbovic; Teri Storino

    2003-04-01

    The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. The technical approach for this quarter includes the application of new methods of Capsicum sp. (pepper) extraction by soxhlet method and analysis of a new set of extracts by thin layer chromatography (TLC) and high performance liquid chromatography (HPLC); isolation and cultivation of MIC-causing microorganisms from corroded pipeline samples; and evaluation of antimicrobial activities of the old set of pepper extracts in comparison with major components of known biocides and corrosion inhibitors. Twelve new extracts from three varieties of Capsicum sp. (Serrano, Habanero, and Chile de Arbol) were obtained by soxhlet extraction using 4 different solvents. Results of TLC done on these extracts showed the presence of capsaicin and some phenolic compounds, while that of HPLC detected capsaicin and dihydrocapsaicin peaks. More tests will be done to determine specific components. Additional isolates from the group of heterotrophic, acid-producing, denitrifying and sulfate-reducing bacteria were obtained from the pipeline samples submitted by gas companies. Isolates of interest will be used in subsequent antimicrobial testing and test-loop simulation system experiments. Results of antimicrobial screening of Capsicum sp. extracts and components of known commercial biocides showed comparable activities when tested against two strains of sulfate-reducing bacteria.

  17. Identification of Staphylococcus epidermidis in the clinical microbiology laboratory by molecular methods.

    PubMed

    Roberts, Amity L

    2014-01-01

    Biochemical assays for the phenotypic identification of coagulase-negative staphylococci in the clinical microbiology laboratory have been well described in previous publications (Becker and Von Eiff Manual of Clinical Microbiology, ASM Press, Washington, pp. 308-330, 2011; Kloos and Wolfshohl J Clin Microbiol 16:509-516, 1982). This discussion focuses on identification of Staphylococcus epidermidis through molecular and proteomic methods. Molecular assays have been shown to be more discriminatory between the coagulase-negative staphylococcal species than are phenotypic assays (Zadoks and Watts Vet Microbiol 134:20-28, 2009; Sheraba et al. BMC Res Notes 3:278, 2010; Patteet et al. Eur J Clin Microbiol Infect Dis 31:747-751, 2012). The molecular and proteomic methods that have shown the greatest utilization potential within the clinical laboratory are as follows: PCR amplification and sequencing of discriminatory genes, real-time polymerase chain reaction with species-specific probes in conjunction with a melt-curve analysis, fluorescence in situ hybridization, and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. PMID:24222453

  18. Molecular microbiological evaluation of subgingival biofilm sampling by paper point and curette.

    PubMed

    Belibasakis, Georgios N; Schmidlin, Patrick R; Sahrmann, Philipp

    2014-04-01

    The present clinical study aimed to investigate if there are differences in microbiological outcomes dependent on the subgingival biofilm collection method. Subgingival biofilm samples were collected from the four deepest pockets (>5 mm) of 17 patients with aggressive periodontitis (AgP) and 33 patients with chronic periodontitis (CP), first by paper point and thereafter by curette. Samples obtained with the same method were pooled together from each patient and forwarded for molecular microbiological analysis by a commercially available assay (IAI Pado Test 4.5) that estimates total bacterial load and levels of Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola and Aggregatibacter actinomycetemcomitans. Data analysis included frequency of detection, quantification and correlation of detection levels between the two sampling methods. P. gingivalis, T. forsythia and T. denticola were detected in >90% of the samples, and their detection levels exhibited a strong correlation between sampling methods. The detection consistency of A. actinomycetemcomitans was 56% between the two sampling methods. A. actinomycetemcomitans was more readily detected by paper point compared with curette collection with a stronger correlation between the two methods in AgP. Subgingival biofilm sampling by curette or paper point does not yield differences in the detection of the three 'red complex' species. However, A. actinomycetemcomitans was more consistently detected by means of paper point collection, which can be crucial in the decision to administer antibiotics as an adjunctive periodontal treatment. PMID:23879704

  19. Molecular epidemiology in environmental carcinogenesis.

    PubMed Central

    Perera, F P; Mooney, L A; Dickey, C P; Santella, R M; Bell, D; Blaner, W; Tang, D; Whyatt, R M

    1996-01-01

    Molecular epidemiology has significant potential in preventing cancer and other diseases caused by environmental exposures (related to lifestyle, occupation, or ambient pollution). This approach attempts to prevent cancer by incorporating laboratory methods to document the molecular dose and preclinical effects of carcinogens, as well as factors that increases individual susceptibility to carcinogens. Recently we have carried out validation studies of biologic markers such as carcinogen--DNA and carcinogen--protein adducts, gene and chromosomal mutations, alterations in target oncogenes or tumor suppressor genes, polymorphisms in putative susceptibility genes (individual P450s, glutathione transferase M1), and serum levels of micronutrients. This research involves adults, infants, and children exposed to varying levels of carcinogens, as well as cancer cases and controls. On a group level, dose-response relationships have frequently been seen between various biomarkers and environmental exposures such as polycyclic aromatic hydrocarbons, cigarette smoke (active and passive), and ambient indoor and workplace air pollution. However, there is significant interindividual variation in biomarkers that appears to reflect a modulating effect on biomarkers (hence potential risk) by genetic and acquired susceptibility factors. Ongoing retrospective and nested case-control studies of lung and breast cancer are examining the association between biomarkers and cancer risk. Results of these studies are encouraging; they suggest that biomarkers, once validated, can be useful in identifying populations and individuals at risk in time to intervene effectively. PMID:8781360

  20. 2001 Gordon Research Conference on Applied and Environmental Microbiology. Final progress report [agenda and attendee list

    SciTech Connect

    Drake, Harold

    2001-07-26

    The Gordon Research Conference on Applied and Environmental Microbiology was held at Connecticut College, New London, Connecticut, July 22-27, 2001. The conference was attended by 121 participants. The attendees represented the spectrum of endeavor in this field, coming from academia, industry, and government laboratories, and included US and foreign scientists, senior researchers, young investigators, and students. Emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate discussion about the key issues in the field today. Session topics included the following: Environmental and applied genomics, Cell-to-cell signaling and multicellular behavior, Emerging technologies and methods, Novel metabolisms and ecosystems, Directed evolution of enzymes and pathways, Symbiotic and trophic relationships, Synthesis and application of novel biopolymers, and Microbes at the oxic-anoxic interface. There was also a special lecture titled ''Under the umbrella of the big tree: microbial biology into the 21st century.''

  1. Aquatic Microbiology Laboratory Manual.

    ERIC Educational Resources Information Center

    Cooper, Robert C.; And Others

    This laboratory manual presents information and techniques dealing with aquatic microbiology as it relates to environmental health science, sanitary engineering, and environmental microbiology. The contents are divided into three categories: (1) ecological and physiological considerations; (2) public health aspects; and (3)microbiology of water…

  2. Estimation of the environmental risk posed by landfills using chemical, microbiological and ecotoxicological testing of leachates.

    PubMed

    Matejczyk, Marek; Płaza, Grażyna A; Nałęcz-Jawecki, Grzegorz; Ulfig, Krzysztof; Markowska-Szczupak, Agata

    2011-02-01

    The leachates from 22 municipal solid waste (MSW) landfill sites in Southern Poland were characterized by evaluation of chemical, microbiological and ecotoxicological parameters. Chemical analyses were mainly focused on the identification of the priority hazardous substances according to Directive on Priority Substances, 2008/105/EC (a daughter directive of the WFD) in leachates. As showed, only five substances (Cd, Hg, hexachlorobutadiene, pentachlorobenzene and PAHs) were detected in the leachates. The compounds tested were absent or present at very low concentrations. Among them, only PAHs were found in all samples in the range from 0.057 to 77.2 μg L⁻¹. The leachates were contaminated with bacteria, including aerobic, psychrophilic and mesophilic bacteria, coliform and fecal coliforms, and spore-forming-bacteria, including Clostridium perfringens, and with filamentous fungi. From the analysis of specific microorganism groups (indicators of environmental pollution by pathogenic or opportunistic pathogenic organisms) it can be concluded that the landfill leachates showed sanitary and epidemiological hazard. In the ecotoxicological study, a battery of tests comprised of 5 bioassays, i.e. Microtox(®), Spirotox, Rotoxkit F™, Thamnotoxkit F™ and Daphtoxkit F™ magna was applied. The leachate samples were classified as toxic in 13.6%, highly toxic in 54.6% and very highly toxic in 31.8%. The Spirotox test was the most sensitive bioassay used. The percentage of class weight score was very high - above 60%; these samples could definitely be considered seriously hazardous and acutely toxic to the fauna and microflora. No correlations were found between the toxicity values and chemical parameters. The toxicity of leachate samples cannot be explained by low levels of the priority pollutants. It seems that other kinds of xenobiotics present in the samples at subacute levels gave the high aggregate toxic effect. The chemical, ecotoxicological and microbiological

  3. Molecular methods for microbiological quality control of meat and meat products: a review.

    PubMed

    Gokulakrishnan, P; Vergis, Jess

    2015-01-01

    Achieving food safety is a global health goal and the food-borne diseases take a major check on global health. Therefore, detection of microbial pathogens in food is the solution to the prevention and recognition of problems related to health and safety. Conventional and standard bacterial detection methods such as culture and colony counting methods and immunology-based methods may take up to several hours or even a few days to yield a result. Obviously, this is inadequate, and recently many researchers are focusing towards the progress of rapid diagnostic methods. The advent of molecular techniques has led to the development of a diverse array of assay for quality control of meat and meat products. Rapid analysis using DNA hybridization and amplification techniques offer more sensitivity and specificity to get results than culture based methods as well as dramatic reduction in the time to get results. Many methods have also achieved the high level automation, facilitating their application as routine sample screening assays. This review is intended to provide an overview of the molecular methods for microbiological quality control of meat and meat products. PMID:24915322

  4. Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS.

    PubMed

    Bechy-Loizeau, Anne-Laure; Flandrois, Jean-Pierre; Abaibou, Hafid

    2015-07-01

    On the ISS, as on Earth, water is an essential element for life and its quality control on a regular basis allows to ensure the health of the crew and the integrity of equipment. Currently, microbial water analysis onboard ISS still relies on the traditional culture-based microbiology methods. Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods. For this reason, the Midass, a fully integrated and automated prototype was designed conjointly by ESA and bioMérieux for a rapid monitoring of the microbiological quality of air. The prototype allows air sampling, sample processing and the amplification/detection of nucleic acids. We describe herein the proof of principle of an analytical approach based on molecular biology that could fulfill the ESA's need for a rapid monitoring of the microbiological quality of recycled water onboard ISS. Both concentration and recovery of microorganisms are the main critical steps when the microfiltration technology is used for water analysis. Among filters recommended standards for monitoring the microbiological quality of the water, the polycarbonate filter was fully in line with the requirements of the ISO 7704-1985 standard in terms of efficacy of capture and recovery of bacteria. Moreover, this filter does not retain nucleic acids on the surface and has no inhibitory effect on their downstream processing steps such as purification and amplification/detection. Although the Midass system was designed for the treatment of air samples, the first results on the integration of PC filters were encouraging. Nevertheless, system modifications are needed to better adapt the Midass system for the monitoring of the microbiological water quality. PMID:26256625

  5. Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS

    NASA Astrophysics Data System (ADS)

    Bechy-Loizeau, Anne-Laure; Flandrois, Jean-Pierre; Abaibou, Hafid

    2015-07-01

    On the ISS, as on Earth, water is an essential element for life and its quality control on a regular basis allows to ensure the health of the crew and the integrity of equipment. Currently, microbial water analysis onboard ISS still relies on the traditional culture-based microbiology methods. Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods. For this reason, the Midass, a fully integrated and automated prototype was designed conjointly by ESA and bioMérieux for a rapid monitoring of the microbiological quality of air. The prototype allows air sampling, sample processing and the amplification/detection of nucleic acids. We describe herein the proof of principle of an analytical approach based on molecular biology that could fulfill the ESA's need for a rapid monitoring of the microbiological quality of recycled water onboard ISS. Both concentration and recovery of microorganisms are the main critical steps when the microfiltration technology is used for water analysis. Among filters recommended standards for monitoring the microbiological quality of the water, the polycarbonate filter was fully in line with the requirements of the ISO 7704-1985 standard in terms of efficacy of capture and recovery of bacteria. Moreover, this filter does not retain nucleic acids on the surface and has no inhibitory effect on their downstream processing steps such as purification and amplification/detection. Although the Midass system was designed for the treatment of air samples, the first results on the integration of PC filters were encouraging. Nevertheless, system modifications are needed to better adapt the Midass system for the monitoring of the microbiological water quality.

  6. Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology

    PubMed Central

    Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K. P.; Woo, Patrick C. Y.

    2015-01-01

    Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study. PMID:26506340

  7. Molecular analysis of point-of-use municipal drinking water microbiology.

    PubMed

    Holinger, Eric P; Ross, Kimberly A; Robertson, Charles E; Stevens, Mark J; Harris, J Kirk; Pace, Norman R

    2014-02-01

    Little is known about the nature of the microbiology in tap waters delivered to consumers via public drinking water distribution systems (DWDSs). In order to establish a broader understanding of the microbial complexity of public drinking waters we sampled tap water from seventeen different cities between the headwaters of the Arkansas River and the mouth of the Mississippi River and determined the bacterial compositions by pyrosequencing small subunit rRNA genes. Nearly 98% of sequences observed among all systems fell into only 5 phyla: Proteobacteria (35%), Cyanobacteria (29%, including chloroplasts), Actinobacteria (24%, of which 85% were Mycobacterium spp.), Firmicutes (6%), and Bacteroidetes (3.4%). The genus Mycobacterium was the most abundant taxon in the dataset, detected in 56 of 63 samples (16 of 17 cities). Among the more rare phylotypes, considerable variation was observed between systems, and was sometimes associated with the type of source water, the type of disinfectant, or the concentration of the environmental pollutant nitrate. Abundant taxa (excepting Cyanobacteria and chloroplasts) were generally similar from system to system, however, regardless of source water type or local land use. The observed similarity among the abundant taxa between systems may be a consequence of the selective influence of chlorine-based disinfection and the common local environments of DWDS and premise plumbing pipes. PMID:24333849

  8. Assessment of chloroethene biodegradation in the subsurface by microbiological, molecular and isotopic tools

    NASA Astrophysics Data System (ADS)

    Schmidt, K. R.; Kranzioch, I.; Heidinger, M.; Ertl, S.; Tiehm, A.

    2012-04-01

    A multiple lines of evidence approach to assess the biodegradation potential of contaminated sites includes - site investigation analysing pollutant distribution (compounds, concentrations, isotopic composition) and hydrochemical conditions (redox conditions) - determination of the presence of pollutant degrading bacteria in the field by microbiological (most probable number, MPN) and molecular (polymerase chain reaction, PCR) methods - analysis of degradation processes in the laboratory by microcosms with determination of site specific isotopic enrichment factors enabling the quantification of biodegradation processes in the field. Results will be shown of the application of such a multiple lines of evidence approach at a chloroethene-contaminated site in Frankenthal, Germany. In anaerobic groundwater microcosms, reductive transformation of perchloroethene (PCE) and trichloroethene (TCE) was observed to mainly proceed to cis-1,2-dichloroethene (cDCE). 16S-PCR analysis showed a wide distribution of halorespiring bacteria capable of PCE degradation to cDCE, whereas Dehalococcoides - the only organisms described so far being able of complete reductive dechlorination down to ethene - was only found in one groundwater sample. Aerobic microcosms showed metabolic degradation of the lower chlorinated compounds cDCE and vinyl chloride (VC). Co-metabolic degradation of cDCE with VC as auxiliary substrate occurred, too. Significant stable carbon isotope fractionation was observed during anaerobic degradation of PCE and TCE as well as during aerobic degradation of cDCE and VC. Compiling the results of the different assessment methods, sequential dechlorination - PCE/TCE to cDCE anaerobically and cDCE to CO2 aerobically - was demonstrated to occur at the Frankenthal site. The extent of biodegradation in the field was calculated based on the enrichment factors determined in microcosms and the 13C-isotopic composition of the contaminants on site. The application of molecular

  9. Comparison of the microbiological quality of environmentally friendly and conventionally grown vegetables sold at retail markets in Korea.

    PubMed

    Ryu, Jee-Hoon; Kim, Minju; Kim, Eun-Gyeong; Beuchat, Larry R; Kim, Hoikyung

    2014-09-01

    Fresh produce is usually eaten raw without cooking or heating, which may increase the probability of foodborne infection. The microbiological quality of 11 types of fresh, raw vegetables (romaine lettuce, sesame leaves, crown daisy, garlic chives, iceberg lettuce, cabbage, broccoli, leek, chili pepper, capsicum, and zucchini) purchased at retail markets in Iksan, Korea as affected by cultivation method (environmentally friendly vegetables [organic, pesticide-free, and low-pesticide vegetables] and conventionally grown vegetables) and harvest season was determined. Escherichia coli O157:H7 and Salmonella were not detected in all samples of vegetables tested. Aerobic mesophiles (>6 log cfu/g) were detected in environmentally friendly romaine lettuce and crown daisy and environmentally friendly and conventionally grown garlic chives, which also contained coliforms (>3 log cfu/g). Sesame leaf and crown daisy (regardless of cultivation method), as well as conventionally grown romaine lettuce and leek, contained >1 log cfu/g of E. coli. The overall microbiological quality of environmentally friendly and conventionally grown vegetables was not significantly different (P > 0.05). However, there were seasonal effects on populations of coliforms and generic E. coli on vegetables. The greatest numbers of microorganisms were isolated from environmentally friendly or conventionally grown vegetables purchased in winter. The vegetables, regardless of cultivation method or season, should be subjected to appropriate antimicrobial treatment to enhance their microbial safety. PMID:25124136

  10. Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

    PubMed Central

    Kell, Douglas; Potgieter, Marnie; Pretorius, Etheresia

    2015-01-01

    For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically ‘nonculturable’ on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as ‘persisters’. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one’s bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit. PMID:26629334

  11. Careers in Microbiology...Horizons Unlimited

    ERIC Educational Resources Information Center

    Goldschmidt Millicent C.; Whitt, Dixie

    1978-01-01

    A broad range of present microbiological work is discussed in order to indicate the many possible careers now open in microbiology. Some areas are immunology, environmental microbiology, agricultural, industrial, and food microbiology, and space microbiology. An employment outlook is also given. (MDR)

  12. Environmental Molecular Sciences Laboratory 2004 Annual Report

    SciTech Connect

    White, Julia C.

    2005-04-17

    This 2004 Annual Report describes the research and accomplishments of staff and users of the W.R. Wiley Environmental Molecular Sciences Laboratory (EMSL), located in Richland, Washington. EMSL is a multidisciplinary, national scientific user facility and research organization, operated by Pacific Northwest National Laboratory (PNNL) for the U.S. Department of Energy's Office of Biological and Environmental Research. The resources and opportunities within the facility are an outgrowth of the U.S. Department of Energy's (DOE) commitment to fundamental research for understanding and resolving environmental and other critical scientific issues.

  13. The Mediterranean non-indigenous ascidian Polyandrocarpa zorritensis: Microbiological accumulation capability and environmental implications.

    PubMed

    Stabili, Loredana; Licciano, Margherita; Longo, Caterina; Lezzi, Marco; Giangrande, Adriana

    2015-12-15

    We investigated the bacterial accumulation and digestion capability of Polyandrocarpa zorritensis, a non-indigenous colonial ascidian originally described in Peru and later found in the Mediterranean. Microbiological analyses were carried out on homogenates from "unstarved" and "starved" ascidians and seawater from the same sampling site (Adriatic Sea, Italy). Culturable heterotrophic bacteria (22 °C), total culturable bacteria (37 °C) and vibrios abundances were determined on Marine Agar 2216, Plate Count Agar and TCBS Agar, respectively. Microbial pollution indicators were measured by the most probable number method. All the examined microbiological groups were accumulated by ascidians but differently digested. An interesting outcome is the capability of P. zorritensis to digest allochthonous microorganisms such as coliforms as well as culturable bacteria at 37 °C, counteracting the effects of microbial pollution. Thus, the potential exploitation of these filter feeders to restore polluted seawater should be taken into consideration in the management of this alien species. PMID:26561443

  14. Taiwanese students' scientific attitudes, environmental perceptions, self-efficacy, and achievement in microbiology courses

    NASA Astrophysics Data System (ADS)

    Lee, Jing-Jin

    One of the important aims of science education is to teach science for every one and to create scientifically literate citizens. In order to become more cognizant of students in the science classroom to better prepare students for an increasingly complex modern society, the study assessed students' science attitudes, science laboratory environment perceptions, self-efficacy in microbiology, and achievement to determine the differences based on gender, knowledge background, enrollment status, and the duration of learning background. Also, the relationships among students' scientific attitudes, perceptions of science laboratory environment, self-efficacy, and achievement were explored. The population for this study included 442 students who took microbiology course at CHCMT in Taiwan. The instruments for data collecting include scientific attitudes inventory, laboratory environment inventory, and self-efficacy inventory for microbiology. A series of t tests and one-way ANOVA, correlation, multiply regression, and path analysis are conducted for data analysis. The results reveal that students' scientific attitude is the only significant factor that affects attitudes. Students' perceptions of the laboratory environment first influenced self-efficacy and attitudes, and then affected achievement. Gender influences students' perceptions of the laboratory environment and self-efficacy. Knowledge background can cause differences in students' scientific attitudes. The duration of students' learning in science can influence students' perceptions of the laboratory environment and achievement. Enrollment status makes a difference in students' scientific attitudes, laboratory environment perceptions, and achievement.

  15. Principles and applications of molecular biology techniques for the microbiological diagnosis of acute post-operative endophthalmitis.

    PubMed

    Cornut, Pierre-Loïc; Boisset, Sandrine; Romanet, Jean-Paul; Maurin, Max; Carricajo, Anne; Benito, Yvonne; Vandenesch, François; Chiquet, Christophe

    2014-01-01

    The systematic microbiological evaluation of endophthalmitis allows the confirmation of the infectious nature of the disease and the possible adaptation of treatment at the individual level and, at the collective level, the epidemiological characterization of the bacterial spectrum of endophthalmitis. Long reserved for research, the use of molecular biology techniques to complement conventional culture techniques has become important for the diagnosis of endophthalmitis in recent years. These new diagnostic techniques are particularly useful for the microbiological study of bacteria that are difficult or impossible to grow because of their intrinsic properties, their presence in only a small inoculum, their sequestration on prosthetic materials, or their inactivation by prior antibiotic treatment. These techniques are based on the polymerase chain reaction (PCR), which allows the amplification and detection of extracted bacterial deoxyribonucleic acid (DNA) that is initially present in minute quantities in an ocular sample. In practice, these conventional or real-time PCRs allow either the a priori detection of bacterial DNA (universal PCR) or the identification of a specific DNA fragment of a bacterial genus or species (specific PCR). New techniques of PCR will allow more rapid bacterial identification and also characterization of genotypic properties, such as genes of virulence or antibiotic resistance. PMID:24359808

  16. Non-linearities in hydrological connectivity and microbiological flux in nested catchments - implications of environmental change

    NASA Astrophysics Data System (ADS)

    Tetzlaff, D.; Soulsby, C.; Birkel, C.; Capell, R.; Speed, M.

    2009-12-01

    The non-linearities of catchment hydrological behaviour are strongly influenced by the connectivity of hillslopes and channel networks, particularly where overland flow is an important runoff mechanism. Such surface connectivity also controls the flux of microbiological pollutants (coliform bacteria) from areas of live stock grazing which can have serious health implications for potable water supplies. We report a nested catchment study where hydrological and tracer monitoring over a two year period has been coupled with regular sampling for faecal indicator organisms (FIOs). The study has been based in catchments with mixed landuse where FIOs are derived from livestock (sheep and cows) in agricultural land and wild animals (red deer) on moorlands. At all scales (3-1800km2), high levels of FIO were transient and episodic and strongly correlated with periods of high hydrological connectivity. We show how this non-linearity in connectivity can be captured within a dynamic hydrological model. The model was used, along with climate change predictions, to assess possible scenarios of change in connectivity and microbiological contamination in catchments with different land use.

  17. [Microbiological quality of indoor air at the School of Building and Environmental Engineering at Białystok University of Technology].

    PubMed

    Butarewicz, Andrzej

    2005-01-01

    The investigation of microbiological rate of indoor air pollution on Faculty of Building and Environmental Engineering at Białystok University of Technology were made by sedimentation method in accordance with Polish standards (PN-89/Z-04111/01,02,03). Six series of measurements were carried out from autumn 2002 to spring 2003. The results show bad microbiological quality of indoor air on Faculty of Building and Environmental Engineering at Białystok University of Technology. It was found that the number of Staphylococcus, Actinomycetales as well as the total count of bacteria were too high and broke the Polish regulations of the clear air. Because of the students' and other workers' safety, monitoring of microbiological pollution of the indoor air must be done and existing emergency to improve the quality of the air must be lead. PMID:16252812

  18. Molecular Biological Methods in Environmental Engineering.

    PubMed

    Zhang, Guocai; Wei, Li; Chang, Chein-Chi; Zhang, Yuhua; Wei, Dong

    2016-10-01

    Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification. 454 high throughput sequencing and Illumina MiSeq sequencing have been the primary and widely recognized methods to analyze the microbial. This review will provide environmental engineers and microbiologists an overview of important advancements in molecular techniques and highlight the application of these methods in diverse environments. PMID:27620079

  19. Wastewater reuse in irrigation: a microbiological perspective on implications in soil fertility and human and environmental health.

    PubMed

    Becerra-Castro, Cristina; Lopes, Ana Rita; Vaz-Moreira, Ivone; Silva, Elisabete F; Manaia, Célia M; Nunes, Olga C

    2015-02-01

    The reuse of treated wastewater, in particular for irrigation, is an increasingly common practice, encouraged by governments and official entities worldwide. Irrigation with wastewater may have implications at two different levels: alter the physicochemical and microbiological properties of the soil and/or introduce and contribute to the accumulation of chemical and biological contaminants in soil. The first may affect soil productivity and fertility; the second may pose serious risks to the human and environmental health. The sustainable wastewater reuse in agriculture should prevent both types of effects, requiring a holistic and integrated risk assessment. In this article we critically review possible effects of irrigation with treated wastewater, with special emphasis on soil microbiota. The maintenance of a rich and diversified autochthonous soil microbiota and the use of treated wastewater with minimal levels of potential soil contaminants are proposed as sine qua non conditions to achieve a sustainable wastewater reuse for irrigation. PMID:25461421

  20. Comparative study of airborne viable particles assessment methods in microbiological environmental monitoring.

    PubMed

    Temprano, G; Garrido, D; Daquino, M

    2004-01-01

    A comparative study was done among available assessment methods to measure airborne viable particles in controlled rooms. Active methods were compared (sieve/nozzle impactor, slit-to-agar, centrifugal, filtration, and impinger). The comparative study was carried out by means of a two-way (factors: day and method) analysis of variance, after to logarithmical transformation of experimental results in order to fulfill the normality test of the variables. Statistically significant differences were found among the results of the five methods (P < 0.0001). In a post hoc study, by means of Tukey's test, no differences were found among centrifugal, filtration, and impinger methods. Differences were found among all the other methods (P < 0.05). It is concluded that centrifugal, filtration, and impinger methods (in which numerical results were higher than in the others) may be the most suitable methods for microbiological monitoring of a clean room. The mean results among the three selected active methods were compared with results on the settle plate (SP) (the passive method). A relationship was established between results of the passive method (CFU/h/plate 90 mmø) and the results of active methods (CFU/m3 air). By means of a lineal regression study, it was obtained a relation factor of 22.7; (95% CI: 19.7, 25.7). This factor is only valid for values between 3 and 16 in CFU/h/plate 90 mmø, and it is put on record that the experimental study took place in a room that fulfills Class D clean room specifications (WHO standards) in microbiological terms. PMID:15368991

  1. Idiopathic environmental intolerances (IEI): from molecular epidemiology to molecular medicine.

    PubMed

    De Luca, C; Scordo, G; Cesareo, E; Raskovic, D; Genovesi, G; Korkina, L

    2010-07-01

    Inherited or acquired impairment of xenobiotics metabolism is a postulated mechanism underlying environment-associated pathologies such as multiple chemical sensitivity, fibromyalgia, chronic fatigue syndrome, dental amalgam disease, and others, also collectively named idiopathic environmental intolerances (IEI). In view of the poor current knowledge of their etiology and pathogenesis, and the absence of recognised genetic and metabolic markers of the diseases. They are often considered "medically unexplained syndromes",. These disabling conditions share the features of polysymptomatic multi-organ syndromes, considered by part of the medical community to be aberrant responses triggered by exposure to low-dose organic and inorganic chemicals and metals, in concentrations far below average reference levels admitted for environmental toxicants. A genetic predisposition to altered biotransformation of environmental chemicals, drugs, and metals, and of endogenous low-molecular weight metabolites, caused by polymorphisms of genes coding for xenobiotic metabolizing enzymes, their receptors and transcription factors appears to be involved in the susceptibility to these environment-associated pathologies, along with epigenetic factors. Free radical/antioxidant homeostasis may also be heavily implicated, indirectly by affecting the regulation of xenobiotic metabolizing enzymes, and directly by causing increased levels of oxidative products, implicated in the chronic damage of cells and tissues, which is in part correlated with clinical symptoms. More systematic studies of molecular epidemiology, toxico- and pharmaco-genomics, elucidating the mechanisms of regulation, expression, induction, and activity of antioxidant/detoxifying enzymes, and the possible role of inflammatory mediators, promise a better understanding of this pathologically increased sensitivity to low-level chemical stimuli, and a solid basis for effective individualized antioxidant- and/or chelator

  2. Multimedia environmental chemical partitioning from molecular information.

    PubMed

    Martínez, Izacar; Grifoll, Jordi; Giralt, Francesc; Rallo, Robert

    2010-12-15

    The prospect of assessing the environmental distribution of chemicals directly from their molecular information was analyzed. Multimedia chemical partitioning of 455 chemicals, expressed in dimensionless compartmental mass ratios, was predicted by SimpleBox 3, a Level III Fugacity model, together with the propagation of reported uncertainty for key physicochemical and transport properties, and degradation rates. Chemicals, some registered in priority lists, were selected according to the availability of experimental property data to minimize the influence of predicted information in model development. Chemicals were emitted in air or water in a fixed geographical scenario representing the Netherlands and characterized by five compartments (air, water, sediments, soil and vegetation). Quantitative structure-fate relationship (QSFR) models to predict mass ratios in different compartments were developed with support vector regression algorithms. A set of molecular descriptors, including the molecular weight and 38 counts of molecular constituents were adopted to characterize the chemical space. Out of the 455 chemicals, 375 were used for training and testing the QSFR models, while 80 were excluded from model development and were used as an external validation set. Training and test chemicals were selected and the domain of applicability (DOA) of the QSFRs established by means of self-organizing maps according to structural similarity. Best results were obtained with QSFR models developed for chemicals belonging to either the class [C] and [C; O], or the class with at least one heteroatom different than oxygen in the structure. These two class-specific models, with respectively 146 and 229 chemicals, showed a predictive squared coefficient of q(2) ≥ 0.90 both for air and water, which respectively dropped to q(2)≈ 0.70 and 0.40 for outlying chemicals. Prediction errors were of the same order of magnitude as the deviations associated to the uncertainty of the

  3. A simple microbiological tool to evaluate the effect of environmental health interventions on hand contamination.

    PubMed

    Devamani, Carol; Norman, Guy; Schmidt, Wolf-Peter

    2014-11-01

    The effects of interventions such as sanitation or hand hygiene on hand contamination are difficult to evaluate. We explored the ability of a simple microbiological test to: (1) detect recontamination after handwashing; (2) reflect risk factors for microbial contamination and (3) be applicable to large populations. The study was done in rural Andhra Pradesh, India, and Maputo, Mozambique. Participants placed all 10 fingertips on a chromogenic agar that stains Enterococcus spp. and E. coli spp. Outcomes were the number of colonies and the number of fingertips with colonies. In the recontamination study, participants were randomised to handwashing with soap and no handwashing, and tested at 30 min intervals afterwards. In two cross sectional studies, risk factors for hand contamination were explored. Recontamination of hands after washing with soap was fast, with baseline levels reached after 1 h. Child care was associated with higher Enterococcus spp. counts, whereas agricultural activities increased E. coli spp. counts. Food preparation was associated with higher counts for both organisms. In Maputo, counts were not strongly associated with water access, latrine type, education or diarrhoea. The method seems unsuitable for the evaluation of handwashing promotion. It may reflect immediately preceding risk practices but not household-level risk factors. PMID:25407420

  4. A Simple Microbiological Tool to Evaluate the Effect of Environmental Health Interventions on Hand Contamination

    PubMed Central

    Devamani, Carol; Norman, Guy; Schmidt, Wolf-Peter

    2014-01-01

    The effects of interventions such as sanitation or hand hygiene on hand contamination are difficult to evaluate. We explored the ability of a simple microbiological test to: (1) detect recontamination after handwashing; (2) reflect risk factors for microbial contamination and (3) be applicable to large populations. The study was done in rural Andhra Pradesh, India, and Maputo, Mozambique. Participants placed all 10 fingertips on a chromogenic agar that stains Enterococcus spp. and E. coli spp. Outcomes were the number of colonies and the number of fingertips with colonies. In the recontamination study, participants were randomised to handwashing with soap and no handwashing, and tested at 30 min intervals afterwards. In two cross sectional studies, risk factors for hand contamination were explored. Recontamination of hands after washing with soap was fast, with baseline levels reached after 1 h. Child care was associated with higher Enterococcus spp. counts, whereas agricultural activities increased E. coli spp. counts. Food preparation was associated with higher counts for both organisms. In Maputo, counts were not strongly associated with water access, latrine type, education or diarrhoea. The method seems unsuitable for the evaluation of handwashing promotion. It may reflect immediately preceding risk practices but not household-level risk factors. PMID:25407420

  5. Microbiological Study of Lactic Acid Fermentation of Caper Berries by Molecular and Culture-Dependent Methods

    PubMed Central

    Pérez Pulido, Rubén; Ben Omar, Nabil; Abriouel, Hikmate; Lucas López, Rosario; Martínez Cañamero, Magdalena; Gálvez, Antonio

    2005-01-01

    Fermentation of capers (the fruits of Capparis sp.) was studied by molecular and culture-independent methods. A lactic acid fermentation occurred following immersion of caper berries in water, resulting in fast acidification and development of the organoleptic properties typical of this fermented food. A collection of 133 isolates obtained at different times of fermentation was reduced to 75 after randomly amplified polymorphic DNA (RAPD)-PCR analysis. Isolates were identified by PCR or 16S rRNA gene sequencing as Lactobacillus plantarum (37 isolates), Lactobacillus paraplantarum (1 isolate), Lactobacillus pentosus (5 isolates), Lactobacillus brevis (9 isolates), Lactobacillus fermentum (6 isolates), Pediococcus pentosaceus (14 isolates), Pediococcus acidilactici (1 isolate), and Enterococcus faecium (2 isolates). Cluster analysis of RAPD-PCR patterns revealed a high degree of diversity among lactobacilli (with four major groups and five subgroups), while pediococci clustered in two closely related groups. A culture-independent analysis of fermentation samples by temporal temperature gradient electrophoresis (TTGE) also indicated that L. plantarum is the predominant species in this fermentation, in agreement with culture-dependent results. The distribution of L. brevis and L. fermentum in samples was also determined by TTGE, but identification of Pediococcus at the species level was not possible. TTGE also allowed a more precise estimation of the distribution of E. faecium, and the detection of Enterococcus casseliflavus (which was not revealed by the culture-dependent analysis). Results from this study indicate that complementary data from molecular and culture-dependent analysis provide a more accurate determination of the microbial community dynamics during caper fermentation. PMID:16332762

  6. Microbiological and ecological responses to global environmental changes in polar regions (MERGE): An IPY core coordinating project

    NASA Astrophysics Data System (ADS)

    Naganuma, Takeshi; Wilmotte, Annick

    2009-11-01

    An integrated program, “Microbiological and ecological responses to global environmental changes in polar regions” (MERGE), was proposed in the International Polar Year (IPY) 2007-2008 and endorsed by the IPY committee as a coordinating proposal. MERGE hosts original proposals to the IPY and facilitates their funding. MERGE selected three key questions to produce scientific achievements. Prokaryotic and eukaryotic organisms in terrestrial, lacustrine, and supraglacial habitats were targeted according to diversity and biogeography; food webs and ecosystem evolution; and linkages between biological, chemical, and physical processes in the supraglacial biome. MERGE hosted 13 original and seven additional proposals, with two full proposals. It respected the priorities and achievements of the individual proposals and aimed to unify their significant results. Ideas and projects followed a bottom-up rather than a top-down approach. We intend to inform the MERGE community of the initial results and encourage ongoing collaboration. Scientists from non-polar regions have also participated and are encouraged to remain involved in MERGE. MERGE is formed by scientists from Argentina, Australia, Austria, Belgium, Brazil, Bulgaria, Canada, Egypt, Finland, France, Germany, Italy, Japan, Korea, Malaysia, New Zealand, Philippines, Poland, Russia, Spain, UK, Uruguay, USA, and Vietnam, and associates from Chile, Denmark, Netherlands, and Norway.

  7. Salty Microbiology

    ERIC Educational Resources Information Center

    Schneegurt, Mark A.; Wedel, Adrianne N.; Pokorski, Edward W.

    2004-01-01

    Using microbiology activities in the classroom is an effective way for teachers to address National Standards in the life sciences. However, common microbiology activities that involve swabbing doorknobs and hands are too risky due to the likelihood of culturing human pathogens. In addition, making sterile media and maintaining sterile conditions…

  8. Pseudomonas fluorescens-like bacteria from the stomach: A microbiological and molecular study

    PubMed Central

    Patel, Saurabh Kumar; Pratap, Chandra Bhan; Verma, Ajay Kumar; Jain, Ashok Kumar; Dixit, Vinod Kumar; Nath, Gopal

    2013-01-01

    AIM: To characterize oxidase- and urease-producing bacterial isolates, grown aerobically, that originated from antral biopsies of patients suffering from acid peptic diseases. METHODS: A total of 258 antral biopsy specimens were subjected to isolation of bacteria followed by tests for oxidase and urease production, acid tolerance and aerobic growth. The selected isolates were further characterized by molecular techniques viz. amplifications for 16S rRNA using universal eubacterial and HSP60 gene specific primers. The amplicons were subjected to restriction analysis and partial sequencing. A phylogenetic tree was generated using unweighted pair group method with arithmetic mean (UPGMA) from evolutionary distance computed with bootstrap test of phylogeny. Assessment of acidity tolerance of bacteria isolated from antrum was performed using hydrochloric acid from 10-7 mol/L to 10-1 mol/L. RESULTS: Of the 258 antral biopsy specimens collected from patients, 179 (69.4%) were positive for urease production by rapid urease test and 31% (80/258) yielded typical Helicobacter pylori (H. pylori) after 5-7 d of incubation under a microaerophilic environment. A total of 240 (93%) antral biopsies yielded homogeneous semi-translucent and small colonies after overnight incubation. The partial 16S rRNA sequences revealed that the isolates had 99% similarity with Pseudomonas species. A phylogenetic tree on the basis of 16S rRNA sequences denoted that JQ927226 and JQ927227 were likely to be related to Pseudomonas fluorescens (P. fluorescens). On the basis of HSP60 sequences applied to the UPGMA phylogenetic tree, it was observed that isolated strains in an aerobic environment were likely to be P. fluorescens, and HSP60 sequences had more discriminatory potential rather than 16S rRNA sequences. Interestingly, this bacterium was acid tolerant for hours at low pH. Further, a total of 250 (96.9%) genomic DNA samples of 258 biopsy specimens and DNA from 240 bacterial isolates were positive

  9. MOLECULAR DIAGNOSTICS - ANOTHER PIECE IN THE ENVIRONMENTAL PUZZLE

    EPA Science Inventory

    Molecular biology offers sensitive and expedient tools for the detection of exposure to environmental stressors. Molecular approaches provide the means for detection of the "first cellular event(s)" in response to environmental changes-specifically, immediate changes in gene expr...

  10. Proteomic tools for environmental microbiology--a roadmap from sample preparation to protein identification and quantification.

    PubMed

    Wöhlbrand, Lars; Trautwein, Kathleen; Rabus, Ralf

    2013-10-01

    The steadily increasing amount of (meta-)genomic sequence information of diverse organisms and habitats has a strong impact on research in microbial physiology and ecology. In-depth functional understanding of metabolic processes and overall physiological adaptation to environmental changes, however, requires application of proteomics, as the context specific proteome constitutes the true functional output of a cell. Considering the enormous structural and functional diversity of proteins, only rational combinations of various analytical approaches allow a holistic view on the overall state of the cell. Within the past decade, proteomic methods became increasingly accessible to microbiologists mainly due to the robustness of analytical methods (e.g. 2DE), and affordability of mass spectrometers and their relative ease of use. This review provides an overview on the complex portfolio of state-of-the-art proteomics and highlights the basic principles of key methods, ranging from sample preparation of laboratory or environmental samples, via protein/peptide separation (gel-based or gel-free) and different types of mass spectrometric protein/peptide analyses, to protein identification and abundance determination. PMID:23894077

  11. Overview of Microbiological Tests Performed During the Design of the International Space Station Environmental Control and Life Support Systems

    NASA Technical Reports Server (NTRS)

    Roman, Monsi C.; Mittelman, Marc W.

    2010-01-01

    The design and manufacturing of the main Environmental Control and Life Support Systems (ECLSS) for the United States segments of the International Space Station (ISS) was an involved process that started in the late 1980's, with the assessment and testing of competing technologies that could be used to clean the air and recycle water. It culminated in 2009 with the delivery and successful activation of the Water Recovery System (WRS) water processor (WP). The ECLSS required the work of a team of engineers and scientist working together to develop systems that could clean and/or recycle human metabolic loads to maintain a clean atmosphere and provide the crew clean water. One of the main goals of the ECLSS is to minimize the time spent by the crew worrying about vital resources not available in the vacuum of space, which allows them to spend most of their time learning to live in a microgravity environment many miles from the comforts of Earth and working on science experiments. Microorganisms are a significant part of the human body as well as part of the environment that we live in. Therefore, the ISS ECLSS design had to take into account the effect microorganisms have on the quality of stored water and wastewater, as well as that of the air systems. Hardware performance issues impacted by the accumulation of biofilm and/or microbiologically influenced corrosion were also studied during the ECLSS development stages. Many of the tests that were performed had to take into account the unique aspects of a microgravity environment as well as the challenge of understanding how to design systems that could not be sterilized or maintained in a sterile state. This paper will summarize the work of several studies that were performed to assess the impacts and/or to minimize the effects of microorganisms in the design of a closed loop life support system.

  12. Isolation and genetic analysis of an environmental bacteriophage: A 10-session laboratory series in molecular virology.

    PubMed

    Williamson, Ryan P; Barker, Brent T; Drammeh, Hamidou; Scott, Jefferson; Lin, Joseph

    2014-01-01

    Bacterial viruses, otherwise known as bacteriophage (or phage), are some of the most abundant viruses found in the environment. They can be easily isolated from water or soil and are ideal for use in laboratory classrooms due to their ease of culture and inherent safety. Here, we describe a series of 10 laboratory exercises where students collect, isolate, and purify the genome of an environmental phage. Once the genome has been extracted, students then clone a fragment of their isolated phage genome into a plasmid and analyze its sequence to identify the phage in their original isolate. These exercises have been carefully designed to apply foundational concepts that will expose students to basic skills in microbiology, molecular biology, and bioinformatics. PMID:25331656

  13. Agricultural Microbiology.

    ERIC Educational Resources Information Center

    Brill, Winston J.

    1981-01-01

    Elucidates strategies for applying microbiological techniques to traditional agricultural practices. Discusses the manipulation of microorganisms that live with plants and also the problems involved in the introduction of new genes into crop plants by recombinant DNA methods. (CS)

  14. Microbiology Made Relevant

    ERIC Educational Resources Information Center

    Cronholm, Lois S.; Metz, Mildred C.

    1976-01-01

    Described are two hospital-based laboratory exercises which helped students perceive the relationship between the principles of microbiology and the practice of nursing. The exercises involved an environmental study focusing on problems of nosocomial infection and a study of patients hospitalized with infectious diseases. (Author/MS)

  15. Which Microbial Communities Are Present? Importance of Selecting Appropriate Primers and Probes for Use in Molecular Microbiological Methods (MMM) in Oilfields

    NASA Astrophysics Data System (ADS)

    Sørensen, Ketil Bernt

    Molecular microbiology techniques play an increasing role in the oil industry. Most of the current applications are based on either Fluorescence in situ Hybridisation (FISH) or polymerase chain reaction (PCR) or some variation thereof. These types of approaches require the use of oligonucleotide primers and probes (i.e. short fragments of DNA that are complementary to the target DNA/RNA of the microorganism of interest). In the case of FISH, the probes are fluorescently labelled in order to identify the target cells. Before undertaking either FISH or PCR approaches, it is important to select the most appropriate primers or probes for targeting the microorganisms of interest in a given environment.

  16. Environmental Molecular Sciences Laboratory Annual Report: Fiscal Year 2006

    SciTech Connect

    Foster, Nancy S.; Showalter, Mary Ann

    2007-03-23

    This report describes the activities and research performed at the Environmental Molecular Sciences Laboratory, a Department of Energy national scientific user facility at Pacific Northwest National Laboratory, during Fiscal Year 2006.

  17. [Microbiological diagnosis of viral respiratory infections].

    PubMed

    Eiros, José M; Ortiz de Lejarazu, Raúl; Tenorio, Alberto; Casas, Inmaculada; Pozo, Francisco; Ruiz, Guillermo; Pérez-Breña, Pilar

    2009-03-01

    Acute respiratory infection is the most common disease occurring over a person's lifetime, with etiological variations determined mainly by age, environmental circumstances, the healthcare setting, and the underlying pathology. More than 200 different viruses distributed in six viral families have been implicated in the pathogenesis of respiratory tract infection. These facts are generating an increasing diagnostic demand that should be incorporated into the healthcare setting without delay. To meet this demand, the Spanish Society of Infectious Diseases and Clinical Microbiology has updated its Standard Procedure for the microbiological diagnosis of viral respiratory infection. This document contains an update primarily of infections caused by influenza viruses, and secondarily, infections due to other conventional and emerging respiratory viruses. In all cases, the methods for direct virological diagnosis (cell culture, and detection of antigens and nucleic acid) are reviewed, with special reference to techniques for molecular detection and genetic characterization. PMID:19306718

  18. Microbiological investigations

    NASA Technical Reports Server (NTRS)

    Ferguson, J. K.; Taylor, G. R.; Mieszkuc, B. J.

    1975-01-01

    The crew microbiology program was conducted to evaluate lunar contamination, to detect potentially pathogenic microoganisms, to identify medically important microorganisms recovered from ill crewmen, to aid in diagnosis and treatment, and to collect microbiological data that would aid in elucidating the response of the crew microbial autoflora to the space flight environment and in evaluating the resultant effect on the crewmember. Microbiological sampling of selected sites in the command module was initiated in support of the quarantine program. During lunar quarantine missions, microbial screening was accomplished for all support personnel to be isolated with the returning crewman. Virology support for the Apollo project consisted of characterization of the viral and mycoplasma flora of the crewmembers and performance of viral serology for crewmembers, crew contacts, and key mission personnel. Procedures and results are discussed in detail.

  19. The Center for Environmental Kinetics Analysis: an NSF- and DOE-funded Environmental Molecular Science Institute (EMSI) at Penn State

    SciTech Connect

    S. L. Brantley; William D. Burgos; Brian A. Dempsey; Peter J. Heaney; James D. Kubicki; Peter C. Lichtner; Bruce E. Logan; Carmen E. Martinez; Karl T. Mueller; Kwadwo A. Osseo-Asare; Ming Tien; Carl I. Steefel, Glenn A. Waychunas; and John M. Zachara

    2007-04-19

    Physicochemical and microbiological processes taking place at environmental interfaces influence natural processes as well as the transport and fate of environmental contaminants, the remediation of toxic chemicals, and the sequestration of anthropogenic CO2. A team of scientists and engineers has been assembled to develop and apply new experimental and computational techniques to expand our knowledge of environmental kinetics. We are also training a cohort of talented and diverse students to work on these complex problems at multiple length scales and to compile and synthesize the kinetic data. Development of the human resources capable of translating molecular-scale information into parameters that are applicable in real world, field-scale problems of environmental kinetics is a major and relatively unique objective of the Institute's efforts. The EMSI team is a partnership among 10 faculty at The Pennsylvania State University (funded by the National Science Foundation Divisions of Chemistry and Earth Sciences), one faculty member at Juniata College, one faculty member at the University of Florida, and four researchers drawn from Los Alamos National Laboratory, Pacific Northwest National Laboratory, and Lawrence Berkeley National Laboratory (funded by the Department of Energy Division of Environmental Remediation Sciences). Interactions among the applied and academic scientists drives research approaches aimed toward solving important problems of national interest. The Institute is organized into three interest groups (IGs) focusing on the processes of dissolution (DIG), precipitation (PIG), and microbial reactions at surfaces (BIG). Some of the research activity from each IG is highlighted to the right. The IGs interact with each other as each interest group studies reactions across the molecular, microscopic, mesoscopic and, in most cases, field scales. For example, abiotic dissolution and precipitation reactions of Fe oxides as studied in the Dissolution IG

  20. Industrial Microbiology.

    ERIC Educational Resources Information Center

    Demain, Arnold L.; Solomon, Nadine A.

    1981-01-01

    Presents an overview of the field of industrial microbiology, providing historical backgrounds of scientific discoveries in the field and descriptions of industrially important microorganisms. Applied research in industry is also detailed, with mention of gene amplification, DNA recombination, pharmaceutical approaches, and detoxification and…

  1. Coral microbiology

    USGS Publications Warehouse

    Rosenberg, Eugene; Kellogg, Christina A.; Rohwer, Forest

    2007-01-01

    In the last 30 years, there has been approximately a 30% loss of corals worldwide, largely due to emerging diseases (Harvell et al., 2002, 2007; Hughes et al., 2003). Coral microbiology is a new field, driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms and to use this knowledge to eventually prevent the spread of coral diseases.

  2. Design of a Tablet Computer App for Facilitation of a Molecular Blood Culture Test in Clinical Microbiology and Preliminary Usability Evaluation

    PubMed Central

    Pape-Haugaard, Louise; Meltzer, Michelle C; Fuchs, Martin; Schønheyder, Henrik C; Hejlesen, Ole

    2016-01-01

    Background User mobility is an important aspect of the development of clinical information systems for health care professionals. Mobile phones and tablet computers have obtained widespread use by health care professionals, offering an opportunity for supporting the access to patient information through specialized applications (apps) while supporting the mobility of the users. The use of apps for mobile phones and tablet computers may support workflow of complex tasks, for example, molecular-based diagnostic tests in clinical microbiology. Multiplex Blood Culture Test (MuxBCT) is a molecular-based diagnostic test used for rapid identification of pathogens in positive blood cultures. To facilitate the workflow of the MuxBCT, a specialized tablet computer app was developed as an accessory to the diagnostic test. The app aims to reduce the complexity of the test by step-by-step guidance of microscopy and to assist users in reaching an exact bacterial or fungal diagnosis based on blood specimen observations and controls. Additionally, the app allows for entry of test results, and communication thereof to the laboratory information system (LIS). Objective The objective of the study was to describe the design considerations of the MuxBCT app and the results of a preliminary usability evaluation. Methods The MuxBCT tablet app was developed and set up for use in a clinical microbiology laboratory. A near-live simulation study was conducted in the clinical microbiology laboratory to evaluate the usability of the MuxBCT app. The study was designed to achieve a high degree of realism as participants carried out a scenario representing the context of use for the MuxBCT app. As the MuxBCT was under development, the scenario involved the use of molecular blood culture tests similar to the MuxBCT for identification of microorganisms from positive blood culture samples. The study participants were observed, and their interactions with the app were recorded. After the study, the

  3. Molecular fingerprints of environmental carcinogens in human cancer.

    PubMed

    Ceccaroli, C; Pulliero, A; Geretto, M; Izzotti, A

    2015-01-01

    Identification of specific molecular changes (fingerprints) is important to identify cancer etiology. Exploitable biomarkers are related to DNA, epigenetics, and proteins. DNA adducts are the turning point between environmental exposures and biological damage. DNA mutational fingerprints are induced by carcinogens in tumor suppressor and oncogenes. In an epigenetic domain, methylation changes occurs in specific genes for arsenic, benzene, chromium, and cigarette smoke. Alteration of specific microRNA has been reported for environmental carcinogens. Benzo(a)pyrene, cadmium, coal, and wood dust hits specific heat-shock proteins and metalloproteases. The multiple analysis of these biomarkers provides information on the carcinogenic mechanisms activated by exposure to environmental carcinogens. PMID:26023758

  4. DEVELOPMENT OF MOLECULAR BIOMARKERS TO MEASURE ENVIRONMENTALLY INDUCED IMMUNE RESPONSES

    EPA Science Inventory

    This study will generate a panel of sensitive molecular biomarkers to measure environmentally induced changes in systemic and local immune responses within small biological samples. Once tested and characterized, these reagents can be immediately incorporated as a part of the...

  5. Plant sentinels and molecular probes that monitor environmental munitions contaminants

    SciTech Connect

    Jackson, P.J.; DeWitt, J.G.; Hill, K.K.; Kuske, C.R.; Kim, D.Y.

    1994-08-01

    Plants accumulate TNT and similar compounds from soil. Their sessile nature requires that plants adapt to environmental changes by biochemical and molecular means. In principle, it is possible to develop a monitoring capability based on expression of any gene that is activated by specific environmental conditions. The authors have identified plant genes activated upon exposure to TNT. Partial gene sequences allow design of DNA probes that measure TNT-induced gene activity. These will be used to develop sensitive assays that monitor gene expression in plants growing in environments possibly contaminated with explosives.

  6. [Post-mortem microbiology analysis].

    PubMed

    Fernández-Rodríguez, Amparo; Alberola, Juan; Cohen, Marta Cecilia

    2013-12-01

    Post-mortem microbiology is useful in both clinical and forensic autopsies, and allows a suspected infection to be confirmed. Indeed, it is routinely applied to donor studies in the clinical setting, as well as in sudden and unexpected death in the forensic field. Implementation of specific sampling techniques in autopsy can minimize the possibility of contamination, making interpretation of the results easier. Specific interpretation criteria for post-mortem cultures, the use of molecular diagnosis, and its fusion with molecular biology and histopathology have led to post-mortem microbiology playing a major role in autopsy. Multidisciplinary work involving microbiologists, pathologists, and forensic physicians will help to improve the achievements of post-mortem microbiology, prevent infectious diseases, and contribute to a healthier population. PMID:23195835

  7. The relationship between molecular structure and biological activity of alkali metal salts of vanillic acid: Spectroscopic, theoretical and microbiological studies

    NASA Astrophysics Data System (ADS)

    Świsłocka, Renata; Piekut, Jolanta; Lewandowski, Włodzimierz

    In this paper we investigate the relationship between molecular structure of alkali metal vanillate molecules and their antimicrobial activity. To this end FT-IR, FT-Raman, UV absorption and 1H, 13C NMR spectra for lithium, sodium, potassium, rubidium and caesium vanillates in solid state were registered, assigned and analyzed. Microbial activity of studied compounds was tested against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Proteus vulgaris, Bacillus subtilis and Candida albicans. In order to evaluate the dependence between chemical structure and biological activity of alkali metal vanillates the statistical analysis was performed for selected wavenumbers from FT-IR spectra and parameters describing microbial activity of vanillates. The geometrical structures of the compounds studied were optimized and the structural characteristics were determined by density functional theory (DFT) using at B3LYP method with 6-311++G** as basis set. The obtained statistical equations show the existence of correlation between molecular structure of vanillates and their biological properties.

  8. The Proteasome Is a Molecular Target of Environmental Toxic Organotins

    PubMed Central

    Shi, Guoqing; Chen, Di; Zhai, Guangshu; Chen, Marina S.; Cui, Qiuzhi Cindy; Zhou, Qunfang; He, Bin; Dou, Q. Ping; Jiang, Guibin

    2009-01-01

    Background Because of the vital importance of the proteasome pathway, chemicals affecting proteasome activity could disrupt essential cellular processes. Although the toxicity of organotins to both invertebrates and vertebrates is well known, the essential cellular target of organotins has not been well identified. We hypothesize that the proteasome is a molecular target of environmental toxic organotins. Objectives Our goal was to test the above hypothesis by investigating whether organotins could inhibit the activity of purified and cellular proteasomes and, if so, the involved molecular mechanisms and downstream events. Results We found that some toxic organotins [e.g., triphenyltin (TPT)] can potently and preferentially inhibit the chymotrypsin-like activity of purified 20S proteasomes and human breast cancer cellular 26S proteasomes. Direct binding of tin atoms to cellular proteasomes is responsible for the observed irreversible inhibition. Inhibition of cellular proteasomes by TPT in several human cell lines results in the accumulation of ubiquitinated proteins and natural proteasome target proteins, accompanied by induction of cell death. Conclusions The proteasome is one of the molecular targets of environmental toxic organotins in human cells, and proteasome inhibition by organotins contributes to their cellular toxicity. PMID:19337512

  9. Building a Collaboratory in Environmental and Molecular Science

    SciTech Connect

    Kouzes, R.T.; Myers, J.D.; Devaney, D.M.; Dunning, T.H.; Wise, J.A.

    1994-03-01

    A Collaboratory is a meta-laboratory that spans multiple geographical areas with collaborators interacting via electronic means. Collaboratories are designed to enable close ties between scientists in a given research area, promote collaborations involving scientists in diverse areas, accelerate the development and dissemination of basic knowledge, and minimize the time-lag between discovery and application. PNL is developing the concept of an Environmental and Molecular Sciences Collaboratory (EMSC) as a natural evolution of the EMSL project. The goal of the EMSC is to increase the efficiency of research and reduce the time required to implement new environmental remediation and preservation technologies. The EMSC will leverage the resources (intellectual and physical) of the EMSL by making them more accessible to remote collaborators as well as by making the resources of remote sites available to local researchers. It will provide a common set of computer hardware and software tools to support remote collaboration, a key step in establishing a collaborative culture for scientists in the theoretical, computational, and experimental molecular sciences across the nation. In short, the EMSC will establish and support an `electronic community of scientists researching and developing innovative environmental preservation and restoration technologies.

  10. Scientific data management in the environmental molecular sciences laboratory

    SciTech Connect

    Bernard, P.R.; Keller, T.L.

    1995-09-01

    The Environmental Molecular Sciences Laboratory (EMSL) is currently under construction at Pacific Northwest Laboratory (PNL) for the U.S. Department of Energy (DOE). This laboratory will be used for molecular and environmental sciences research to identify comprehensive solutions to DOE`s environmental problems. Major facilities within the EMSL include the Molecular Sciences Computing Facility (MSCF), a laser-surface dynamics laboratory, a high-field nuclear magnetic resonance (NMR) laboratory, and a mass spectrometry laboratory. The EMSL is scheduled to open early in 1997 and will house about 260 resident and visiting scientists. It is anticipated that at least six (6) terabytes of data will be archived in the first year of operation. An object-oriented database management system (OODBMS) and a mass storage system will be integrated to provide an intelligent, automated mechanism to manage data. The resulting system, called the DataBase Computer System (DBCS), will provide total scientific data management capabilities to EMSL users. A prototype mass storage system based on the National Storage Laboratory`s (NSL) UniTree has been procured and is in limited use. This system consists of two independent hierarchies of storage devices. One hierarchy of lower capacity, slower speed devices provides support for smaller files transferred over the Fiber Distributed Data Interface (FDDI) network. Also part of the system is a second hierarchy of higher capacity, higher speed devices that will be used to support high performance clients (e.g., a large scale parallel processor). The ObjectStore OODBMS will be used to manage metadata for archived datasets, maintain relationships between archived datasets, and -hold small, duplicate subsets of archived datasets (i.e., derivative data). The interim system is called DBCS, Phase 0 (DBCS-0). The production system for the EMSL, DBCS Phase 1 (DBCS-1), will be procured and installed in the summer of 1996.

  11. Kinetic Modeling of Microbiological Processes

    SciTech Connect

    Liu, Chongxuan; Fang, Yilin

    2012-08-26

    Kinetic description of microbiological processes is vital for the design and control of microbe-based biotechnologies such as waste water treatment, petroleum oil recovery, and contaminant attenuation and remediation. Various models have been proposed to describe microbiological processes. This editorial article discusses the advantages and limiation of these modeling approaches in cluding tranditional, Monod-type models and derivatives, and recently developed constraint-based approaches. The article also offers the future direction of modeling researches that best suit for petroleum and environmental biotechnologies.

  12. Legionnaires’ disease from a cooling tower in a community outbreak in Lidköping, Sweden- epidemiological, environmental and microbiological investigation supported by meteorological modelling

    PubMed Central

    2012-01-01

    Background An outbreak of Legionnaires’ Disease took place in the Swedish town Lidköping on Lake Vänern in August 2004 and the number of pneumonia cases at the local hospital increased markedly. As soon as the first patients were diagnosed, health care providers were informed and an outbreak investigation was launched. Methods Classical epidemiological investigation, diagnostic tests, environmental analyses, epidemiological typing and meteorological methods. Results Thirty-two cases were found. The median age was 62 years (range 36 – 88) and 22 (69%) were males. No common indoor exposure was found. Legionella pneumophila serogroup 1 was found at two industries, each with two cooling towers. In one cooling tower exceptionally high concentrations, 1.2 × 109 cfu/L, were found. Smaller amounts were also found in the other tower of the first industry and in one tower of the second plant. Sero- and genotyping of isolated L. pneumophila serogroup 1 from three patients and epidemiologically suspected environmental strains supported the cooling tower with the high concentration as the source. In all, two L. pneumophila strains were isolated from three culture confirmed cases and both these strains were detected in the cooling tower, but one strain in another cooling tower as well. Meteorological modelling demonstrated probable spread from the most suspected cooling tower towards the town centre and the precise location of four cases that were stray visitors to Lidköping. Conclusions Classical epidemiological, environmental and microbiological investigation of an LD outbreak can be supported by meteorological modelling methods. The broad competence and cooperation capabilities in the investigation team from different authorities were of paramount importance in stopping this outbreak. PMID:23171054

  13. Investigating the presence of fungal agents in febrile neutropenic patients with hematological malignancies using different microbiological, serological, and molecular methods

    PubMed Central

    Sönmez, Ahu; Eksi, Fahriye; Pehlivan, Mustafa; Sahin, Handan Haydaroglu

    2015-01-01

    This study aimed to investigate fungal agents in febrile neutropenic patients with hematological malignancies. Direct microscopy and cultures were performed on clinical samples collected from febrile neutropenic episodes. The galactomannan (GM) antigen was tested using enzyme-linked immunosorbent assays, and Aspergillus fumigatus and Candida albicans deoxyribonucleic acid (DNA) assessed using real-time polymerase chain reaction (PCR) in consecutive serum samples. Of the 199 episodes investigated, 1.5% were classified as definite invasive aspergillosis (IA), 4.0% as IA with high probability, and 4.0% as IA with low probability. Additionally, candidaemia was detected in eight episodes (4.1%). The GM antigen was found negative for 86.4% of episodes, as one positive for 7.0% of episodes, as two or more consecutive positives for 5.5% of episodes, and as positive in any two serum samples in 1.0% of episodes. While no C. albicans DNA was detected in 98.5% of 199 ­episodes, one positive result was obtained in 1.0% of episodes, and two or more consecutive positives in 0.5% of episodes. A. fumigatus PCR results were found negative in 81.9% of episodes, as one positive in 16.1% of episodes, as positive in any two serum samples in 1.0% of episodes, and consecutively positive in 1.0% of episodes. GM antigen tests were found consecutively positive in all three patients diagnosed as having definite IA. These findings indicate that conventional, serological, and molecular methods should be used in combination to detect fungal agents in febrile neutropenic patients. PMID:26295293

  14. Molecular and genetic ecotoxicologic approaches to aquatic environmental bioreporting.

    PubMed Central

    Beaty, B J; Black, W C; Carlson, J O; Clements, W H; DuTeau, N; Harrahy, E; Nuckols, J; Kenneth, E; Olson, K E; Rayms-Keller, A

    1998-01-01

    Molecular and population genetic ecotoxicologic approaches are being developed for the utilization of arthropods as bioreporters of heavy metal mixtures in the environment. The explosion of knowledge in molecular biology, molecular genetics, and biotechnology provides an unparalleled opportunity to use arthropods as bioreporter organisms. Interspecific differences in aquatic arthropod populations have been previously demonstrated in response to heavy metal insult in the Arkansas River (AR) California Gulch Superfund site (CGSS). Population genetic analyses were conducted on the mayfly Baetis tricaudatus. Genetic polymorphisms were detected in polymerase chain reaction amplified 16S mitochondrial rDNA (a selectively neutral gene) of B tricaudatus using single-strand conformation polymorphism analysis. Genetic differences may have resulted from impediments to gene flow in the population caused by mortality arising from exposure to heavy metal mixture pollution. In laboratory studies a candidate metal-responsive mucinlike gene, which is metal and dose specific, has been identified in Chironomus tentans and other potential AR-CGSS bioreporter species. Population genetic analyses using the mucinlike gene may provide insight into the role of this selectable gene in determining the breeding structure of B. tricaudatus in the AR-CGSS and may provide mechanistic insight into determinants of aquatic arthropod response to heavy metal insult. Metal-responsive (MR) genes and regulatory sequences are being isolated, characterized, and assayed for differential gene expression in response to heavy metal mixture pollution in the AR-CGSS. Identified promoter sequences can then be engineered into previously developed MR constructs to provide sensitive in vitro assays for environmental bioreporting of heavy metal mixtures. The results of the population genetic studies are being entered into an AR geographic information system that contains substantial biological, chemical, and

  15. ENVIRONMENTAL EFFECTS OF WESTERN COAL SURFACE MINING. PART IV--CHEMICAL AND MICROBIOLOGICAL INVESTIGATIONS OF A SURFACE COAL MINE SETTLING POND

    EPA Science Inventory

    Chemical and microbiological investigations of the settling pond system at the West Decker Coal Mine in southeastern Montana were undertaken during 1975-1977. Concentrations of total dissolved solids, bicarbonate, sodium, sulfate, and nitrogen species in pond water were elevated ...

  16. Molecular targets of epigenetic regulation and effectors of environmental influences

    SciTech Connect

    Choudhuri, Supratim; Cui Yue; Klaassen, Curtis D.

    2010-06-15

    The true understanding of what we currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DNA methylation, chromatin modification, as well as on the expression of small non-coding RNAs (ncRNAs) have expanded the scope of research on the etiology of various diseases including cancer. The current review briefly discusses the molecular mechanisms of epigenetic regulation and expands the discussion with examples on the role of environment, such as the immediate environment during development, in inducing epigenetic changes and modulating gene expression.

  17. Effect of culture intensity and probiotics application on microbiological and environmental parameters in Litopenaeus vannamei culture ponds.

    PubMed

    Patil, Prasanna Kumar; Muralidhar, M; Solanki, Haresh G; Patel, Pretesh P; Patel, Krishna; Gopla, Chavali

    2016-01-01

    The present study examined the complex interaction among stocking density and extent of probiotic use with production and environmental parameters in Litopenaeus vannamei culture ponds to suggest suitable management strategies. The study was conducted inL. vannamei culture ponds with stocking density of 35 nos sq m(-1) (Group I) and 56 nos sq m(-1) (Group II) and probiotic application @16.5 kg ha(-1) and 157 kg ha(-1), respectively. There was no significant difference noted between the two groups of ponds in respect to ammonia oxidizing bacteria (AOB) in sediment and nitrite oxidizing bacteria (NOB) in water samples, whereas significantly higher levels of AOB in water samples of high intensity culture ponds (Group II) and NOB in sediment samples of Group I were observed. The levels of sulphur oxidizing bacteria (SOB) and sulphur reducing bacteria (SRB) in Group I pond water and in Group II sediment were significantly higher than their corresponding levels in the other group. In both the groups, ammonia, nitrite and sulphide concentrations were below toxic limits prescribed for shrimp farming. Comparing the production parameters at harvest revealed that low intensity culture ponds (Group I) had higher growth rate, average body weight and significantly lower FCR and higher survival rate than high intensity culture ponds (Group II). The results indicated that application of microbial products in higher quantities did not benefit significantly, and there is a need to regulate quantum and schedule of biological product usage for economically sustainable shrimp culture. PMID:26930856

  18. Environmental surveillance and molecular characterization of Legionella in tropical Singapore.

    PubMed

    Lim, Y H; Relus Kek, Y L; Lim, P Y; Yap, H M; Vivien Goh, T L; Ng, L C

    2011-04-01

    Legionnaires' disease is often acquired by inhalation of legionellae from a contaminated environmental source. In recent years, Singapore has seen an increase in the use of aerosol-generating fixtures such as mist fans and spa pools. Poorly maintained and designed water fixtures could pose a public health threat to the community. In this study, we provided an update on the prevalence of Legionella in mist fans (N=28), household water heaters with storage tanks (N=19) and instantaneous heaters (N=30); and extended the survey to spa pools (N=29) and aerosol-generating fixtures in nursing homes (N=116). The prevalence of Legionella were 21.1% in water heaters with storage tanks, 24.1% in spa pools, 14.2% in mist fans and 3.3% in instantaneous heaters. Legionella was not detected in nursing homes. A total of 37 isolates were subjected to molecular characterization using Sequence-Based Typing (SBT) protocol from the European Working Group on Legionella Infections (EWGLI). This is the first study on the use of SBT protocol on environmental strains isolated from tropical South East Asia. The Legionella flora was very heterogenous. The overall diversity of the allelic profile was found to be 0.970 (95% CI 0.946 - 0.994). All known STs of our isolates have been associated with clinical cases in EWGLI database. The phylogenetic analysis showed that our novel environmental isolates were clustered with clinical STs that were previously reported in Europe, Japan, United Kingdom and United States etc. (in EWGLI database), suggesting that Legionella found in the environment of Singapore may potentially cause human disease. PMID:21602781

  19. Quantum microbiology.

    PubMed

    Trevors, J T; Masson, L

    2011-01-01

    During his famous 1943 lecture series at Trinity College Dublin, the reknown physicist Erwin Schrodinger discussed the failure and challenges of interpreting life by classical physics alone and that a new approach, rooted in Quantum principles, must be involved. Quantum events are simply a level of organization below the molecular level. This includes the atomic and subatomic makeup of matter in microbial metabolism and structures, as well as the organic, genetic information code of DNA and RNA. Quantum events at this time do not elucidate, for example, how specific genetic instructions were first encoded in an organic genetic code in microbial cells capable of growth and division, and its subsequent evolution over 3.6 to 4 billion years. However, due to recent technological advances, biologists and physicists are starting to demonstrate linkages between various quantum principles like quantum tunneling, entanglement and coherence in biological processes illustrating that nature has exerted some level quantum control to optimize various processes in living organisms. In this article we explore the role of quantum events in microbial processes and endeavor to show that after nearly 67 years, Schrödinger was prophetic and visionary in his view of quantum theory and its connection with some of the fundamental mechanisms of life. PMID:21368338

  20. Phenotypic and molecular diversity of Meyerozyma guilliermondii strains isolated from food and other environmental niches, hints for an incipient speciation.

    PubMed

    Corte, Laura; di Cagno, Raffaella; Groenewald, Marizeth; Roscini, Luca; Colabella, Claudia; Gobbetti, Marco; Cardinali, Gianluigi

    2015-06-01

    Meyerozyma guilliermondii is a yeast species widely isolated from several natural environments and from fruit; in medical microbiology it is known as the teleomorph of the opportunistic pathogen Candida guilliermondii, which causes about 2% of the human blood infections. This yeast is also promising in a variety of biotechnological applications as vitamins production and post-harvest control. The question if isolates from different sources are physiologically and genetically similar, or if the various environments induced significant differences, is crucial for the understanding of this species structure and to select strains appropriate for each application. This question was addressed using LSU and ITS sequencing for taxonomic assignment, i-SSR (GACA4) for the molecular characterization and FTIR for the metabolomic fingerprint. All data showed that fruit and environmental isolates cluster separately with a general good agreement between metabolomics and molecular analysis. An additional RAPD analysis was able to discriminate strains according to the isolation position within the pineapple fruit. Although all strains are members of the M. guilliermondii species according to the current standards, the distribution of large variability detected suggests that some specialization occurred in the niches inhabited by this yeast and that food related strains can be differentiated from the medical isolates. PMID:25791010

  1. Use of Case Studies to Introduce Undergraduate Students to Principles of Food Microbiology, Molecular Biology, and Epidemiology of Food-Borne Disease

    ERIC Educational Resources Information Center

    Ponder, Monica A.; Sumner, Susan

    2009-01-01

    Mock outbreaks of infectious disease offer the ability to introduce principles of food microbiology, ecology, and epidemiology to undergraduate students using an inquiry driven process. Students were presented with an epidemiological case study detailing patient history, clinical presentation, and foods recently consumed. The students then had to…

  2. Marine molluscs in environmental monitoring. I. Cellular and molecular responses

    NASA Astrophysics Data System (ADS)

    Bresler, Vladimir; Abelson, Avigdor; Fishelson, Lev; Feldstein, Tamar; Rosenfeld, Michael; Mokady, Ofer

    2003-10-01

    levels of biological organization—the molecular and cellular level—the parameters measured may have the capacity not only for biomonitoring environmental quality, but also for early warning.

  3. Microbiology of aggressive periodontitis.

    PubMed

    Könönen, Eija; Müller, Hans-Peter

    2014-06-01

    For decades, Aggregatibacter actinomycetemcomitans has been considered the most likely etiologic agent in aggressive periodontitis. Implementation of DNA-based microbiologic methodologies has considerably improved our understanding of the composition of subgingival biofilms, and advanced open-ended molecular techniques even allow for genome mapping of the whole bacterial spectrum in a sample and characterization of both the cultivable and not-yet-cultivable microbiota associated with periodontal health and disease. Currently, A. actinomycetemcomitans is regarded as a minor component of the resident oral microbiota and as an opportunistic pathogen in some individuals. Its specific JP2 clone, however, shows properties of a true exogenous pathogen and has an important role in the development of aggressive periodontitis in certain populations. Still, limited data exist on the impact of other microbes specifically in aggressive periodontitis. Despite a wide heterogeneity of bacteria, especially in subgingival samples collected from patients, bacteria of the red complex in particular, and those of the orange complex, are considered as potential pathogens in generalized aggressive periodontitis. These types of bacterial findings closely resemble those found for chronic periodontitis, representing a mixed polymicrobial infection without a clear association with any specific microorganism. In aggressive periodontitis, the role of novel and not-yet-cultivable bacteria has not yet been elucidated. There are geographic and ethnic differences in the carriage of periodontitis-associated microorganisms, and they need to be taken into account when comparing study reports on periodontal microbiology in different study populations. In the present review, we provide an overview on the colonization of potential periodontal pathogens in childhood and adolescence, and on specific microorganisms that have been suspected for their role in the initiation and progression of aggressive

  4. Epigenetic: a molecular link between testicular cancer and environmental exposures

    PubMed Central

    Vega, Aurelie; Baptissart, Marine; Caira, Françoise; Brugnon, Florence; Lobaccaro, Jean-Marc A.; Volle, David H.

    2012-01-01

    In the last decades, studies in rodents have highlighted links between in utero and/or neonatal exposures to molecules that alter endocrine functions and the development of genital tract abnormalities, such as cryptorchidism, hypospadias, and impaired spermatogenesis. Most of these molecules, called endocrine disrupters exert estrogenic and/or antiandrogenic activities. These data led to the hypothesis of the testicular dysgenesis syndrome which postulates that these disorders are one clinical entity and are linked by epidemiological and pathophysiological relations. Furthermore, infertility has been stated as a risk factor for testicular cancer (TC). The incidence of TC has been increasing over the past decade. Most of testicular germ cell cancers develop through a pre-invasive carcinoma in situ from fetal germ cells (primordial germ cell or gonocyte). During their development, fetal germ cells undergo epigenetic modifications. Interestingly, several lines of evidence have shown that gene regulation through epigenetic mechanisms (DNA and histone modifications) plays an important role in normal development as well as in various diseases, including TC. Here we will review chromatin modifications which can affect testicular physiology leading to the development of TC; and highlight potential molecular pathways involved in these alterations in the context of environmental exposures. PMID:23230429

  5. Paradigm change in evolutionary microbiology.

    PubMed

    O'Malley, Maureen A; Boucher, Yan

    2005-03-01

    Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn's account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn's relevance to this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn's account may capture aspects of the pattern (or outcome) of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn's application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. PMID:16120264

  6. Microbiological Tests Performed During the Design of the International Space Station Environmental Control and Life Support Systems. Part 1, Bulk Phase. Part 1; Bulk Phase

    NASA Technical Reports Server (NTRS)

    Roman, Monsi C.; Mittelman, Marc W.

    2010-01-01

    The design and manufacturing of the main Environmental Control and Life Support Systems (ECLSS) for the United States segments of the International Space Station (ISS) was an involved process that started in the mid 1980s, with the assessment and testing of competing technologies that could be used to clean the air and recycle water. It culminated in 2009 with the delivery and successful activation of the Water Recovery System (WRS) water processor (WP). The ECLSS required the work of a team of engineers and scientist working together to develop systems that could clean and/or recycle human metabolic loads to maintain a clean atmosphere and provide the crew clean water. One of the main goals of the ECLSS is to minimize the time spent by the crew worrying about vital resources not available in the vacuum of space, which allows them to spend most of their time learning to live in a microgravity environment many miles from the comforts of Earth and working on science experiments. Microorganisms are a significant part of the human body as well as part of the environment that we live in. Therefore, the ISS ECLSS design had to take into account the effect microorganisms have on the quality of stored water and wastewater, as well as that of the air systems. Hardware performance issues impacted by the accumulation of biofilm and/or microbiologically influenced corrosion were also studied during the ECLSS development stages. Many of the tests that were performed had to take into account the unique aspects of a microgravity environment as well as the challenge of understanding how to design systems that could not be sterilized or maintained in a sterile state. This paper will summarize the work of several studies that were performed to assess the impacts and/or to minimize the effects of microorganisms in open, semi-closed and closed loop life support system. The biofilm and biodeterioration studies that were performed during the design and test periods will be presented in

  7. Automation in Clinical Microbiology

    PubMed Central

    Ledeboer, Nathan A.

    2013-01-01

    Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories. PMID:23515547

  8. Microbiology & Toxicology: Space Environment

    NASA Video Gallery

    One key aspect in maintaining crew health and performance during spaceflight missions is the provision of a habitable environment with acceptably low concentrations of microbiological and toxicolog...

  9. ENVIRONMENTAL FACTORS AND CHEMICAL AND MICROBIOLOGICAL WATER QUALITY CONSTITUTENTS RELATED TO THE PRESENCE OF ENTERIC VIRUSES IN GROUND WATER FROM SMALL PUBLIC WATER SUPPLIES IN SOUTHEASTERN MICHIGAN

    EPA Science Inventory

    A study of small public ground-water-supply wells that produce water from discontinuous sand and gravel aquifers was done from July 1999 through July 2001 in southeastern Michigan. Samples were collected to determine the occurrence of viral pathogens and microbiological indicato...

  10. ENVIRONMENTAL FACTORS AND CHEMICAL AND MICROBIOLOGICAL CONSTITUENTS RELATED TO THE PRESENECE OF VIRUSES IN GROUND WATER FROM SMALL PUBLIC WATER SUPPLIES IN SOUTHEASTERN MICHIGAN

    EPA Science Inventory

    Thirty-eight public ground-water-supply wells serving fewer than 3,300 people were sampled from July 1999 through July 2001 in southeastern Michigan to determine (1) the occurrence of viral pathogens and microbiological indicators, (2) the adequacy of indicators as predictors of...

  11. Egg Microbiology Basics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbiology is the study of living microorganisms. This includes any single living animal not visible to the naked eye most of which are less than 0.1 mm in diameter. Bacteria, yeasts, molds, viruses, some algae and protozoans are considered microorganisms. Microbiology is a diverse field and fo...

  12. Microbiology of Water.

    ERIC Educational Resources Information Center

    Geldreich, Edwin E.

    1978-01-01

    Presents a literature review of microbiology of water, covering publications of 1967-77. This review covers: (1) microbial indicators of pollution; and (2) microbiology of rivers, potable waters, natural lakes, and impoundments. A list of 192 references is also presented. (HM)

  13. Microbiology, philosophy and education.

    PubMed

    O'Malley, Maureen A

    2016-09-01

    There are not only many links between microbiological and philosophical topics, but good educational reasons for microbiologists to explore the philosophical issues in their fields. I examine three broad issues of classification, causality and model systems, showing how these philosophical dimensions have practical implications. I conclude with a discussion of the educational benefits for recognising the philosophy in microbiology. PMID:27465488

  14. Microbiology of Waste Treatment.

    ERIC Educational Resources Information Center

    Unz, Richard F.

    1978-01-01

    Presents a literature review of the microbiology of waste treatment, covering publications of 1976-77. This review includes topics such as: (1) sanitary microbiology; (2) wastewater disinfectant; (3) viruses in wastewater; and (4) wastewater microbial populations. A list of 142 references is also presented. (HM)

  15. Emerging Technologies for the Clinical Microbiology Laboratory

    PubMed Central

    Buchan, Blake W.

    2014-01-01

    SUMMARY In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory. PMID:25278575

  16. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

    PubMed Central

    Narihiro, Takashi; Sekiguchi, Yuji

    2011-01-01

    Summary For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers. PMID:21375721

  17. Microbiology and Moisture Uptake of Desert Soils

    NASA Astrophysics Data System (ADS)

    Kress, M. E.; Bryant, E. P.; Morgan, S. W.; Rech, S.; McKay, C. P.

    2005-12-01

    We have initiated an interdisciplinary study of the microbiology and water content of desert soils to better understand microbial activity in extreme arid environments. Water is the one constituent that no organism can live without; nevertheless, there are places on Earth with an annual rainfall near zero that do support microbial ecosystems. These hyperarid deserts (e.g. Atacama and the Antarctic Dry Valleys) are the closest terrestrial analogs to Mars, which is the subject of future exploration motivated by the search for life beyond Earth. We are modeling the moisture uptake by soils in hyperarid environments to quantify the environmental constraints that regulate the survival and growth of micro-organisms. Together with the studies of moisture uptake, we are also characterizing the microbial population in these soils using molecular and culturing methods. We are in the process of extracting DNA from these soils using MoBio extraction kits. This DNA will be used as a template to amplify bacterial and eukaryotic ribosomal DNA to determine the diversity of the microbial population. We also have been attempting to determine the density of organisms by culturing on one-half strength R2A agar. The long-range goal of this research is to identify special adaptations of terrestrial life that allow them to inhabit extreme arid environments, while simultaneously quantifying the environmental parameters that enforce limits on these organisms' growth and survival.

  18. Determining molecular responses to environmental change in soybeans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As the global climate changes, plants will be challenged by environmental stresses that are more extreme and more frequent. The average yield loss due to environmental stresses is currently estimated to be more than 50% for major crop species and is the major limitation to world food production. The...

  19. MOLECULAR MODELING OF THE INTERACTION OF ENVIRONMENTAL CHEMICALS WITH MACROMOLECULES IN THE ENDOCRINE SYSTEM

    EPA Science Inventory

    This research will use experimentally determined structures of the estrogen receptor. The structure of estrogen and other (environmental) ligands will be used as starting points for computer docking experiments. Programs utilizing a classical molecular mechanics algorithm to qu...

  20. Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

    ERIC Educational Resources Information Center

    Oerther, Daniel B.

    2002-01-01

    Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

  1. Next Generation Microbiology Requirements

    NASA Technical Reports Server (NTRS)

    Ott, C. M.; Oubre, C. M.; Elliott, T. F.; Castro, V. A.; Pierson, D. L.

    2012-01-01

    As humans continue to explore deep into space, microorganisms will travel with them. The primary means to mitigate the risk of infectious disease are a combination of prudent spacecraft design and rigorous operational controls. The effectiveness of these methods are evaluated by microbiological monitoring of spacecraft, food, water, and the crew that is performed preflight, in-flight, and post-flight. Current NASA requirements associated with microbiological monitoring are based on culture-based methodology where microorganisms are grown on a semi-solid growth medium and enumerated. Subsequent identification of the organisms requires specialized labor and large equipment, which historically has been performed on Earth. Requirements that rely strictly on culture-based units limit the use of non-culture based monitoring technology. Specifically, the culture-based "measurement criteria" are Colony Forming Units (CFU, representing the growth of one microorganism at a single location on the agar medium) per a given volume, area, or sample size. As the CFU unit by definition is culture-based, these requirements limit alternative technologies for spaceflight applications. As spaceflight missions such as those to Mars extend further into space, culture-based technology will become difficult to implement due to the (a) limited shelf life of the culture media, (b) mass/volume necessary to carry these consumables, and (c) problems associated with the production of biohazardous material in the habitable volume of the spacecraft. In addition, an extensive amount of new knowledge has been obtained during the Space Shuttle, NASA-Mir, and International Space Station Programs, which gave direction for new or modified microbial control requirements for vehicle design and mission operations. The goal of this task is to develop and recommend a new set of requirements for vehicle design and mission operations, including microbiological monitoring, based upon "lessons learned" and new

  2. Molecular Modeling of Environmentally Important Processes: Reduction Potentials

    ERIC Educational Resources Information Center

    Lewis, Anne; Bumpus, John A.; Truhlar, Donald G.; Cramer, Christopher J.

    2004-01-01

    The increasing use of computational quantum chemistry in the modeling of environmentally important processes is described. The employment of computational quantum mechanics for the prediction of oxidation-reduction potential for solutes in an aqueous medium is discussed.

  3. Subsurface Microbiology and Biogeochemistry

    SciTech Connect

    Fredrickson, Jim K.; Fletcher, Madilyn

    2001-05-01

    Jim contributed a chapter to this book, in addition to co-editing it with Madilyn Fletcher. Fredrickson, J. K., and M. Fletcher. (eds.) 2001 Subsurface Microbiology and Biogeochemistry. Wiley-Liss, Inc., New York.

  4. Microbiology in Introductory Biology.

    ERIC Educational Resources Information Center

    Callery, Michael L.; And Others

    1980-01-01

    Describes a microbiology unit developed for an introductory college biology course in which the identity of an unknown bacterium is determined. Also described is an interactive taxonomy computer program which aids in the identity of the unknown organism. (CS)

  5. Clinical Microbiology Informatics

    PubMed Central

    Sintchenko, Vitali; Rauch, Carol A.; Pantanowitz, Liron

    2014-01-01

    SUMMARY The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future. PMID:25278581

  6. A microbiological view of sterile service production.

    PubMed

    Atfield, R D

    1991-06-01

    The primary purpose of a Sterile Services Department is the prevention of infection. A specific guide to Good Manufacturing Practice (GMP) has been published by the Institute of Sterile Service Management to assist managers to ensure that the final products are of the nature and quality intended. The testing and monitoring of machinery, such as autoclaves, has an obvious microbiological relevance but other practices, such as expire dates and presterilization of used items, are of dubious microbiological advantage and can act against the main aim. GMP recommendations on environmental controls have received disproportionate attention to the remainder of the document, particularly relating to packing rooms. The standard should not be seen as a primarily microbiological measure but as a sensible control to limit the ingress of unwanted dust, flies and people and provide basic ventilation. Tests indicate that the standard for particle counts can be achieved without structural alteration in some departments. Microbiological counts are similar to those within operating theatres and additional protective clothing is of no apparent advantage. Process failure is the main cause of risks to the patient, and other practices, although both relevant and important, should not be given a false microbiological significance as these can detract and distract attention from the main issue. PMID:1679826

  7. Use of case studies to introduce undergraduate students to principles of food microbiology, molecular biology, and epidemiology of food-borne disease.

    PubMed

    Ponder, Monica A; Sumner, Susan

    2009-05-01

    Mock outbreaks of infectious disease offer the ability to introduce principles of food microbiology, ecology, and epidemiology to undergraduate students using an inquiry driven process. Students were presented with an epidemiological case study detailing patient history, clinical presentation, and foods recently consumed. The students then had to form hypotheses about the causative agents and attempt to identify the vehicle of transmission from foods their patient consumed. Students applied biochemical testing protocols to explore bacterial metabolism that are used to identify pathogens. After biochemically identifying their case's causative agent, the students were introduced to rapid methods that are used by health departments. Students extracted DNA, performed PCR reactions to amplify the 16s rDNA gene and identified it by comparing the PCR product sequence to a database using BLAST. Rapid methods, which do not employ time-consuming culturing methods, are increasingly being used; this exercise ensures that students have the technical skills necessary to compete in an increasingly technological global market. PMID:21567725

  8. Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery.

    PubMed

    Toyota, Taro; Banno, Taisuke; Nitta, Sachiko; Takinoue, Masahiro; Nomoto, Tomonori; Natsume, Yuno; Matsumura, Shuichi; Fujinami, Masanori

    2014-01-01

    This review briefly summarizes recent developments in the construction of biologically/environmentally compatible chemical machinery composed of soft matter. Since environmental and living systems are open systems, chemical machinery must continuously fulfill its functions not only through the influx and generation of molecules but also via the degradation and dissipation of molecules. If the degradation or dissipation of soft matter molecular building blocks and biomaterial molecules/polymers can be achieved, soft matter particles composed of them can be used to realize chemical machinery such as selfpropelled droplets, drug delivery carriers, tissue regeneration scaffolds, protocell models, cell-/tissuemarkers, and molecular computing systems. PMID:25341502

  9. The Development of New User Research Capabilities in Environmental Molecular Science: Workshop Report

    SciTech Connect

    Felmy, Andrew R.; Baer, Donald R.; Fredrickson, Jim K.; Gephart, Roy E.; Rosso, Kevin M.

    2006-10-31

    On August 1, and 2, 2006, 104 scientists representing 40 institutions including 24 Universities and 5 National Laboratories gathered at the W.R. Wiley Environmental Molecular Sciences Laboratory, a National scientific user facility, to outline important science challenges for the next decade and identify major capabilities needed to pursue advanced research in the environmental molecular sciences. EMSL’s four science themes served as the framework for the workshop. The four science themes are 1) Biological Interactions and Interfaces, 2) Geochemistry/Biogeochemistry and Surface Science, 3) Atmospheric Aerosol Chemistry, and 4) Science of Interfacial Phenomena.

  10. Molecular Signatures of Methanogens in Cultures and Environmental Samples

    NASA Astrophysics Data System (ADS)

    Summons, R. E.; Embaye, T.; Jahnke, L. L.; Baumgartner, M.

    2002-12-01

    The core lipids of methanogens comprise C20 and C40 isoprenoid chains, linked through ether bonds to glycerol. Additional structural diversity is encoded into the polar head groups that are attached to the glycerol ether cores. These compounds are potentially very useful as taxonomic markers in microbial mats and other environmental samples while the nature of the hydrocarbon chains provide a means to identify methanogenic inputs to ancient sediments. The structural diversity of methanogen polar lipids is most valuable when it can be directly correlated to 16S rRNA phylogeny. On the other hand, this diversity can also leads to analytical challenges because there is no single approach that works for all structural types. While some intact methanogen lipids have been identified using mass spectrometry and NMR spectroscopy, the most common means of analysing the lipid cores involves cleavage of the ether bonds using HI and subsequent reduction of the alkyl iodides to hydrocarbons with LiAlH4. One class of methanogenic lipids, the 3?-hydroxyarchaeols, escaped detection for some years because strong acid treatments in the analysis protocols destroyed hydroxyl-containing isoprenoid chains. We have been systematically re-examining the lipids of methanogens, using milder procedures involving weak acid hydrolysis of polar head groups, derivatisation to form trimethylsilyl ethers and analysis by GC-MS. As well as archaeol, sn-2- and sn-3-hydroxyarchaeol, we have tentatively identified a dihydroxyarchaeol in several Methanococcus sp. For Methanococcus thermolithotrophicus an analysis of the total lipid extracts using BBr3 as an ether cleavage reagent followed by LiBEt3H, reduction revealed a very complex mixture consisting of phytane, phytenes, biphytane, biphytenes and a suite of related alcohols. The latter compounds were analysed by GC-MS as their trimethylsilyl ethers and found to comprise a mixture tentatively identified as phytan-N-ol and biphytan-N-ol where N= 3 or 7

  11. Microbiology of ensiling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in our understanding of silage microbiology are reviewed. The ability to extract microbial DNA from silages, amplify portions of DNA, and then separate those portions by the strains of microorganisms that have produced them has been at the core of the changes that have occurred recen...

  12. Microbiology--Safety Considerations.

    ERIC Educational Resources Information Center

    Hoffmann, Sheryl K.

    This paper discusses the risk assessment associated with microbiology instruction based on grade level, general control measures, appropriate activities for middle school and high school students, the preparation and sterilization of equipment, and safe handling techniques. Appended are instructions and figures on making wire loops and the…

  13. Making Microbiology Even Smaller!

    ERIC Educational Resources Information Center

    Young, Linda Mull; Motz, Vicki Abrams

    2013-01-01

    We outline protocols for producing slant-minis (SLINIs) and mini-deeps (MEEPs) and examples of their use in simple microbiology experiments suitable for high school students. The principal benefits of these protocols are decreased cost associated with significantly reduced media use; easier, less expensive disposal of waste; and increased safety…

  14. Microbiological test results of the environmental control and life support systems vapors compression distillation subsystem recycle tank components following various pretreatment protocols

    NASA Technical Reports Server (NTRS)

    Huff, Tim

    1993-01-01

    Microbiological samples were collected from the recycle tank of the vapor compression distillation (VCD) subsystem of the water recovery test at NASA MSFC following a 68-day run. The recycle tank collects rejected urine brine that was pretreated with a commercially available oxidant (Oxone) and sulfuric acid and pumps it back to the processing component of the VCD. Samples collected included a water sample and two swab samples, one from the particulate filter surface and a second from material floating on the surface of the water. No bacteria were recovered from the water sample. Both swab samples contained a spore-forming bacterium, Bacillus insolitus. A filamentous fungus was isolated from the floating material. Approximately 1 month after the pretreatment chemicals were changed to sodium hypochlorite and sulfuric acid, a swab of the particulate filter was again analyzed for microbial content. One fungus was isolated, and spore-forming bacteria were observed. These results indicate the inability of these pretreatments to inhibit surface attachment. The implications of the presence of these organisms are discussed.

  15. Environmental impact assessment of Attenda abattoir, Ogbomoso southwestern Nigeria on surface and groundwater quality using geo-electrical imaging and microbiological analysis.

    PubMed

    Adelowo, Olawale Olufemi; Akinlabi, Ismail A; Fagade, Obasola Ezekiel

    2012-07-01

    The impact of Attenda abattoir, Ogbomoso southwestern Nigeria on four water sources was investigated using geoelectrical imaging and microbiological analysis. 2D electrical resistivity imaging indicated groundwater contamination by leachate from the abattoir. Electrical resistivity values measured by the traverse run directly on the waste dump and other areas impacted by the waste from the abattoir are generally very low (6.68-16.7 Ωm) in comparison to other positions (135-288 Ωm). The total viable bacteria count of the water samples ranged from 0.49 × 10(6) to 2.85 × 10(8) cfu/ml and all samples are contaminated with coliforms with the most probable number (MPN)/100 ml ranging from 110 to ≥ 1,600 MPN/100 ml. Among bacteria isolated from the study site (n = 95), resistance to eight antibiotics ranged from 35.8% to 94%. In addition, 85% of Streptococcus agalactiae (n = 31) and Staphylococci (n = 9) showed haemolytic activity while 92% of all isolates showed β-lactamase activity. These results suggest that operations of the abattoir may impact negatively on surrounding aquatic ecosystem and endanger the health of surrounding residents who use water from the wells for domestic purposes. Furthermore, such aquatic ecosystems may serve as reservoir of antibiotic resistant bacteria. PMID:22105848

  16. The aryl hydrocarbon receptor: a molecular pathway for the environmental control of the immune response.

    PubMed

    Quintana, Francisco J

    2013-03-01

    Environmental factors have significant effects on the development of autoimmune diseases. The ligand-activated transcription factor aryl hydrocarbon receptor (AHR) is controlled by endogenous and environmental small molecules. Hence, AHR provides a molecular pathway by which endogenous and environmental signals can influence the immune response and the development of autoimmune diseases. AHR also provides a target for therapeutic intervention in immune-mediated disorders. In this review, we discuss the role of AHR in the regulation of T-cell differentiation and autoimmunity. PMID:23190340

  17. DEVELOPMENT OF MOLECULAR MARKERS OF RESPONSE TO ASSESS THE SENSITIVITY OF CHILDREN TO ENVIRONMENTAL CHEMICALS

    EPA Science Inventory

    Development of Molecular Markers of Response to Assess the Sensitivity of Children to Environmental Chemicals

    J.Allen, C. Blackman, M. Blaze, D. Delker, D. DeMarini, C. Doerr, R. Grindstaff, S.
    Hester, C. Jones, A. Kligerman, G. Knapp, M. Kohan, C. Nelson, R. Owen, J. P...

  18. Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations

    EPA Science Inventory

    Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental wat...

  19. Environmental changes and microbiological health risks. Satellite-derived turbidity: an indicator of "health hazard" for surface water in West Africa (Bagre lake, Burkina Faso).

    NASA Astrophysics Data System (ADS)

    Robert, E.; Grippa, M.; Kergoat, L.; Martinez, J.; Pinet, S.; Gal, L.; Soumaguel, N.

    2015-12-01

    A significant correlation exists between the concentration of parasites, bacteria and some water quality parameters including surface suspended solids (SSS) and turbidity. Suspended particles can carry viruses and pathogenic bacteria affecting human health and foster their development. High SSS, associated with high turbidity, can therefore be considered as a vector of microbiological contaminants, causing diarrheal diseases. Few studies have focused on the turbidity parameter in rural Africa, while many cases of intestinal parasitic infections are due to the consumption of unsafe water from ponds, lakes, and rivers. Monitoring turbidity may therefore contribute to health hazard monitoring. Turbidity refers to the optical properties of water and is known to impact water reflectance in the visible and near-infrared domain. Ideally, its spatial and temporal variability requires the use of high temporal resolution (MODIS) and spatial resolution (Landsat, SPOT, Sentinel-2). Here we investigate turbidity in West-Africa. Various algorithms and indices proposed in the literature for inland waters are applied to MODIS series and to Landsat 7 and 8 CDR images, and SPOT5 images. The data and algorithms are evaluated with field measurements: turbidity, SSS, and hyperspectral ground radiometry. We show that turbidity of the Bagre Lake displays a strong increase over 2000-2015, associated with the corresponding increase of the red and NIR reflectances, as well as a reduction of the seasonal variations. Water level derived from the Jason 2 altimeter does not explain such variations. The most probable hypothesis is a change in land use (increase in bare and degraded soils), that leads to an increase in the particles transported by surface runoff to the lake. Such an increase in turbidity reinforces the health risk. We will discuss the link between turbidity and health in view of data from health centers on diarrheal diseases as well as data on practices and uses of populations.

  20. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    PubMed Central

    Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

    2015-01-01

    We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC) and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs), bisphenols (BPs), and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA) and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK) signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors. PMID:26512648

  1. Microbiology operations and facilities aboard restructured Space Station Freedom

    NASA Technical Reports Server (NTRS)

    Cioletti, Louis A.; Mishra, S. K.; Pierson, Duane L.

    1992-01-01

    With the restructure and funding changes for Space Station Freedom, the Environmental Health System (EHS)/Microbiology Subsystem revised its scheduling and operational requirements for component hardware. The function of the Microbiology Subsystem is to monitor the environmental quality of air, water, and internal surfaces and, in part, crew health on board Space Station. Its critical role shall be the identification of microbial contaminants in the environment that may cause system degradation, produce unsanitary or pathogenic conditions, or reduce crew and mission effectiveness. EHS/Microbiology operations and equipment shall be introduced in concert with a phased assembly sequence, from Man Tended Capability (MTC) through Permanently Manned Capability (PMC). Effective Microbiology operations and subsystem components will assure a safe, habitable, and useful spacecraft environment for life sciences research and long-term manned exploration.

  2. Molecularly imprinted adsorbents for selective separation and/or concentration of environmental pollutants.

    PubMed

    Kubo, Takuya; Hosoya, Ken; Otsuka, Koji

    2014-01-01

    This review describes the development of molecularly imprinted materials for selective separation and/or concentration of environmental pollutants, the quantitative concentration of which is usually difficult to determine because of their low level of concentration and existence of a large number of contaminants in environmental water. The fragment imprinting technique allowed for the selective separation of endocrine disrupters and halogenated aromatic compounds, including bisphenol A, and chlorinated/brominated aromatic compounds by the specific structural recognition based on the breeds, position, and number of the substituents. Also, the interval immobilization technique provided the specific materials enabling selective concentration based on the interval recognition of ionic functional groups in the targeting compounds, so that the effective determinations were achieved for natural toxins and pharmaceuticals in environmental water. Additionally, a selective photodegradation of toxins and a stimulus responsible hydrogel by the similar molecular recognition ability were successfully carried out. We have summarized these techniques including our recent studies. PMID:24420250

  3. Evaluation in Cameroon of a Novel, Simplified Methodology to Assist Molecular Microbiological Analysis of V. cholerae in Resource-Limited Settings

    PubMed Central

    Debes, Amanda K.; Ateudjieu, Jerome; Guenou, Etiene; Lopez, Anna Lena; Bugayong, Mark Philip; Retiban, Pearl Joy; Garrine, Marcelino; Mandomando, Inacio; Li, Shan; Stine, O. Colin; Sack, David A.

    2016-01-01

    Background Vibrio cholerae is endemic in South Asia and Africa where outbreaks of cholera occur widely and are particularly associated with poverty and poor sanitation. Knowledge of the genetic diversity of toxigenic V. cholerae isolates, particularly in Africa, remains scarce. The constraints in improving this understanding is not only the lack of regular cholera disease surveillance, but also the lack of laboratory capabilities in endemic countries to preserve, store and ship isolates in a timely manner. We evaluated the use of simplified sample preservation methods for molecular characterization using multi-locus variable-number tandem-repeat analysis (MLVA) for differentiation of Vibrio cholerae genotypes. Methods and Findings Forty-seven V. cholerae isolates and 18 enriched clinical specimens (e.g. stool specimens after enrichment in broth) from cholera outbreaks in Cameroon were preserved on Whatman filter paper for DNA extraction. The samples were collected from two geographically distinct outbreaks in the Far North of Cameroon (FNC) in June 2014 and October 2014. In addition, a convenience sample of 14 isolates from the Philippines and 8 from Mozambique were analyzed. All 87 DNAs were successfully analyzed including 16 paired samples, one a cultured isolate and the other the enriched specimen from which the isolate was collected. Genotypic results were identical between 15 enriched specimens and their culture isolates and the other pair differed at single locus. Two closely related, but distinct clonal complexes were identified among the Cameroonian specimens from 2014. Conclusions Collecting V. cholerae using simplified laboratory methods in remote and low-resource settings allows for subsequent advanced molecular characterization of V. cholerae O1. These simplified DNA preservation methods identify V. cholerae and make possible timely information regarding the genetic diversity of V. cholerae; our results set the stage for continued molecular

  4. Microbiological analysis of cosmetics.

    PubMed

    Herrera, Anavella Gaitan

    2004-01-01

    Cosmetics are products of chemical or natural origin dedicated specifically for use in skin and mucosa. The constant development of the cosmetic industry has generated the necessity to carry out microbiological analysis on the raw materials used in the industrial production of cosmetics as well as the final products, with the purpose of obtaining products of good microbiological quality. Cosmetic products are recognized to be substrates for the survival and development of a large variety of microorganisms, since they possess some of the nutrients that facilitate growth such as: lipids, polysaccharides, alcohol, proteins, amino acids, glucosides, esteroids, peptides, and vitamins. Also, the conditions of readiness (oxygenation, pH, temperature, osmotic degree, superficial activity, perfume, and essential oils) present in the cosmetic products favor microbial multiplication. Routine analyses to determine the microbiological quality of a cosmetic product include the following: Count of mesophilic aerobic microorganisms. Most probable number (MPN) of total coliforms. Count of molds and yeasts. Absence/presence of Staphylococcus aureus probe. Absence/presence of Pseudomonas aeruginosa probe. PMID:15156038

  5. A Critical Assessment of Microbiological Biogas to Biomethane Upgrading Systems.

    PubMed

    Rittmann, Simon K-M R

    2015-01-01

    Microbiological biogas upgrading could become a promising technology for production of methane (CH(4)). This is, storage of irregular generated electricity results in a need to store electricity generated at peak times for use at non-peak times, which could be achieved in an intermediate step by electrolysis of water to molecular hydrogen (H(2)). Microbiological biogas upgrading can be performed by contacting carbon dioxide (CO(2)), H(2) and hydrogenotrophic methanogenic Archaea either in situ in an anaerobic digester, or ex situ in a separate bioreactor. In situ microbiological biogas upgrading is indicated to require thorough bioprocess development, because only low volumetric CH(4) production rates and low CH(4) fermentation offgas content have been achieved. Higher volumetric production rates are shown for the ex situ microbiological biogas upgrading compared to in situ microbiological biogas upgrading. However, the ex situ microbiological biogas upgrading currently suffers from H(2) gas liquid mass transfer limitation, which results in low volumetric CH(4) productivity compared to pure H(2)/CO(2) conversion to CH(4). If waste gas utilization from biological and industrial sources can be shown without reduction in volumetric CH(4) productivity, as well as if the aim of a single stage conversion to a CH(4) fermentation offgas content exceeding 95 vol% can be demonstrated, ex situ microbiological biogas upgrading with pure or enrichment cultures of methanogens could become a promising future technology for almost CO(2)-neutral biomethane production. PMID:26337846

  6. Circadian Clocks in the Cnidaria: Environmental Entrainment, Molecular Regulation, and Organismal Outputs

    PubMed Central

    Reitzel, Adam M.; Tarrant, Ann M.; Levy, Oren

    2013-01-01

    The circadian clock is a molecular network that translates predictable environmental signals, such as light levels, into organismal responses, including behavior and physiology. Regular oscillations of the molecular components of the clock enable individuals to anticipate regularly fluctuating environmental conditions. Cnidarians play important roles in benthic and pelagic marine environments and also occupy a key evolutionary position as the likely sister group to the bilaterians. Together, these attributes make members of this phylum attractive as models for testing hypotheses on roles for circadian clocks in regulating behavior, physiology, and reproduction as well as those regarding the deep evolutionary conservation of circadian regulatory pathways in animal evolution. Here, we review and synthesize the field of cnidarian circadian biology by discussing the diverse effects of daily light cycles on cnidarians, summarizing the molecular evidence for the conservation of a bilaterian-like circadian clock in anthozoan cnidarians, and presenting new empirical data supporting the presence of a conserved feed-forward loop in the starlet sea anemone, Nematostella vectensis. Furthermore, we discuss critical gaps in our current knowledge about the cnidarian clock, including the functions directly regulated by the clock and the precise molecular interactions that drive the oscillating gene-expression patterns. We conclude that the field of cnidarian circadian biology is moving rapidly toward linking molecular mechanisms with physiology and behavior. PMID:23620252

  7. Towards the development of multifunctional molecular indicators combining soil biogeochemical and microbiological variables to predict the ecological integrity of silvicultural practices.

    PubMed

    Peck, Vincent; Quiza, Liliana; Buffet, Jean-Philippe; Khdhiri, Mondher; Durand, Audrey-Anne; Paquette, Alain; Thiffault, Nelson; Messier, Christian; Beaulieu, Nadyre; Guertin, Claude; Constant, Philippe

    2016-05-01

    The impact of mechanical site preparation (MSP) on soil biogeochemical structure in young larch plantations was investigated. Soil samples were collected in replicated plots comprising simple trenching, double trenching, mounding and inverting site preparation. Unlogged natural mixed forest areas were used as a reference. Analysis of soil nutrients, abundance of bacteria and gas exchanges unveiled no significant difference among the plots. However, inverting site preparation resulted in higher variations of gas exchanges when compared with trenching, mounding and unlogged natural forest. A combination of the biological and physicochemical variables was used to define a multifunctional classification of the soil samples into four distinct groups categorized as a function of their deviation from baseline ecological conditions. According to this classification model, simple trenching was the approach that represented the lowest ecological risk potential at the microsite level. No relationship was observed between MSP method and soil bacterial community structure as assessed by high-throughput sequencing of bacterial 16S rRNA gene; however, indicator genotypes were identified for each multifunctional soil class. This is the first identification of multifunctional molecular indicators for baseline and disturbed ecological conditions in soil, demonstrating the potential of applied microbial ecology to guide silvicultural practices and ecological risk assessment. PMID:26853704

  8. [Revolution in diagnostic microbiology. Needs, driving forces and consequences].

    PubMed

    Bukholm, G; Rollag, H

    1995-11-10

    Introducing molecular biological technology into medical microbiology promotes deeper insight into the epidemiology, pathogenesis, diagnostics and treatment of infectious diseases. New technology has helped to highlight the complicated biological interaction between host and microbes and has created a need for more advanced technology both in microbiological diagnostics and in microbiological science. Extra-professional factors like the high prestige of new techniques have also been of considerable significance. Medical microbiologists will become an important link between the inventors of new technology and the physicians who diagnose and treat the patients. Through these contacts and their diagnostic laboratory work, they will become important generators and communicators of knowledge. In this connection it will be important to represent reason in introducing technology in medical microbiological diagnostics. Since patients are expected to play a more active part in health care, communicating knowledge to patients and the population in general will become an obligation. PMID:7491583

  9. Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

    SciTech Connect

    Nourbakhsh-Rey, Mehrnoush; Libault, Marc

    2016-01-01

    The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. Lastly, in this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.

  10. Epidemiological transition of colorectal cancer in developing countries: Environmental factors, molecular pathways, and opportunities for prevention

    PubMed Central

    Bishehsari, Faraz; Mahdavinia, Mahboobeh; Vacca, Michele; Malekzadeh, Reza; Mariani-Costantini, Renato

    2014-01-01

    Colorectal cancer (CRC) is one of the leading causes of cancer and cancer-related mortality worldwide. The disease has been traditionally a major health problem in industrial countries, however the CRC rates are increasing in the developing countries that are undergoing economic growth. Several environmental risk factors, mainly changes in diet and life style, have been suggested to underlie the rise of CRC in these populations. Diet and lifestyle impinge on nuclear receptors, on the intestinal microbiota and on crucial molecular pathways that are implicated in intestinal carcinogenesis. In this respect, the epidemiological transition in several regions of the world offers a unique opportunity to better understand CRC carcinogenesis by studying the disease phenotypes and their environmental and molecular associations in different populations. The data from these studies may have important implications for the global prevention and treatment of CRC. PMID:24876728

  11. Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

    PubMed Central

    2016-01-01

    The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hair cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. In this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses. PMID:27088086

  12. Microbiological concerns and methodological approaches related to bacterial water quality in spaceflight

    NASA Technical Reports Server (NTRS)

    Pyle, Barry H.; Mcfeters, Gordon A.

    1992-01-01

    A number of microbiological issues are of critical importance to crew health and system performance in spacecraft water systems. This presentation reviews an army of these concerns which include factors that influence water treatment and disinfection in spaceflight such as biofilm formation and the physiological responses of bacteria in clean water systems. Factors associated with spaceflight like aerosol formation under conditions of microgravity are also discussed within the context of airborne infections such as Legionellosis. Finally, a spectrum of analytical approaches is reviewed to provide an evaluation of methodological alternatives that have been suggested or used to detect microorganisms of interest in water systems. These range from classical approaches employing colony formation on specific microbiological growth media to direct (i.e. microscopic) and indirect (e.g. electrochemical) methods as well as the use of molecular approaches and gene probes. These techniques are critically evaluated for their potential utility in determining microbiological water quality through the detection of microorganisms under the influence of ambient environmental stress inherent in spaceflight water systems.

  13. Environmental Molecular Sciences Laboratory Operations System: Version 4.0 - system requirements specification

    SciTech Connect

    Kashporenko, D.

    1996-07-01

    This document is intended to provide an operations standard for the Environmental Molecular Sciences Laboratory OPerations System (EMSL OPS). It is directed toward three primary audiences: (1) Environmental Molecular Sciences Laboratory (EMSL) facility and operations personnel; (2) laboratory line managers and staff; and (3) researchers, equipment operators, and laboratory users. It is also a statement of system requirements for software developers of EMSL OPS. The need for a finely tuned, superior research environment as provided by the US Department of Energy`s (DOE) Environmental Molecular Sciences Laboratory has never been greater. The abrupt end of the Cold War and the realignment of national priorities caused major US and competing overseas laboratories to reposition themselves in a highly competitive research marketplace. For a new laboratory such as the EMSL, this means coming into existence in a rapidly changing external environment. For any major laboratory, these changes create funding uncertainties and increasing global competition along with concomitant demands for higher standards of research product quality and innovation. While more laboratories are chasing fewer funding dollars, research ideas and proposals, especially for molecular-level research in the materials and biological sciences, are burgeoning. In such an economically constrained atmosphere, reduced costs, improved productivity, and strategic research project portfolio building become essential to establish and maintain any distinct competitive advantage. For EMSL, this environment and these demands require clear operational objectives, specific goals, and a well-crafted strategy. Specific goals will evolve and change with the evolution of the nature and definition of DOE`s environmental research needs. Hence, EMSL OPS is designed to facilitate migration of these changes with ease into every pertinent job function, creating a facile {open_quotes}learning organization.{close_quotes}

  14. Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology

    SciTech Connect

    Victor de Lorenzo; Juan Luis Ramos; Jerome Kukor; Gerben J. Zylstra

    2004-02-15

    One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.

  15. Molecular environmental science : an assessment of research accomplishments, available synchrotron radiation facilities, and needs.

    SciTech Connect

    Brown, G. E., Jr.; Sutton, S. R.; Bargar, J. R.; Shuh, D. K.; Fenter, P. A.; Kemner, K. M.

    2004-10-20

    Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and their reactions with

  16. Molecular Environmental Science: An Assessment of Research Accomplishments, Available Synchrotron Radiation Facilities, and Needs

    SciTech Connect

    Brown, G

    2004-02-05

    Synchrotron-based techniques are fundamental to research in ''Molecular Environmental Science'' (MES), an emerging field that involves molecular-level studies of chemical and biological processes affecting the speciation, properties, and behavior of contaminants, pollutants, and nutrients in the ecosphere. These techniques enable the study of aqueous solute complexes, poorly crystalline materials, solid-liquid interfaces, mineral-aqueous solution interactions, microbial biofilm-heavy metal interactions, heavy metal-plant interactions, complex material microstructures, and nanomaterials, all of which are important components or processes in the environment. Basic understanding of environmental materials and processes at the molecular scale is essential for risk assessment and management, and reduction of environmental pollutants at field, landscape, and global scales. One of the main purposes of this report is to illustrate the role of synchrotron radiation (SR)-based studies in environmental science and related fields and their impact on environmental problems of importance to society. A major driving force for MES research is the need to characterize, treat, and/or dispose of vast quantities of contaminated materials, including groundwater, sediments, and soils, and to process wastes, at an estimated cost exceeding 150 billion dollars through 2070. A major component of this problem derives from high-level nuclear waste. Other significant components come from mining and industrial wastes, atmospheric pollutants derived from fossil fuel consumption, agricultural pesticides and fertilizers, and the pollution problems associated with animal waste run-off, all of which have major impacts on human health and welfare. Addressing these problems requires the development of new characterization and processing technologies--efforts that require information on the chemical speciation of heavy metals, radionuclides, and xenobiotic organic compounds and their reactions with

  17. Using Domestic and Free-Ranging Arctic Canid Models for Environmental Molecular Toxicology Research.

    PubMed

    Harley, John R; Bammler, Theo K; Farin, Federico M; Beyer, Richard P; Kavanagh, Terrance J; Dunlap, Kriya L; Knott, Katrina K; Ylitalo, Gina M; O'Hara, Todd M

    2016-02-16

    The use of sentinel species for population and ecosystem health assessments has been advocated as part of a One Health perspective. The Arctic is experiencing rapid change, including climate and environmental shifts, as well as increased resource development, which will alter exposure of biota to environmental agents of disease. Arctic canid species have wide geographic ranges and feeding ecologies and are often exposed to high concentrations of both terrestrial and marine-based contaminants. The domestic dog (Canis lupus familiaris) has been used in biomedical research for a number of years and has been advocated as a sentinel for human health due to its proximity to humans and, in some instances, similar diet. Exploiting the potential of molecular tools for describing the toxicogenomics of Arctic canids is critical for their development as biomedical models as well as environmental sentinels. Here, we present three approaches analyzing toxicogenomics of Arctic contaminants in both domestic and free-ranging canids (Arctic fox, Vulpes lagopus). We describe a number of confounding variables that must be addressed when conducting toxicogenomics studies in canid and other mammalian models. The ability for canids to act as models for Arctic molecular toxicology research is unique and significant for advancing our understanding and expanding the tool box for assessing the changing landscape of environmental agents of disease in the Arctic. PMID:26730740

  18. Discovery of characteristic molecular signatures for the simultaneous prediction and detection of environmental pollutants.

    PubMed

    Song, Mi-Kyung; Choi, Han-Seam; Park, Yong-Keun; Ryu, Jae-Chun

    2014-02-01

    Gene expression data may be very promising for the classification of toxicant types, but the development and application of transcriptomic-based gene classifiers for environmental toxicological applications are lacking compared to the biomedical sciences. Also, simultaneous classification across a set of toxicant types has not been investigated extensively. In the present study, we determined the transcriptomic response to three types of ubiquitous toxicants exposure in two types of human cell lines (HepG2 and HL-60), which are useful in vitro human model for evaluation of toxic substances that may affect human hepatotoxicity (e.g., polycyclic aromatic hydrocarbon [PAH] and persistent organic pollutant [POP]) and human leukemic myelopoietic proliferation (e.g., volatile organic compound [VOC]). The findings demonstrate characteristic molecular signatures that facilitated discrimination and prediction of the toxicant type. To evaluate changes in gene expression levels after exposure to environmental toxicants, we utilized 18 chemical substances; nine PAH toxicants, six VOC toxicants, and three POP toxicants. Unsupervised gene expression analysis resulted in a characteristic molecular signature for each toxicant group, and combination analysis of two separate multi-classifications indicated 265 genes as surrogate markers for predicting each group of toxicants with 100 % accuracy. Our results suggest that these expression signatures can be used as predictable and discernible surrogate markers for detection and prediction of environmental toxicant exposure. Furthermore, this approach could easily be extended to screening for other types of environmental toxicants. PMID:24197968

  19. Water microbiology. Bacterial pathogens and water.

    PubMed

    Cabral, João P S

    2010-10-01

    Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water-cholera, typhoid fever and bacillary dysentery-is presented, focusing on the biology and ecology of the causal agents and on the diseases' characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters. PMID:21139855

  20. Water Microbiology. Bacterial Pathogens and Water

    PubMed Central

    Cabral, João P. S.

    2010-01-01

    Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water—cholera, typhoid fever and bacillary dysentery—is presented, focusing on the biology and ecology of the causal agents and on the diseases’ characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters. PMID:21139855

  1. Control of metallic corrosion through microbiological route.

    PubMed

    Maruthamuthu, S; Ponmariappan, S; Mohanan, S; Palaniswamy, N; Palaniappan, R; Rengaswamy, N S

    2003-09-01

    Involvement of biofilm or microorganisms in corrosion processes is widely acknowledged. Although majority of the studies on microbiologically induced corrosion (MIC) have concentrated on aerobic/anaerobic bacteria. There are numerous aerobic bacteria, which could hinder the corrosion process. The microbiologically produced exopolymers provide the structural frame work for the biofilm. These polymers combine with dissolved metal ions and form organometallic complexes. Generally heterotrophic bacteria contribute to three major processes: (i) synthesis of polymers (ii) accumulation of reserve materials like poly-beta-hydroxy butrate (iii) production of high molecular weight extracellular polysaccharides. Poly-beta-hydroxy butyrate is a polymer of D(-)beta-hydroxy butrate and has a molecular weight between 60,000 and 2,50,000. Some extracellular polymers also have higher molecular weights. It seems that higher molecular weight polymer acts as biocoating. In the present review, role of biochemistry on corrosion inhibition and possibilities of corrosion inhibition by various microbes are discussed. The role of bacteria on current demand during cathodic protection is also debated. In addition, some of the significant contributions made by CECRI in this promising area are highlighted. PMID:15242295

  2. Microbiologically active nanocomposite media

    NASA Astrophysics Data System (ADS)

    Petranovskii, Vitalii; Panina, Lyudmila; Bogomolova, Eugenia; Belostotskaya, Galina

    2003-07-01

    The most recent approach to the development of novel antimicrobial and antifungal agents is based on the application of synthetic and natural zeolites, because zeolites are known to be the carrier and slow releaser of the heavy metals with olygodynamic properties. The microbiological activity of the ion-exchanged zeolites is attributed to the ionic state of the metal sreleased from the zeolites by ion re-exchange. In the present work we used low cost natural clinoptilolite (Cli) as a substrate for copper and silver in different states. The state of oxidation of the exchanged metal in zeolite with supported Cu and Ag species (in the form of cations, small clusters, sub-coloidal particles, large particles) in order to fit them to fulfill the following criteria: to demonstrate their high protective abilities against fungi and long-term stability. The study of structure of samples with XRD, UV-visible spectroscopy, FTIR, their stability with temperature and during storage was carried out for obtaining the correct correlation with microbiological activity.

  3. Microbiology of chronic rhinosinusitis.

    PubMed

    Brook, I

    2016-07-01

    Most sinus infections are viral and only a small percentage develop bacterial infection. Rhino-, influenza, and para-influenza viruses are the most frequent viral causes of sinusitis. The most common bacterial isolates from children and adult patients with community-acquired acute bacterial sinusitis are Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pyogenes. Staphylococcus aureus and anaerobic organisms (Prevotella and Porphyromonas, Fusobacterium, and Peptostreptococcus spp.) are the commonest isolates in chronic rhinosinusitis (CRS). Aerobic and anaerobic beta lactamase-producing bacteria (BLPB) were recovered from over a third of these patients. Methicillin-resistant S. aureus (MRSA) accounted for over 60 % of S. aureus isolates. Pseudomonas aeruginosa and other aerobic and facultative Gram-negative rods are frequently recovered in nosocomial sinusitis, the immunocompromised host, individuals with human immunodeficiency virus infection, and in cystic fibrosis. The CRS infection evolves the formation of a biofilm that might play a significant role in the pathogenesis and persistence of CRS. The microbiology of sinusitis is influenced by previous antimicrobial therapy, vaccinations, and the presence of normal flora capable of interfering with the growth of pathogens. Recognition of the unique microbiology of CRS and their antimicrobial susceptibility is of great importance when selecting antimicrobial therapy. PMID:27086363

  4. Recent advances in silage microbiology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in our understanding of silage microbiology are reviewed. The ability to extract microbial DNA from silages, amplify portions of DNA, and use the amplified regions to identify strains of microorganisms is at the core of the changes occurring recently in silage microbiology. These dev...

  5. Impact of sampling depth and plant species on local environmental conditions, microbiological parameters and bacterial composition in a mercury contaminated salt marsh.

    PubMed

    Cleary, D F R; Oliveira, V; Gomes, N C M; Pereira, A; Henriques, I; Marques, B; Almeida, A; Cunha, A; Correia, A; Lillebø, A I

    2012-02-01

    We compare the environmental characteristics and bacterial communities associated with two rushes, Juncus maritimus and Bolboschoenus maritimus, and adjacent unvegetated habitat in a salt marsh subjected to historical mercury pollution. Mercury content was higher in vegetated than unvegetated habitat and increased with sampling depth. There was also a significant relationship between mercury concentration and bacterial composition. Habitat (Juncus, Bolboschoenus or unvegetated), sample depth, and the interaction between both, however, explained most of the variation in composition (~70%). Variation in composition with depth was most prominent for the unvegetated habitat, followed by Juncus, but more constrained for Bolboschoenus habitat. This constraint may be indicative of a strong plant-microbe ecophysiological adaptation. Vegetated habitat contained distinct bacterial communities associated with higher potential activity of aminopeptidase, β-glucosidase and arylsulphatase and incorporation rates of (14)C-glucose and (14)C-acetate. Communities in unvegetated habitat were, in contrast, associated with both higher pH and proportion of sulphate reducing bacteria. PMID:22177286

  6. Evolution across the Curriculum: Microbiology

    PubMed Central

    Burmeister, Alita R.; Smith, James J.

    2016-01-01

    An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives. Journal of Microbiology & Biology Education PMID:27158306

  7. Evolution across the Curriculum: Microbiology.

    PubMed

    Burmeister, Alita R; Smith, James J

    2016-05-01

    An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives. Journal of Microbiology & Biology Education. PMID:27158306

  8. Regulation of migration in Mythimna separata (Walker) in China: A review integrating environmental, physiological, hormonal, genetic, and molecular factors

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Each year the oriental armyworm, Mythimna separata, undertakes a seasonal, long-distance, multigeneration roundtrip migration between Southern and Northern China. The developmental decision to migrate is facultative and controlled by environmental, physiological, hormonal, genetic, and molecular fac...

  9. Treatment bed microbiological control

    NASA Technical Reports Server (NTRS)

    Janauer, Gilbert E.; Fitzpatrick, Timothy W.; Kril, Michael B.; Wilber, Georgia A.; Sauer, Richard L.

    1987-01-01

    The effects of microbial fouling on treatment bed (TB) performance are being studied. Fouling of activated carbon (AC) and ion exchange resins (IEX) by live and devitalized bacteria can cause decreased capacity for selected sorbates with AC and IEX TB. More data are needed on organic species removal in the trace region of solute sorption isotherms. TB colonization was prevented by nonclassical chemical disinfectant compositions (quaternary ammonium resins) applied in suitable configurations. Recently, the protection of carbon beds via direct disinfectant impregnation has shown promise. Effects (of impregnation) upon bed sorption/removal characteristics are to be studied with representative contaminants. The potential need to remove solutes added or produced during water disinfection and/or TB microbiological control must be investigated.

  10. Microbiology of sinusitis.

    PubMed

    Brook, Itzhak

    2011-03-01

    Most sinus infections are viral, and only a small proportion develops a secondary bacterial infection. Rhinoviruses, influenza viruses, and parainfluenza viruses are the most common causes of sinusitis. The most common bacteria isolated from pediatric and adult patients with community-acquired acute purulent sinusitis are Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pyogenes. Staphylococcus aureus and anaerobic bacteria (Prevotella and Porphyromonas, Fusobacterium and Peptostreptococcus spp.) are the main isolates in chronic sinusitis. Pseudomonas aeruginosa and other aerobic and facultative gram-negative rods are commonly isolated from patients with nosocomial sinusitis, the immunocompromised host, those with HIV infection, and in cystic fibrosis. Fungi and Pseudomonas aeruginosa are the most common isolates in neutropenic patients. The microbiology of sinusitis is influenced by the previous antimicrobial therapy, vaccinations, and the presence of normal flora capable of interfering with the growth of pathogens. PMID:21364226

  11. Charge Transport in Molecular Junctions: A Study of Level-Alignment, Thermoelectric Properties, and Environmental Effects

    NASA Astrophysics Data System (ADS)

    Kotiuga, Michele

    Here, we use and develop first-principles methods based on density functional theory (DFT) and beyond to understand and predict charge transport phenomena in the novel class of nanostructured devices: molecular junctions. Molecular junctions, individual molecules contacted to two metallic leads, which can be systematically altered by modifying the chemistry of each component, serve as test beds for the study of transport at the nanoscale. To date, various experimental methods have been designed to reliably assemble and measure transport properties of molecular junctions. Furthermore, theoretical methods built on DFT designed to yield quantitative agreement with these experiments for certain classes of molecular junctions have been developed. In order to gain insight into a broader range of molecular junctions and environmental effects associated with the surrounding solution, this dissertation will employ, explore and extend first-principles DFT calculations coupled with approximate self-energy corrections known to yield quantitative agreement with experiments for certain classes of molecular junctions. To start we examine molecular junctions in which the molecule is strongly hybridized with the leads: a challenging limit for the existing methodology. Using a physically motivated tight-binding model, we find that the experimental trends observed for such molecules can be explained by the presence of a so-called "gateway" state associated with the chemical bond that bridges the molecule and the lead. We discuss the ingredients of a self-energy corrected DFT based approach to quantitatively predict conductance in the presence of these hybridization effects. We also develop and apply an approach to account for the surrounding environment on the conductance, which has been predominantly ignored in past transport calculations due to computational complexity. Many experiments are performed in a solution of non-conducting molecules; far from benign, this solution is known

  12. High molecular weight bioemulsifiers, main properties and potential environmental and biomedical applications.

    PubMed

    Mnif, Inès; Ghribi, Dhouha

    2015-05-01

    High molecular weight bioemulsifiers are amphipathic polysaccharides, proteins, lipopolysaccharides, lipoproteins, or complex mixtures of these biopolymers, produced by a wide variety of microorganisms. They are characterized by highly structural diversity and have the ability to decrease the surface and interfacial tension at the surface and interface respectively and/or emulsify hydrophobic compounds. Emulsan, fatty acids, phospholipids, neutral lipids, exopolysaccharides, vesicles and fimbriae are among the most popular high molecular weight bioemulsifiers. They have great physic-chemical properties like tolerance to extreme conditions of pH, temperature and salinity, low toxicity and biodegradability. Owing their emulsion forming and breaking capacities, solubilization, mobilization and dispersion activities and their viscosity reduction activity; they possess great environmental application as enhancer of hydrocarbon biodegradation and for microbial enhanced oil recovery. Besides, they are applied in biomedical fields for their antimicrobial and anti-adhesive activities and involvement in immune responses. PMID:25739564

  13. Molecular biomarkers to assess health risks due to environmental contaminants exposure.

    PubMed

    Poblete-Naredo, Irais; Albores, Arnulfo

    2016-01-01

    Biomarkers, or bioindicators, are metric tools that, when compared with reference values, allow specialists to perform risk assessments and provide objective information to decision makers to design effective strategies to solve health or environmental problems by efficiently using the resources assigned. Health risk assessment is a multidisciplinary exercise, and molecular biology is a discipline that greatly contributes to these evaluations because the genome, transcriptome, proteome and metabolome could be affected by xenobiotics causing measurable changes that might be useful biomarkers. Such changes may greatly depend on individual genetic background; therefore, the polymorphic distribution of exposed populations becomes an essential feature for adequate data interpretation. The aim of this paper is to offer an up-to-date review of the role of different molecular biomarkers in health risk assessments. PMID:27622493

  14. Technical Tension Between Achieving Particulate and Molecular Organic Environmental Cleanliness: Data from Astromaterial Curation Laboratories

    NASA Technical Reports Server (NTRS)

    Allton, J. H.; Burkett, P. J.

    2011-01-01

    NASA Johnson Space Center operates clean curation facilities for Apollo lunar, Antarctic meteorite, stratospheric cosmic dust, Stardust comet and Genesis solar wind samples. Each of these collections is curated separately due unique requirements. The purpose of this abstract is to highlight the technical tensions between providing particulate cleanliness and molecular cleanliness, illustrated using data from curation laboratories. Strict control of three components are required for curating samples cleanly: a clean environment; clean containers and tools that touch samples; and use of non-shedding materials of cleanable chemistry and smooth surface finish. This abstract focuses on environmental cleanliness and the technical tension between achieving particulate and molecular cleanliness. An environment in which a sample is manipulated or stored can be a room, an enclosed glovebox (or robotic isolation chamber) or an individual sample container.

  15. Total internal reflection ellipsometry and SPR detection of low molecular weight environmental toxins

    NASA Astrophysics Data System (ADS)

    Nabok, A. V.; Tsargorodskaya, A.; Hassan, A. K.; Starodub, N. F.

    2005-06-01

    The environmental toxins, such as herbicides simazine and atrazine, and T2 mycotoxin were registered with the optical methods of surface plasmon resonance (SPR) and recently developed total internal reflection ellipsometry (TIRE). The immune assay approach was exploited for in situ registration of the above low molecular weight toxins with specific antibodies immobilised onto the gold surface via (poly)allylamine hydrochloride layer using electrostatic self-assembly (ESA) technique. The comparison of two methods of SPR and TIRE shows a higher sensitivity of the latter.

  16. Pulmonary fibrosis in response to environmental cues and molecular targets involved in its pathogenesis.

    PubMed

    Yoshida, Toshinori; Ohnuma, Aya; Horiuchi, Haruka; Harada, Takanori

    2011-03-01

    Chronic lung injury resulting from a variety of different causes is frequently associated with the develop ment of pulmonary fibrosis in humans. Although the etiology of pulmonary fibrosis is generally unknown, several sources of evidence support the hypothesis that a number of environmental and occupational agents play an etiologic role in the pathogenesis of this disease. The agents discussed in this review include beryllium, nylon flock, textile printing aerosols, polyvinyl chloride and didecyldimethylammonium chloride. The authors also describe a variety of animal models, including genetically modified mice, in order to investigate the molecular mechanism of pulmonary fibrosis, focusing on chemokine receptors, regulatory T cells and transforming growth factor-β and bone morphogenetic protein signaling. Overall, we propose the concept of toxicological pulmonary fibrosis as a lung disease induced in response to environmental cues. PMID:22272040

  17. Pulmonary Fibrosis in Response to Environmental Cues and Molecular Targets Involved in Its Pathogenesis

    PubMed Central

    Yoshida, Toshinori; Ohnuma, Aya; Horiuchi, Haruka; Harada, Takanori

    2011-01-01

    Chronic lung injury resulting from a variety of different causes is frequently associated with the develop ment of pulmonary fibrosis in humans. Although the etiology of pulmonary fibrosis is generally unknown, several sources of evidence support the hypothesis that a number of environmental and occupational agents play an etiologic role in the pathogenesis of this disease. The agents discussed in this review include beryllium, nylon flock, textile printing aerosols, polyvinyl chloride and didecyldimethylammonium chloride. The authors also describe a variety of animal models, including genetically modified mice, in order to investigate the molecular mechanism of pulmonary fibrosis, focusing on chemokine receptors, regulatory T cells and transforming growth factor-β and bone morphogenetic protein signaling. Overall, we propose the concept of toxicological pulmonary fibrosis as a lung disease induced in response to environmental cues. PMID:22272040

  18. Meta-analysis in microbiology.

    PubMed

    Pabalan, N; Jarjanazi, H; Steiner, T S

    2014-01-01

    The use of meta-analysis in microbiology may facilitate decision-making that impacts public health policy. Directed at clinicians and researchers in microbiology, this review outlines the steps in performing this statistical technique, addresses its biases and describes its value in this discipline. The survey to estimate extent of the use of meta-analyses in microbiology shows the remarkable growth in the use of this research methodology, from a minimal Asian output to a level comparable with those of Europe and North America in the last 7 years. PMID:25008812

  19. Investigation of the molecular epidemiology of Acinetobacter baumannii isolated from patients and environmental contamination.

    PubMed

    Ying, Chunmei; Li, Yongli; Wang, Yaping; Zheng, Bing; Yang, Chengde

    2015-09-01

    The objective of this work was to investigate correlations between Acinetobacter baumannii isolates from neurosurgical intensive care unit patients and its environment. This is a prospective, observational study. The minimal inhibitory concentrations of antimicrobial agents against 27 clinical and 28 environmental isolates were determined by the agar dilution method. Molecular genotyping was performed by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of carbapenemase and metallo-β-lactamase genes were analyzed by specific PCRs and DNA sequencing. From the clinical A. baumannii isolates, 25.9% were found resistant to minocycline, 51.9% to cefoperazone-sulbactam, 59.3% to imipenem and 70% resistant to other antimicrobial agents. Environmental isolates were more sensitive compared with clinical isolates (P<0.05). Twenty-seven clinical isolates comprised three ERIC-PCR genotypes, four major PFGE pulsotypes and five distinct MLST sequence types (STs) (ST208, ST368, ST191, ST195, ST540), all belonging to CC92 with only one locus (gpi) difference among them. Twenty-eight environmental isolates showed more diverse genetic types than clinical isolates and comprised six ERIC-PCR groups, nine PFGE groups and two main STs (ST208, ST229). Four clinical and 15 environmental isolates could not be identified by MLST and were assigned to non-clonal STs. We identified the presence of the blaOXA-23 carbapenemase encoding gene in most of the clinical (21/27) but fewer in the environmental isolates (3/28). The A. baumannii strains isolated from patients were genetically similar to the environmental strains, with CC92 members as the major fraction but with different antibiotic susceptibilities. PMID:25873322

  20. Environmental effects and aquatic organisms: investigations of molecular mechanisms of carcinogenesis.

    PubMed Central

    Van Beneden, R J

    1997-01-01

    Cancers of the reproductive system are among the leading causes of mortality in women in the United States. While both genetic and environmental factors have been implicated in their etiology, the extent of the contribution of environmental factors to human diseases remains controversial. To better address the role of environmental exposures in cancer etiology, there has been an increasing focus on the development of nontraditional, environmentally relevant models. Our research involves the development of one such model. Gonadal tumors have been described in the softshell clam (Mya arenaria) in Maine and the hardshell clam (Mercenaria spp.) from Florida. Prevalence of these tumors is as high as 40% in some populations in eastern Maine and 60% in some areas along the Indian River in Florida. The average tumor prevalence in Maine and Florida is approximately 20 and 11%, respectively. An association has been suggested between the use of herbicides and the incidence of gonadal tumors in the softshell clam in Maine. The role of environmental exposures in the development of the tumors in Mercenaria in Florida is unknown; however, there is evidence that genetic factors may contribute to its etiology. Epidemiologic studies of human populations in these same areas show a higher than average mortality rate due to cancers of the reproductive system in women, including both ovarian and breast cancer. The relationship, if any, among these observations is unknown. Our studies on the molecular basis of this disease in clams may provide additional information on environmental exposures and their possible link to cancer in clams and other organisms, including humans. Images Figure 1. A Figure 1. B PMID:9168012

  1. Physiological and Molecular Aspects of Tolerance to Environmental Constraints in Grain and Forage Legumes.

    PubMed

    Adnane, Bargaz; Mainassara, Zaman-Allah; Mohamed, Farissi; Mohamed, Lazali; Jean-Jacques, Drevon; Rim, Maougal T; Georg, Carlsson

    2015-01-01

    Despite the agronomical and environmental advantages of the cultivation of legumes, their production is limited by various environmental constraints such as water or nutrient limitation, frost or heat stress and soil salinity, which may be the result of pedoclimatic conditions, intensive use of agricultural lands, decline in soil fertility and environmental degradation. The development of more sustainable agroecosystems that are resilient to environmental constraints will therefore require better understanding of the key mechanisms underlying plant tolerance to abiotic constraints. This review provides highlights of legume tolerance to abiotic constraints with a focus on soil nutrient deficiencies, drought, and salinity. More specifically, recent advances in the physiological and molecular levels of the adaptation of grain and forage legumes to abiotic constraints are discussed. Such adaptation involves complex multigene controlled-traits which also involve multiple sub-traits that are likely regulated under the control of a number of candidate genes. This multi-genetic control of tolerance traits might also be multifunctional, with extended action in response to a number of abiotic constraints. Thus, concrete efforts are required to breed for multifunctional candidate genes in order to boost plant stability under various abiotic constraints. PMID:26287163

  2. Isolation and identification of Salmonella spp. in environmental water by molecular technology in Taiwan

    NASA Astrophysics Data System (ADS)

    Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Shen, Tsung Yu; Kao, Po Min; Shen, Shu Min; Chen, Jung Sheng

    2013-04-01

    Salmonella spp. is one of the most important causal agents of waterborne diseases. The taxonomy of Salmonella is very complicated and its genus comprises more than 2,500 serotypes. The detection of Salmonella in environmental water samples by routines culture methods using selective media and characterization of suspicious colonies based on biochemical tests and serological assay are generally time consuming. To overcome this drawback, it is desirable to use effective method which provides a higher discrimination and more rapid identification about Salmonella in environmental water. The aim of this study is to investigate the occurrence of Salmonella using molecular technology and to identify the serovars of Salmonella isolates from 70 environmental water samples in Taiwan. The analytical procedures include membrane filtration, non-selective pre-enrichment, selective enrichment of Salmonella. After that, we isolated Salmonella strains by selective culture plates. Both selective enrichment and culture plates were detected by Polymerase Chain Reaction (PCR). Finally, the serovars of Salmonella were confirmed by using biochemical tests and serological assay. In this study, 15 water samples (21.4%) were identified as Salmonella by PCR. The positive water samples will further identify their serotypes by culture method. The presence of Salmonella in environmental water indicates the possibility of waterborne transmission in drinking watershed. Consequently, the authorities need to provide sufficient source protection and to maintain the system for disease prevention. Keywords: Salmonella spp., serological assay, PCR

  3. Molecular epidemiology in environmental health: the potential of tumor suppressor gene p53 as a biomarker.

    PubMed Central

    Semenza, J C; Weasel, L H

    1997-01-01

    One of the challenges in environmental health is to attribute a certain health effect to a specific environmental exposure and to establish a cause-effect relationship. Molecular epidemiology offers a new approach to addressing these challenges. Mutations in the tumor suppressor gene p53 can shed light on past environmental exposure, and carcinogenic agents and doses can be distinguished on the basis of mutational spectra and frequency. Mutations in p53 have successfully been used to establish links between dietary aflatoxin exposure and liver cancer, exposure to ultraviolet light and skin cancer, smoking and cancers of the lung and bladder, and vinyl chloride exposure and liver cancer. In lung cancer, carcinogens from tobacco smoke have been shown to form adducts with DNA. The location of these adducts correlates with those positions in the p53 gene that are mutated in lung cancer, confirming a direct etiologic link between exposure and disease. Recent investigations have also explored the use of p53 as a susceptibility marker for cancer. Furthermore, studies in genetic toxicology have taken advantage of animals transgenic for p53 to screen for carcinogens in vivo. In this review, we summarize recent developments in p53 biomarker research and illustrate applications to environmental health. PMID:9114284

  4. Physiological and Molecular Aspects of Tolerance to Environmental Constraints in Grain and Forage Legumes

    PubMed Central

    Bargaz, Adnane; Zaman-Allah, Mainassara; Farissi, Mohamed; Lazali, Mohamed; Drevon, Jean-Jacques; Maougal, Rim T.; Carlsson, Georg

    2015-01-01

    Despite the agronomical and environmental advantages of the cultivation of legumes, their production is limited by various environmental constraints such as water or nutrient limitation, frost or heat stress and soil salinity, which may be the result of pedoclimatic conditions, intensive use of agricultural lands, decline in soil fertility and environmental degradation. The development of more sustainable agroecosystems that are resilient to environmental constraints will therefore require better understanding of the key mechanisms underlying plant tolerance to abiotic constraints. This review provides highlights of legume tolerance to abiotic constraints with a focus on soil nutrient deficiencies, drought, and salinity. More specifically, recent advances in the physiological and molecular levels of the adaptation of grain and forage legumes to abiotic constraints are discussed. Such adaptation involves complex multigene controlled-traits which also involve multiple sub-traits that are likely regulated under the control of a number of candidate genes. This multi-genetic control of tolerance traits might also be multifunctional, with extended action in response to a number of abiotic constraints. Thus, concrete efforts are required to breed for multifunctional candidate genes in order to boost plant stability under various abiotic constraints. PMID:26287163

  5. MICROBIOLOGY: METHODOLOGY AND QUALITY ASSURANCE

    EPA Science Inventory

    Research on the microbiological quality of water continues to concentrate on improved methods for the detection, enumeration, and identification of pollution indicators, pathogens, and other microbial groups. A complete handbook of basic laboratory procedures, replete with resour...

  6. Teaching microbiology to undergraduate students in the humanities and the social sciences.

    PubMed

    Oren, Aharon

    2015-10-01

    This paper summarizes my experiences teaching a 28-hour course on the bacterial world for undergraduate students in the humanities and the social sciences at the Hebrew University of Jerusalem. This course was offered in the framework of a program in which students must obtain credit points for courses offered by other faculties to broaden their education. Most students had little biology in high school and had never been exposed to the basics of chemistry. Using a historical approach, highlighting the work of pioneers such as van Leeuwenhoek, Koch, Fleming, Pasteur, Winogradsky and Woese, I covered a broad area of general, medical, environmental and evolutionary microbiology. The lectures included basic concepts of organic and inorganic chemistry necessary to understand the principles of fermentations and chemoautotrophy, and basic molecular biology to explain biotechnology using transgenic microorganisms and molecular phylogeny. Teaching the basics of microbiology to intelligent students lacking any background in the natural sciences was a rewarding experience. Some students complained that, in spite of my efforts, basic concepts of chemistry remained beyond their understanding. But overall the students' evaluation showed that the course had achieved its goal. PMID:26363013

  7. The environmental and molecular sciences laboratory project: Continuous evolution in leadership

    SciTech Connect

    Knutson, D.E.; McClusky, J.K.

    1995-09-01

    The United States is embarking on an environmental cleanup effort that dwarfs previous scientific enterprise. Using current best available technology, the projected costs of cleaning up the tens of abounds of toxic waste sites, including DOE sites, is estimated to exceed one trillion dollars. That level of expenditure contains no guarantee that the sites can be restored to their original condition, and no consensus on ``how clean is clean enough.`` ``Ultimately, the scientific challenge is to determine as accurately as possible each term in the path that links the source of the contaminant with the particular biological end points or health effects and to understand the mechanisms that connect them. However, the present state of scientific knowledge regarding the effects of exogenous chemicals on human biology is very limited. Understanding the connections at the molecular level is, at best, a blurred picture and often a black box.`` Long term environmental research at the molecular level is needed to resolve the concerns, and form the building blocks for a structure of cost effective process improvement and regulatory reform.

  8. Molecular-Level Investigations of Nucleation Mechanisms and Kinetics of Formation of Environmental Nanoparticles

    SciTech Connect

    Young-Shin Jun; Glenn A. Waychunas

    2007-04-19

    Environmental nanoparticles are often poorly-crystalline or metastable structures, whose kinetics of formation and growth are poorly understood. Further, the sorption or growth of nanoparticles on mineral surfaces may control the mineral surface's reactivity and modify its ability to influence contaminant transport. Due to the characteristic length scale, a holistic understanding of the nucleation mechanisms and kinetics of nanoparticle formation on mineral surfaces is difficult to achieve with traditional methodology. In this work, our intent is to determine the molecular nature of nucleation on surfaces, the kinetics of surface nucleation and growth, and the effect of crystal surface topology using new synchrotron-based techniques. We have approached these objectives by: (1) combining state-of-the-art crystal-truncation rod diffraction (CTR) and grazing incidence x-ray absorption fine structure spectroscopy (GIXAS) techniques to investigate the three-dimensional molecular-scale geometry of silicate monomer sorption on the r-plane of hematite; and (2) developing a new grazing-incidence small angle x-ray scattering (GISAXS) setup at SSRL (0.08 nm{sup -1} < q < 8 nm{sup -1}) to explore the initial development of environmental nanoparticles on various mineral surfaces. This study also includes complementary techniques such as atomic force microscopy (AFM), bulk SAXS, dynamic light scattering (DLS), XRD, and TEM.

  9. Low-Volatility Model Demonstrates Humidity Affects Environmental Toxin Deposition on Plastics at a Molecular Level.

    PubMed

    Hankett, Jeanne M; Collin, William R; Yang, Pei; Chen, Zhan; Duhaime, Melissa

    2016-02-01

    Despite the ever-increasing prevalence of plastic debris and endocrine disrupting toxins in aquatic ecosystems, few studies describe their interactions in freshwater environments. We present a model system to investigate the deposition/desorption behaviors of low-volatility lake ecosystem toxins on microplastics in situ and in real time. Molecular interactions of gas-phase nonylphenols (NPs) with the surfaces of two common plastics, poly(styrene) and poly(ethylene terephthalate), were studied using quartz crystal microbalance and sum frequency generation vibrational spectroscopy. NP point sources were generated under two model environments: plastic on land and plastic on a freshwater surface. We found the headspace above calm water provides an excellent environment for NP deposition and demonstrate significant NP deposition on plastic within minutes at relevant concentrations. Further, NP deposits and orders differently on both plastics under humid versus dry environments. We attributed the unique deposition behaviors to surface energy changes from increased water content during the humid deposition. Lastly, nanograms of NP remained on microplastic surfaces hours after initial NP introduction and agitating conditions, illustrating feasibility for plastic-bound NPs to interact with biota and surrounding matter. Our model studies reveal important interactions between low-volatility environmental toxins and microplastics and hold potential to correlate the environmental fate of endocrine disrupting toxins in the Great Lakes with molecular behaviors. PMID:26752114

  10. Decipher the Molecular Response of Plant Single Cell Types to Environmental Stresses

    DOE PAGESBeta

    Nourbakhsh-Rey, Mehrnoush; Libault, Marc

    2016-01-01

    The analysis of the molecular response of entire plants or organs to environmental stresses suffers from the cellular complexity of the samples used. Specifically, this cellular complexity masks cell-specific responses to environmental stresses and logically leads to the dilution of the molecular changes occurring in each cell type composing the tissue/organ/plant in response to the stress. Therefore, to generate a more accurate picture of these responses, scientists are focusing on plant single cell type approaches. Several cell types are now considered as models such as the pollen, the trichomes, the cotton fiber, various root cell types including the root hairmore » cell, and the guard cell of stomata. Among them, several have been used to characterize plant response to abiotic and biotic stresses. Lastly, in this review, we are describing the various -omic studies performed on these different plant single cell type models to better understand plant cell response to biotic and abiotic stresses.« less

  11. Vadose zone microbiology

    SciTech Connect

    Kieft, Thomas L.; Brockman, Fred J.

    2001-01-17

    The vadose zone is defined as the portion of the terrestrial subsurface that extends from the land surface downward to the water table. As such, it comprises the surface soil (the rooting zone), the underlying subsoil, and the capillary fringe that directly overlies the water table. The unsaturated zone between the rooting zone and the capillary fringe is termed the "intermediate zone" (Chapelle, 1993). The vadose zone has also been defined as the unsaturated zone, since the sediment pores and/or rock fractures are generally not completely water filled, but instead contain both water and air. The latter characteristic results in the term "zone of aeration" to describe the vadose zone. The terms "vadose zone," "unsaturated zone", and "zone of aeration" are nearly synonymous, except that the vadose zone may contain regions of perched water that are actually saturated. The term "subsoil" has also been used for studies of shallow areas of the subsurface immediately below the rooting zone. This review focuses almost exclusively on the unsaturated region beneath the soil layer since there is already an extensive body of literature on surface soil microbial communities and process, e.g., Paul and Clark (1989), Metting (1993), Richter and Markowitz, (1995), and Sylvia et al. (1998); whereas the deeper strata of the unsaturated zone have only recently come under scrutiny for their microbiological properties.

  12. Microbiological methodology in astrobiology

    NASA Astrophysics Data System (ADS)

    Abyzov, S. S.; Gerasimenko, L. M.; Hoover, R. B.; Mitskevich, I. N.; Mulyukin, A. L.; Poglazova, M. N.; Rozanov, A. Y.

    2005-09-01

    Searching for life in astromaterials to be delivered from the future missions to extraterrestrial bodies is undoubtedly related to studies of the properties and signatures of living microbial cells and microfossils on Earth. The Antarctic glacier and Earth permafrost habitats, where living microbial cells preserved viability for millennia years due to entering the anabiotic state, are often regarded as terrestrial analogs of Martian polar subsurface layers. For the future findings of viable microorganisms in samples from extraterrestrial objects, it is important to use a combined methodology that includes classical microbiological methods, plating onto nutrient media, direct epifluorescence and electron microscopy examinations, detection of the elemental composition of cells, PCR and FISH methods. Of great importance is to ensure authenticity of microorganisms (if any in studied samples) and to standardize the protocols used to minimize a risk of external contamination. Although the convincing evidence of extraterrestrial microbial life will may come from the discovery of living cells in astromaterials, biomorphs and microfossils must also be regarded as a target in search of life evidence bearing in mind a scenario that living microorganisms had not been preserved and underwent mineralization. Regarding the vital importance of distinguishing between biogenic and abiogenic signatures and between living and fossil microorganisms in analyzed samples, it is worthwhile to use previously developed approaches based on electron microscopy examinations and analysis of elemental composition of biomorphs in situ.

  13. Superresolution microscopy for microbiology

    PubMed Central

    Coltharp, Carla; Xiao, Jie

    2014-01-01

    Summary This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of super-resolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate super-resolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments. PMID:22947061

  14. IPMP 2013 - A comprehensive data analysis tool for predictive microbiology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Predictive microbiology is an area of applied research in food science that uses mathematical models to predict the changes in the population of pathogenic or spoilage microorganisms in foods undergoing complex environmental changes during processing, transportation, distribution, and storage. It f...

  15. Critical Readiness Review EHS Water Quality and Microbiology

    NASA Technical Reports Server (NTRS)

    Woo, Cindy

    2010-01-01

    Presentation reviews the status in reference to the Environmental, Health and Safety (EHS) of the water quality and microbiology for the International Space Station. It includes information about crew training, hardware delivery, and those items that will be returned for study.

  16. Molecular Typing of Environmental and Clinical Strains of Vibrio vulnificus Isolated in the Northeastern USA

    PubMed Central

    Reynaud, Yann; Pitchford, Steven; De Decker, Sophie; Wikfors, Gary H.; Brown, Christopher L.

    2013-01-01

    Vibrio vulnificus is a ubiquitous marine bacterium that is responsible for infections and some seafood-related illnesses and deaths in the United States, mainly in individuals with compromised health status in the Gulf of Mexico region. Most phylogenetic studies focus on V. vulnificus strains isolated in the southern United States, but almost no genetic data are available on northeastern bacterial isolates of clinical or environmental origin. Our goal in this study was to examine the genetic diversity of environmental strains isolated from commercially-produced oysters and in clinical strains of known pathogenicity in northeastern United States. We conducted analyses of a total of eighty-three strains of V. vulnificus, including 18 clinical strains known to be pathogenic. A polyphasic, molecular-typing approach was carried out, based upon established biotypes, vcg, CPS, 16S rRNA types and three other genes possibly associated with virulence (arylsulfatase A, mtlABC, and nanA). An established Multi Locus Sequence Typing (MLST) method was also performed. Phylogenetic analyses of these markers and MLST results produced similar patterns of clustering of strains into two main lineages (we categorized as ‘LI’ and ‘LII’), with clinical and environmental strains clustering together in both lineages. Lineage LII was comprised primarily but not entirely of clinical bacterial isolates. Putative virulence markers were present in both clinical and environmental strains. These results suggest that some northeastern environmental strains of V. vulnificus are phylogenetically close to clinical strains and probably are capable of virulence. Further studies are necessary to assess the risk of human illness from consuming raw oysters harvested in the northeastern US. PMID:24386187

  17. Skylab environmental and crew microbiology studies

    NASA Technical Reports Server (NTRS)

    Taylor, G. R.; Graves, R. C.; Brockett, R. M.; Ferguson, J. K.; Mieszkuc, B. J.

    1977-01-01

    Microbial flora samples were collected from crewmembers before, during, and after missions in order to obtain data on the microbial response to space flight environment. Data showed that, while gross contamination of the Skylab environment was demonstrated and there were several in-flight disease events, such events are not limiting hazards for long term manned space flights. Intercrew transfer of pathogens was demonstrated, but evidence of postflight microbial shock was not found.

  18. Environmental microbiology as related to planetary quarantine

    NASA Technical Reports Server (NTRS)

    Pflug, I. J.

    1974-01-01

    Continued experimental work related to dry heat resistance of microorganisms. One phase of this research has been concerned with the viability and dry heat resistance of indigenous microflora associated with small soil particles. The second part of this report is an analysis of the present status of dry heat sterilization. An attempt is made to integrate results for both laboratory grown spores and spores in soil.

  19. Environmental microbiology as related to planetary quarantine

    NASA Technical Reports Server (NTRS)

    Iflug, I. J.

    1971-01-01

    The results of studies to determine the effect of soil particle size on the survival time at 125 C of the microflora associated with these particles are discussed. The data suggest that longer survival times exist for the microflora associated with larger particles. The studies indicate that microorganisms associated with soil are difficult to kill and that organisms associated with large particles are harder to kill than those associated with small particles. Sterlization requirements increase as the level of contamination increases. Soil particles and their accompanying microflora are the most critical contaminants.

  20. Molecular Characterization of Polio from Environmental Samples: ISSP, The Israeli Sewage Surveillance Protocol.

    PubMed

    Shulman, Lester M; Manor, Yossi; Hindiyeh, Musa; Sofer, Danit; Mendelson, Ella

    2016-01-01

    Polioviruses are enteric viruses that cause paralytic poliomyelitis in less than 0.5 % of infections and are asymptomatic in >90 % infections of naïve hosts. Environmental surveillance monitors polio in populations rather than in individuals. When this very low morbidity to infection ratio, drops drastically in highly vaccinated populations, environmental surveillance employing manual or automatic sampling coupled with molecular analysis carried out in well-equipped central laboratories becomes the surveillance method of choice since polioviruses are excreted by infected individuals regardless of whether or not the infection is symptomatic. This chapter describes a high throughput rapid turn-around time method for molecular characterization of polioviruses from sewage. It is presented in five modules: (1) Sewage collection and concentration of the viruses in the sewage; (2) Cell cultures for identification of virus in the concentrated sewage; (3) Nucleic acid extractions directly from sewage and from tissue cultures infected with aliquots of concentrated sewage; (4) Nucleic Acid Amplification for poliovirus serotype identification and intratypic differentiation (discriminating wild and vaccine derived polioviruses form vaccine strains); and (5) Molecular characterization of viral RNA by qRT-PCR, TR-PCR, and Sequence analysis. Monitoring silent or symptomatic transmission of vaccine-derived polioviruses or wild polioviruses is critical for the endgame of poliovirus eradication. We present methods for adapting standard kits and validating the changes for this purpose based on experience gained during the recent introduction and sustained transmission of a wild type 1 poliovirus in Israel in 2013 in a population with an initial IPV vaccine coverage >90 %. PMID:26983731

  1. Molecular typing of environmental Cryptococcus neoformans/C. gattii species complex isolates from Manaus, Amazonas, Brazil.

    PubMed

    Alves, Gleica Soyan Barbosa; Freire, Ana Karla Lima; Bentes, Amaury Dos Santos; Pinheiro, José Felipe de Souza; de Souza, João Vicente Braga; Wanke, Bodo; Matsuura, Takeshi; Jackisch-Matsuura, Ani Beatriz

    2016-08-01

    Cryptococcus neoformans and Cryptococcus gattii are the main causative agents of cryptococcosis, a systemic fungal disease that affects internal organs and skin, and which is acquired by inhalation of spores or encapsulated yeasts. It is currently known that the C. neoformans/C. gattii species complex has a worldwide distribution, however, some molecular types seem to prevail in certain regions. Few environmental studies of Cryptococcus have been conducted in the Brazilian Amazon. This is the first ecological study of the pathogenic fungi C. neoformans/C. gattii species complex in the urban area of Manaus, Amazonas, Brazil. A total of 506 samples from pigeon droppings (n = 191), captive bird droppings (n = 60) and tree hollows (n = 255) were collected from June 2012 to January 2014 at schools and public buildings, squares, pet shops, households, the zoo and the bus station. Samples were plated on niger seed agar (NSA) medium supplemented with chloramphenicol and incubated at 25°C for 5 days. Dark-brown colonies were isolated and tested for thermotolerance at 37°C, cycloheximide resistance and growth on canavanine-glycine-bromothymol blue agar. Molecular typing was done by PCR-RFLP. Susceptibility to the antifungal drugs amphotericin B, fluconazole, itraconazole and ketoconazole was tested using Etest(®) strips. In total, 13 positive samples were obtained: one tree hollow (C. gattiiVGII), nine pigeon droppings (C. neoformansVNI) and three captive bird droppings (C. neoformansVNI). The environmental cryptococcal isolates found in this study were of the same molecular types as those responsible for infections in Manaus. PMID:27005969

  2. Flow-Injection Preconcentration of Chloramphenicol Using Molecularly Imprinted Polymer for HPLC Determination in Environmental Samples

    PubMed Central

    Kowalski, Damian; Poboży, Ewa; Trojanowicz, Marek

    2011-01-01

    The residue of antibiotic chloramphenicol (CAP) is important issue for food quality control and also for the environmental monitoring. It is banned for use in food-producing animals and has very limited use in human medicine, because of its severe impact on human health. Determination of trace level of CAP in environmental samples requires a very sensitive analytical method and efficient preconcentration procedure. CAP can be efficiently preconcentrated in flow-injection system using flow-through reactor packed with molecularly imprinted polymer (MIP), but determination of CAP in eluate from MIP requires the application of chromatographic separation, which was made in reversed-phase HPLC system with UV detection. In optimized conditions the limit of detection for 100 mL sample in HPLC with offline preconcentration on MIP was evaluated as 0.66 mg/L. In hyphenated FIA-HPLC system with zone sampling the LOD for developed method was evaluated as 15 ng/L, which indicates the possibility of using it for analysis of environmental samples. PMID:21584273

  3. Microbiological Methodology in Astrobiology

    NASA Technical Reports Server (NTRS)

    Abyzov, S. S.; Gerasimenko, L. M.; Hoover, R. B.; Mitskevich, I. N.; Mulyukin, A. L.; Poglazova, M. N.; Rozanov, A. Y.

    2005-01-01

    Searching for life in astromaterials to be delivered from the future missions to extraterrestrial bodies is undoubtedly related to studies of the properties and signatures of living microbial cells and microfossils on Earth. As model terrestrial analogs of Martian polar subsurface layers are often regarded the Antarctic glacier and Earth permafrost habitats where alive microbial cells preserved viability for millennia years due to entering the anabiotic state. For the future findings of viable microorganisms in samples from extraterrestrial objects, it is important to use a combined methodology that includes classical microbiological methods, plating onto nutrient media, direct epifluorescence and electron microscopy examinations, detection of the elemental composition of cells, radiolabeling techniques, PCR and FISH methods. Of great importance is to ensure authenticity of microorganisms (if any in studied samples) and to standardize the protocols used to minimize a risk of external contamination. Although the convincing evidence of extraterrestrial microbial life will may come from the discovery of living cells in astromaterials, biomorphs and microfossils must also be regarded as a target in search of life evidence bearing in mind a scenario that alive microorganisms had not be preserved and underwent mineralization. Under the laboratory conditions, processes that accompanied fossilization of cyanobacteria were reconstructed, and artificially produced cyanobacterial stromatolites resembles by their morphological properties those found in natural Earth habitats. Regarding the vital importance of distinguishing between biogenic and abiogenic signatures and between living and fossil microorganisms in analyzed samples, it is worthwhile to use some previously developed approaches based on electron microscopy examinations and analysis of elemental composition of biomorphs in situ and comparison with the analogous data obtained for laboratory microbial cultures and

  4. Molecular epidemiologic research on the effects of environmental pollutants on the fetus.

    PubMed Central

    Perera, F P; Jedrychowski, W; Rauh, V; Whyatt, R M

    1999-01-01

    Evidence shows that fetuses and infants are more affected than adults by a variety of environmental toxicants because of differential exposure, physiologic immaturity, and a longer lifetime over which disease initiated in early life can develop. In this article we review data on the effects of in utero exposure to common environmental contaminants, including polycyclic aromatic hydrocarbons (PAH), particulate matter and environmental tobacco smoke (ETS). We then summarize results from our molecular epidemiologic study to assess risks from in utero exposures to ambient air pollution and ETS. This research study, conducted in Poland, used biomarkers to measure the internal and bioeffective dose of toxicants and individual susceptibility factors. The study included 160 mothers and 160 newborns. Ambient air pollution was significantly associated (p= 0.05) with the amount of PAH bound to DNA (PAH-DNA adducts) in both maternal and infant cord white blood cells (WBC). Newborns with elevated PAH-DNA adducts (greater than the median) had significantly decreased birth weight (p= 0.05), birth length (p= 0.02), and head circumference (p= 0.0005) compared to the newborns with lower adducts (n= 135). Maternal and infant cotinine levels were increased by active and passive cigarette smoke exposure of the mother (p= 0.01). An inverse correlation was seen between newborn plasma cotinine (nanograms per milliliter) and birth weight (p= 0.0001) and length (p= 0.003). Adducts were elevated in placental tissue and WBC of newborns who were heterozygous or homozygous for the cytochrome P4501A1 MspI restriction fragment length polymorphism (RFLP) compared to newborns without the RFLP. Levels of PAH-DNA and cotinine were higher in newborns than mothers. These results document that there is significant transplacental transfer of PAH and ETS constituents from mother to fetus; that PAH-DNA adduct levels in maternal and newborn WBC were increased with environmental exposure to PAH from ambient

  5. Molecular Epidemiology of Nontuberculous Mycobacteria Isolates from Clinical and Environmental Sources of a Metropolitan City

    PubMed Central

    Akbar Velayati, Ali; Farnia, Parissa; Mozafari, Mohadese; Malekshahian, Donya; Seif, Shima; Rahideh, Snaz; Mirsaeidi, Mehdi

    2014-01-01

    Introduction While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran. Material and Methods A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations. Results Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (P<0.05). Out of 5314 positive clinical samples for mycobacteria, 175 (3.2%) isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078) in 2004 to 3.8% (39 out of 1005) in 2014 (P = 0.0001). The major clinical isolates were M. simiae (51; 29.1%), M. kansasii (26; 14.8%), M. chelonae (28; 16%), and M. fortuitum (13; 7.4%). Conclusions Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation. PMID:25485795

  6. Quality control analytical methods: strategies to ensure a robust quality-control microbiology program.

    PubMed

    Griffiths, Tricia; Connors, Anne

    2013-01-01

    As the regulatory environment for compounding pharmacies continues to evolve, facilities can take immediate steps to strengthen their quality-control microbiology and environmental monitoring programs. Robust programs that are timely, comprehensive, and effective will minimize risk and help support positive patient outcomes. This article provides a roadmap for putting in place a robust quality-control microbiology program in the face of United States Pharmacopeia Chapter 797 standards, and highlights several technologies for environmental monitoring that support a successful program. PMID:23696174

  7. Molecular basis of natural variation and environmental control of trichome patterning.

    PubMed

    Hauser, Marie-Theres

    2014-01-01

    Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

  8. Center for Molecular Electronics, University of Missouri, St. Louis. Environmental Assessment

    SciTech Connect

    Not Available

    1994-06-01

    The Department of Energy (DOE) proposes to authorize the University of Missouri, St. Louis to proceed with the detailed design and construction of the proposed Center for Molecular Electronics. The proposed Center would consist of laboratories and offices housed in a three-story building on the University campus. The proposed modular laboratories would be adaptable for research activities principally related to physics, chemistry, and electrical engineering. Proposed research would include the development and application of thin-film materials, semi-conductors, electronic sensors and devices, and high-performance polymers. Specific research for the proposed Center has not yet been formulated, therefore, specific procedures for any particular process or study cannot be described at this time. The proposed construction site is an uncontaminated panel of land located on the University campus. This report contains information about the environmental assessment that was performed in accordance with this project.

  9. Environmental and Climatic Determinants of Molecular Diversity and Genetic Population Structure in a Coenagrionid Damselfly

    PubMed Central

    Wellenreuther, Maren; Sánchez-Guillén, Rosa A.; Cordero-Rivera, Adolfo; Svensson, Erik I.; Hansson, Bengt

    2011-01-01

    Identifying environmental factors that structure intraspecific genetic diversity is of interest for both habitat preservation and biodiversity conservation. Recent advances in statistical and geographical genetics make it possible to investigate how environmental factors affect geographic organisation and population structure of molecular genetic diversity within species. Here we present a study on a common and wide ranging insect, the blue tailed damselfly Ischnuraelegans, which has been the target of many ecological and evolutionary studies. We addressed the following questions: (i) Is the population structure affected by longitudinal or latitudinal gradients?; (ii) Do geographic boundaries limit gene flow?; (iii) Does geographic distance affect connectivity and is there a signature of past bottlenecks?; (iv) Is there evidence of a recent range expansion and (vi) what is the effect of geography and climatic factors on population structure? We found low to moderate genetic sub-structuring between populations (mean FST = 0.06, Dest = 0.12), and an effect of longitude, but not latitude, on genetic diversity. No significant effects of geographic boundaries (e.g. water bodies) were found. FST-and Dest-values increased with geographic distance; however, there was no evidence for recent bottlenecks. Finally, we did not detect any molecular signatures of range expansions or an effect of geographic suitability, although local precipitation had a strong effect on genetic differentiation. The population structure of this small insect has probably been shaped by ecological factors that are correlated with longitudinal gradients, geographic distances, and local precipitation. The relatively weak global population structure and high degree of genetic variation within populations suggest that I. elegans has high dispersal ability, which is consistent with this species being an effective and early coloniser of new habitats. PMID:21655216

  10. Molecular epidemiology of environmental MRSA at an equine teaching hospital: introduction, circulation and maintenance

    PubMed Central

    2014-01-01

    The role that environmental contamination might play as a reservoir and a possible source of Methicillin-resistant Staphylococcus aureus (MRSA) for patients and personnel at equine veterinary hospitals remains undefined, as the environment has only been monitored during outbreaks or for short periods. Therefore, the objectives of this study were to determine the monthly presence, distribution, and characteristics of environmental MRSA at an equine hospital, and to establish patterns of contamination over time using molecular epidemiological analyses. For this purpose, a yearlong active MRSA surveillance was performed targeting the environment and incoming patients. Antimicrobial susceptibility testing, SCCmec typing, PFGE typing, and dendrographic analysis were used to characterize and analyze these isolates. Overall, 8.6% of the surfaces and 5.8% of the horses sampled were positive for MRSA. The most common contaminated surfaces were: computers, feed-water buckets, and surgery tables-mats. Ninety percent of the isolates carried SCCmec type IV, and 62.0% were classified as USA500. Molecular analysis showed that new pulsotypes were constantly introduced into the hospital throughout the year. However, maintenance of strains in the environment was also observed when unique clones were detected for 2 consecutive months on the same surfaces. Additionally, pulsotypes were circulating throughout several areas and different contact surfaces of the hospital. Based on these results, it is evident that MRSA is constantly introduced and frequently found in the equine hospital environment, and that some contact surfaces could act as “hot-spots”. These contaminated surfaces should be actively targeted for strict cleaning and disinfection as well as regular monitoring. PMID:24641543

  11. Molecular epidemiology of environmental MRSA at an equine teaching hospital: introduction, circulation and maintenance.

    PubMed

    van Balen, Joany; Mowery, Jade; Piraino-Sandoval, Micha; Nava-Hoet, Rocio C; Kohn, Catherine; Hoet, Armando E

    2014-01-01

    The role that environmental contamination might play as a reservoir and a possible source of Methicillin-resistant Staphylococcus aureus (MRSA) for patients and personnel at equine veterinary hospitals remains undefined, as the environment has only been monitored during outbreaks or for short periods. Therefore, the objectives of this study were to determine the monthly presence, distribution, and characteristics of environmental MRSA at an equine hospital, and to establish patterns of contamination over time using molecular epidemiological analyses. For this purpose, a yearlong active MRSA surveillance was performed targeting the environment and incoming patients. Antimicrobial susceptibility testing, SCCmec typing, PFGE typing, and dendrographic analysis were used to characterize and analyze these isolates. Overall, 8.6% of the surfaces and 5.8% of the horses sampled were positive for MRSA. The most common contaminated surfaces were: computers, feed-water buckets, and surgery tables-mats. Ninety percent of the isolates carried SCCmec type IV, and 62.0% were classified as USA500. Molecular analysis showed that new pulsotypes were constantly introduced into the hospital throughout the year. However, maintenance of strains in the environment was also observed when unique clones were detected for 2 consecutive months on the same surfaces. Additionally, pulsotypes were circulating throughout several areas and different contact surfaces of the hospital. Based on these results, it is evident that MRSA is constantly introduced and frequently found in the equine hospital environment, and that some contact surfaces could act as "hot-spots". These contaminated surfaces should be actively targeted for strict cleaning and disinfection as well as regular monitoring. PMID:24641543

  12. Molecularly imprinted fluorescent hollow nanoparticles as sensors for rapid and efficient detection λ-cyhalothrin in environmental water.

    PubMed

    Wang, Jixiang; Qiu, Hao; Shen, Hongqiang; Pan, Jianming; Dai, Xiaohui; Yan, Yongsheng; Pan, Guoqing; Sellergren, Börje

    2016-11-15

    Molecularly imprinted fluorescent polymers have shown great promise in biological or chemical separations and detections, due to their high stability, selectivity and sensitivity. In this work, molecularly imprinted fluorescent hollow nanoparticles, which could rapidly and efficiently detect λ-cyhalothrin (a toxic insecticide) in water samples, was reported. The molecularly imprinted fluorescent sensor showed excellent sensitivity (the limit of detection low to 10.26nM), rapid detection rate (quantitative detection of λ-cyhalothrin within 8min), regeneration ability (maintaining good fluorescence properties after 8 cycling operation) and appreciable selectivity over several structural analogs. Moreover, the fluorescent sensor was further used to detect λ-cyhalothrin in real samples form the Beijing-Hangzhou Grand Canal Water. Despite the relatively complex components of the environmental water, the molecularly imprinted fluorescent hollow nanosensor still showed good recovery, clearly demonstrating the potential value of this smart sensor nanomaterial in environmental monitoring. PMID:27208472

  13. Isolation, Identification and Molecular Typing of Cryptococcus neoformans from Pigeon Droppings and Other Environmental Sources in Tripoli, Libya.

    PubMed

    Ellabib, Mohamed S; Aboshkiwa, Mohamed A; Husien, Walid M; D'Amicis, Roberta; Cogliati, Massimo

    2016-08-01

    Cryptococcus neoformans and C. gattii are the major cause of fungal meningitis, a potentially lethal mycosis. Since pigeon excreta and other environmental sources can be considered a significant environmental reservoir of this species in urban areas, 100 samples of pigeon excreta and 420 samples from Eucalyptus camaldulensis and Olea europaea (olive tree) around the city of Tripoli, Libya, were collected. C. neoformans was isolated and identified using standard biochemical assays from 46 samples: 34 from pigeon droppings, 3 from Eucalyptus trees and 9 from olive trees. Molecular typing revealed that all isolates from pigeon droppings belonged to molecular type VNI (C. neoformans var. grubii) and mating type αA, whereas those from trees included also the molecular type VNII and VNIII (AD hybrids). The present study reports, for the first time, information about the distribution of species, mating types and molecular types of C. neoformans/C. gattii species complex in Libya. PMID:26943725

  14. THE RELATION BETWEEN MID-PLANE PRESSURE AND MOLECULAR HYDROGEN IN GALAXIES: ENVIRONMENTAL DEPENDENCE

    SciTech Connect

    Feldmann, Robert; Hernandez, Jose; Gnedin, Nickolay Y.

    2012-12-20

    Molecular hydrogen (H{sub 2}) is the primary component of the reservoirs of cold, dense gas that fuel star formation in our Galaxy. While the H{sub 2} abundance is ultimately regulated by physical processes operating on small scales in the interstellar medium (ISM), observations have revealed a tight correlation between the ratio of molecular to atomic hydrogen in nearby spiral galaxies and the pressure in the mid-plane of their disks. This empirical relation has been used to predict H{sub 2} abundances in galaxies with potentially very different ISM conditions, such as metal-deficient galaxies at high redshifts. Here, we test the validity of this approach by studying the dependence of the pressure-H{sub 2} relation on environmental parameters of the ISM. To this end, we follow the formation and destruction of H{sub 2} explicitly in a suite of hydrodynamical simulations of galaxies with different ISM parameters. We find that a pressure-H{sub 2} relation arises naturally in our simulations for a variety of dust-to-gas ratios or strengths of the interstellar radiation field in the ISM. Fixing the dust-to-gas ratio and the UV radiation field to values measured in the solar neighborhood results in fair agreement with the relation observed in nearby galaxies with roughly solar metallicity. However, the parameters (slope and normalization) of the pressure-H{sub 2} relation vary in a systematical way with ISM properties. A particularly strong trend is the decrease of the normalization of the relation with a lowering of the dust-to-gas ratio of the ISM. We show how this trend and other properties of the pressure-H{sub 2} relation arise from the atomic-to-molecular phase transition in the ISM caused by a combination of H{sub 2} formation, destruction, and shielding mechanisms.

  15. Molecular identification, antifungal susceptibility profile, and biofilm formation of clinical and environmental Rhodotorula species isolates.

    PubMed

    Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona E; Colombo, Arnaldo Lopes

    2013-01-01

    Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC(50)/MIC(90), 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula

  16. Molecular Identification, Antifungal Susceptibility Profile, and Biofilm Formation of Clinical and Environmental Rhodotorula Species Isolates

    PubMed Central

    Nunes, Jorge Meneses; Bizerra, Fernando César; Ferreira, Renata Carmona e

    2013-01-01

    Rhodotorula species are emergent fungal pathogens capable of causing invasive infections, primarily fungemia. They are particularly problematic in immunosuppressed patients when using a central venous catheter. In this study, we evaluated the species distribution of 51 clinical and 8 environmental Rhodotorula species isolates using the ID32C system and internal transcribed spacer (ITS) sequencing. Antifungal susceptibility testing and biofilm formation capability using a crystal violet staining assay were performed. Using ITS sequencing as the gold standard, the clinical isolates were identified as follows: 44 R. mucilaginosa isolates, 2 R. glutinis isolates, 2 R. minuta isolates, 2 R. dairenensis isolates, and 1 Rhodosporidium fluviale isolate. The environmental isolates included 7 R. mucilaginosa isolates and 1 R. slooffiae isolate. Using the ID32C system, along with a nitrate assimilation test, only 90.3% of the isolates tested were correctly identified. In the biofilm formation assay, R. mucilaginosa and R. minuta exhibited greater biofilm formation ability compared to the other Rhodotorula species; the clinical isolates of R. mucilaginosa showed greater biofilm formation compared to the environmental isolates (P = 0.04). Amphotericin B showed good in vitro activity (MIC ≤ 1 μg/ml) against planktonic cells, whereas voriconazole and posaconazole showed poor activity (MIC50/MIC90, 2/4 μg/ml). Caspofungin and fluconazole MICs were consistently high for all isolates tested (≥64 μg/ml and ≥ 4 μg/ml, respectively). In this study, we emphasized the importance of molecular methods to correctly identify Rhodotorula species isolates and non-R. mucilaginosa species in particular. The antifungal susceptibility profile reinforces amphotericin B as the antifungal drug of choice for the treatment of Rhodotorula infections. To our knowledge, this is the first study evaluating putative differences in the ability of biofilm formation among different Rhodotorula species

  17. Microbiological aspects of clean room technology as applied to surgery, with special reference to unidirectional airflow systems

    NASA Technical Reports Server (NTRS)

    Wardle, M. D.

    1974-01-01

    The microbiological aspects of clean room technology as applied to surgery were reviewed. The following pertinent subject areas were examined: (1) clean room technology per se and its utilization for surgery, (2) microbiological monitoring of the clean room surgical environment, (3) clean rooms and their impact on operating room environmental microbiology, and (4) the effect of the technology on surgical wound infection rates. Conclusions were drawn for each topic investigated.

  18. Molecular ecology of bacterial populations in environmental hazardous-chemical control. Final report, 1 Dec 88-30 Nov 91

    SciTech Connect

    Sayler, G.S.

    1991-11-30

    Basic research was conducted to develop and explore the use of modern molecular biology techniques in understanding the dynamics of microbial populations engaged in biodegradation of environmental pollutants. The research focused on (1) the use of environmental DNA extraction and gene probing techniques to quantify the presence and distribution of degradative genes in the environment, (2) characterizing new-degradative organisms and plasmids for eventual development of new catabolic gene probes for environmental use, and (3) construction of novel bioluminescent reporter bacteria to act as biosensors of catabolic activity in the environment.

  19. Veterinary Microbiology, 3rd Edition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Veterinary Microbiology, Third Edition is organized into four sections and begins with an updated and expanded introductory section on infectious disease pathogenesis, diagnosis and clinical management. The second section covers bacterial and fungal pathogens, and the third section describes viral d...

  20. Soil Microbiology, Ecology, and Biochemistry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The 4th edition of Soil Microbiology, Ecology, and Biochemistry Edited by Eldor Paul continues in the vein of the 3rd edition by providing an excellent, broad-reaching introduction to soil biology. The new edition improves on the previous by providing extensive supplementary materials, links to outs...

  1. 42 CFR 493.909 - Microbiology.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 5 2010-10-01 2010-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are...

  2. 42 CFR 493.821 - Condition: Microbiology.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 5 2010-10-01 2010-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes...

  3. 42 CFR 493.909 - Microbiology.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 5 2011-10-01 2011-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are...

  4. 42 CFR 493.821 - Condition: Microbiology.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 5 2011-10-01 2011-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes...

  5. 42 CFR 493.909 - Microbiology.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 5 2013-10-01 2013-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are...

  6. 42 CFR 493.909 - Microbiology.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 5 2012-10-01 2012-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are...

  7. 42 CFR 493.909 - Microbiology.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 5 2014-10-01 2014-10-01 false Microbiology. 493.909 Section 493.909 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.909 Microbiology. The subspecialties under the specialty of microbiology for which a program may offer proficiency testing are...

  8. 42 CFR 493.821 - Condition: Microbiology.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 5 2012-10-01 2012-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes...

  9. 42 CFR 493.821 - Condition: Microbiology.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 42 Public Health 5 2013-10-01 2013-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes...

  10. 42 CFR 493.821 - Condition: Microbiology.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 42 Public Health 5 2014-10-01 2014-10-01 false Condition: Microbiology. 493.821 Section 493.821 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES... These Tests § 493.821 Condition: Microbiology. The specialty of microbiology includes, for purposes...

  11. 21 CFR 866.2540 - Microbiological incubator.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540...

  12. 21 CFR 866.2540 - Microbiological incubator.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540...

  13. 21 CFR 866.2540 - Microbiological incubator.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540...

  14. 21 CFR 866.2540 - Microbiological incubator.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540...

  15. 21 CFR 866.2540 - Microbiological incubator.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbiological incubator. 866.2540 Section 866.2540 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2540...

  16. Molecularly imprinted ionic liquid magnetic microspheres for the rapid isolation of organochlorine pesticides in environmental water.

    PubMed

    Qiao, Fengxia; Gao, Mengmeng; Yan, Hongyuan

    2016-04-01

    A new type of molecularly imprinted ionic liquid magnetic microspheres was synthesized by aqueous suspension polymerization, using 4,4'-dichlorobenzhydrol as a dummy template, and 1-allyl-3-ethylimidazolium hexafluorophosphate and methacrylic acid as co-functional monomers. The results of morphology and magnetic property evaluation of the obtained microspheres demonstrated that it was monodispersed spherical, possessed a rough surface, and an outstanding magnetic properties. Binding experiments revealed that it had a substantial adsorption capacity and strong recognition ability to organochlorine pesticides (OCPs) in aqueous solution. Then the microspheres were applied as an adsorbent of magnetic dispersive solid-phase extraction for the selective recognition and rapid determination of OCPs in environmental water. Under the optimum conditions, good linearity of the three types of OCPs (dicofol, tetradifon, and p,p'-dichlorodiphenyldichloroethane) was achieved in the range of 1.0-100 ng/mL (r ≥ 0.9994). The recoveries at three spiking levels ranged from 82.6 to 100.4% with the RSDs less than 6.9%. PMID:26791136

  17. The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms

    PubMed Central

    de Storme, Nico; Geelen, Danny

    2014-01-01

    In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved. PMID:23731015

  18. Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology

    PubMed Central

    Miller, Melissa B.; Tang, Yi-Wei

    2009-01-01

    Summary: The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles. PMID:19822891

  19. Molecular toxicity of cerium oxide nanoparticles to the freshwater alga Chlamydomonas reinhardtii is associated with supra-environmental exposure concentrations

    PubMed Central

    Taylor, Nadine S.; Merrifield, Ruth; Williams, Tim D.; Chipman, J. Kevin; Lead, Jamie R.; Viant, Mark R.

    2016-01-01

    Abstract Ceria nanoparticles (NPs) are widely used as fuel catalysts and consequently are likely to enter the environment. Their potential impacts on. biota at environmentally relevant concentrations, including uptake and toxicity, remain to be elucidated and quantitative data on which to assess risk are sparse. Therefore, a definitive assessment of the molecular and phenotypic effects of ceria NPs was undertaken, using well-characterised mono-dispersed NPs as their toxicity is likely to be higher, enabling a conservative hazard assessment. Unbiased transcriptomics and metabolomics approaches were used to investigate the potential toxicity of tightly constrained 4–5 nm ceria NPs to the unicellular green alga, Chlamydomonas reinhardtii, a sentinel freshwater species. A wide range of exposure concentrations were investigated from predicted environmental levels, to support hazard assessment, to supra-environmental levels to provide insight into molecular toxicity pathways. Ceria NPs were internalised into intracellular vesicles within C. reinhardtii, yet caused no significant effect on algal growth at any exposure concentration. Molecular perturbations were only detected at supra-environmental ceria NP-concentrations, primarily down-regulation of photosynthesis and carbon fixation with associated effects on energy metabolism. For acute exposures to small mono-dispersed particles, it can be concluded there should be little concern regarding their dispersal into the environment for this trophic level. PMID:25740379

  20. Microbiological Contamination of Spacecraft

    NASA Technical Reports Server (NTRS)

    Pierson, D. L.; Bruce, R. J.; Groves, T. O.; Novikova, N. D.; Viktorov, A. N.

    2000-01-01

    The International Space Station (ISS) Phase1 Program resulted in seven US astronauts residing aboard the Russian Space Station Mir between March 1995 and May 1998. Collaboration between U.S. and Russian scientists consisted of collection and analyses of samples from the crewmembers and the Mir and Shuttle environments before, during, and after missions that lasted from 75 to 209 days in duration. The effects of long-duration space flight on the microbial characteristics of closed life support systems and the interactions of microbes with the spacecraft environment and crewmembers were investigated. Air samples were collected using a Russian or U.S.-supplied sampler (SAS, RCS, or Burkard,) while surface samples were collected using contact slides (Hycon) or swabs. Mir recycled condensate and stored potable water sources were analyzed using the U.S.-supplied Water Experiment Kit. In-flight analysis consisted of enumeration of levels of bacteria and fungi. Amounts of microorganisms seen in the air and on surfaces were mostly within acceptability lin1its; observed temporal fluctuations in levels of microbes probably reflect changes in environmental conditions (e.g., humidity). All Mir galley hot water samples were within the standards set for Mir and the ISS. Microbial isolates were returned to Earth for identification of bacterial and fungal isolates. Crew samples (nose, throat, skin, urine, and feces) were analyzed using methods approved for the medical evaluations of Shuttle flight crews. No significant changes in crew microbiota were found during space flight or upon return relative to preflight results. Dissemination of microbes between the crew and environment was demonstrated by D A fingerprinting. Some biodegradation of spacecraft materials was observed. Accumulation of condensate allowed for the recovery of a wide range of bacteria and fungi as well as some protozoa and dust mites.

  1. Microbiological treatment of radioactive wastes

    SciTech Connect

    Francis, A.J.

    1992-12-31

    The ability of microorganisms which are ubiquitous throughout nature to bring about information of organic and inorganic compounds in radioactive wastes has been recognized. Unlike organic contaminants, metals cannot be destroyed, but must be either removed or converted to a stable form. Radionuclides and toxic metals in wastes may be present initially in soluble form or, after disposal may be converted to a soluble form by chemical or microbiological processes. The key microbiological reactions include (i) oxidation/reduction; (ii) change in pH and Eh which affects the valence state and solubility of the metal; (iii) production of sequestering agents; and (iv) bioaccumulation. All of these processes can mobilize or stabilize metals in the environment.

  2. Microbiological testing of Skylab foods.

    NASA Technical Reports Server (NTRS)

    Heidelbaugh, N. D.; Mcqueen, J. L.; Rowley, D. B.; Powers , E. M.; Bourland, C. T.

    1973-01-01

    Review of some of the unique food microbiology problems and problem-generating circumstances the Skylab manned space flight program involves. The situations these problems arise from include: extended storage times, variations in storage temperatures, no opportunity to resupply or change foods after launch of the Skylab Workshop, first use of frozen foods in space, first use of a food-warming device in weightlessness, relatively small size of production lots requiring statistically valid sampling plans, and use of food as an accurately controlled part in a set of sophisticated life science experiments. Consideration of all of these situations produced the need for definite microbiological tests and test limits. These tests are described along with the rationale for their selection. Reported test results show good compliance with the test limits.

  3. Microbiological Spoilage of Cereal Products

    NASA Astrophysics Data System (ADS)

    Cook, Frederick K.; Johnson, Billie L.

    A wide range of cereal products, including bakery items, refrigerated dough, fresh pasta products, dried cereal products, snack foods, and bakery mixes, are manufactured for food consumption. These products are subject to physical, chemical, and microbiological spoilage that affects the taste, aroma, leavening, appearance, and overall quality of the end consumer product. Microorganisms are ubiquitous in nature and have the potential for causing food spoilage and foodborne disease. However, compared to other categories of food products, bakery products rarely cause food poisoning. The heat that is applied during baking or frying usually eliminates pathogenic and spoilage microorganisms, and low moisture contributes to product stability. Nevertheless, microbiological spoilage of these products occurs, resulting in substantial economic losses.

  4. Clinical microbiology of coryneform bacteria.

    PubMed Central

    Funke, G; von Graevenitz, A; Clarridge, J E; Bernard, K A

    1997-01-01

    Coryneform bacteria are aerobically growing, asporogenous, non-partially-acid-fast, gram-positive rods of irregular morphology. Within the last few years, there has been a massive increase in the number of publications related to all aspects of their clinical microbiology. Clinical microbiologists are often confronted with making identifications within this heterogeneous group as well as with considerations of the clinical significance of such isolates. This review provides comprehensive information on the identification of coryneform bacteria and outlines recent changes in taxonomy. The following genera are covered: Corynebacterium, Turicella, Arthrobacter, Brevibacterium, Dermabacter. Propionibacterium, Rothia, Exiguobacterium, Oerskovia, Cellulomonas, Sanguibacter, Microbacterium, Aureobacterium, "Corynebacterium aquaticum," Arcanobacterium, and Actinomyces. Case reports claiming disease associations of coryneform bacteria are critically reviewed. Minimal microbiological requirements for publications on disease associations of coryneform bacteria are proposed. PMID:8993861

  5. New Technologies in Clinical Microbiology

    PubMed Central

    Wolk, Donna M.; Dunne, W. Michael

    2011-01-01

    Rapid identification of microorganisms in the clinical microbiology laboratory can be of great value for selection of optimal patient management strategies for infections caused by bacteria, viruses, fungi, mycobacteria, and parasites. Rapid identification of microorganisms in clinical samples enables expedient de-escalation from broad-spectrum agents to targeted antimicrobial therapy. The switch to tailored therapy minimizes risks of antibiotics, namely, disruption of normal flora, toxic side effects, and selective pressure. There is a critical need for new technologies in clinical microbiology, particularly for bloodstream infections, in which associated mortality is among the highest of all infections. Just as importantly, there is a need for the clinical laboratory community to embrace the practices of evidence-based interventional laboratory medicine and collaborate in translational research projects to establish the clinical utility, cost benefit, and impact of new technologies.

  6. Applications of neural networks to real-time data processing at the Environmental and Molecular Sciences Laboratory (EMSL)

    SciTech Connect

    Keller, P.E.; Kouzes, R.T.; Kangas, L.J.

    1993-06-01

    Detailed design of the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory (PNL) is nearing completion and construction is scheduled to begin later this year. This facility will assist in the environmental restoration and waste management mission at the Hanford Site. This paper identifies several real-time data processing applications within the EMSL where neural networks can potentially be beneficial. These applications include real-time sensor data acquisition and analysis, spectral analysis, process control, theoretical modeling, and data compression.

  7. TyPol - a new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior.

    PubMed

    Servien, Rémi; Mamy, Laure; Li, Ziang; Rossard, Virginie; Latrille, Eric; Bessac, Fabienne; Patureau, Dominique; Benoit, Pierre

    2014-09-01

    Following legislation, the assessment of the environmental risks of 30000-100000 chemical substances is required for their registration dossiers. However, their behavior in the environment and their transfer to environmental components such as water or atmosphere are studied for only a very small proportion of the chemical in laboratory tests or monitoring studies because it is time-consuming and/or cost prohibitive. Therefore, the objective of this work was to develop a new methodology, TyPol, to classify organic compounds, and their degradation products, according to both their behavior in the environment and their molecular properties. The strategy relies on partial least squares analysis and hierarchical clustering. The calculation of molecular descriptors is based on an in silico approach, and the environmental endpoints (i.e. environmental parameters) are extracted from several available databases and literature. The classification of 215 organic compounds inputted in TyPol for this proof-of-concept study showed that the combination of some specific molecular descriptors could be related to a particular behavior in the environment. TyPol also provided an analysis of similarities (or dissimilarities) between organic compounds and their degradation products. Among the 24 degradation products that were inputted, 58% were found in the same cluster as their parents. The robustness of the method was tested and shown to be good. TyPol could help to predict the environmental behavior of a "new" compound (parent compound or degradation product) from its affiliation to one cluster, but also to select representative substances from a large data set in order to answer some specific questions regarding their behavior in the environment. PMID:24997973

  8. Molecular ecology meets remote sensing: environmental drivers to population structure of humpback dolphins in the Western Indian Ocean

    PubMed Central

    Mendez, M; Subramaniam, A; Collins, T; Minton, G; Baldwin, R; Berggren, P; Särnblad, A; Amir, O A; Peddemors, V M; Karczmarski, L; Guissamulo, A; Rosenbaum, H C

    2011-01-01

    Genetic analyses of population structure can be placed in explicit environmental contexts if appropriate environmental data are available. Here, we use high-coverage and high-resolution oceanographic and genetic sequence data to assess population structure patterns and their potential environmental influences for humpback dolphins in the Western Indian Ocean. We analyzed mitochondrial DNA data from 94 dolphins from the coasts of South Africa, Mozambique, Tanzania and Oman, employing frequency-based and maximum-likelihood algorithms to assess population structure and migration patterns. The genetic data were combined with 13 years of remote sensing oceanographic data of variables known to influence cetacean dispersal and population structure. Our analyses show strong and highly significant genetic structure between all putative populations, except for those in South Africa and Mozambique. Interestingly, the oceanographic data display marked environmental heterogeneity between all sampling areas and a degree of overlap between South Africa and Mozambique. Our combined analyses therefore suggest the occurrence of genetically isolated populations of humpback dolphins in areas that are environmentally distinct. This study highlights the utility of molecular tools in combination with high-resolution and high-coverage environmental data to address questions not only pertaining to genetic population structure, but also to relevant ecological processes in marine species. PMID:21427750

  9. Microbiology of nitrogen cycle in animal manure compost

    PubMed Central

    Maeda, Koki; Hanajima, Dai; Toyoda, Sakae; Yoshida, Naohiro; Morioka, Riki; Osada, Takashi

    2011-01-01

    Summary Composting is the major technology in the treatment of animal manure and is a source of nitrous oxide, a greenhouse gas. Although the microbiological processes of both nitrification and denitrification are involved in composting, the key players in these pathways have not been well identified. Recent molecular microbiological methodologies have revealed the presence of dominant Bacillus species in the degradation of organic material or betaproteobacterial ammonia‐oxidizing bacteria on nitrification on the surface, and have also revealed the mechanism of nitrous oxide emission in this complicated process to some extent. Some bacteria, archaea or fungi still would be considered potential key players, and the contribution of some pathways, such as nitrifier denitrification or heterotrophic nitrification, might be involved in composting. This review article discusses these potential microbial players in nitrification–denitrification within the composting pile and highlights the relevant unknowns through recent activities that focus on the nitrogen cycle within the animal manure composting process. PMID:21375720

  10. Microbiology of ‘Candidatus Accumulibacter’ in activated sludge

    PubMed Central

    He, Shaomei; McMahon, Katherine D.

    2011-01-01

    Summary ‘Candidatus Accumulibacter’ is a biotechnologically important bacterial group that can accumulate large amounts of intracellular polyphosphate, contributing to biological phosphorus removal in wastewater treatment. Since its first molecular identification more than a decade ago, this bacterial group has drawn significant research attention due to its high abundance in many biological phosphorus removal systems. In the past 6 years, our understanding of Accumulibacter microbiology and ecophysiology has advanced rapidly, largely owing to genomic information obtained through shotgun metagenomic sequencing efforts. In this review, we focus on the metabolism, physiology, fine‐scale population structure and ecological distribution of Accumulibacter, aiming to integrate the information learned so far and to present a more complete picture of the microbiology of this important bacterial group. PMID:21338476

  11. Soft X-Ray Microscopy and Spectroscopy at the Molecular Environmental Science Beamline at the Advanced Light Source

    SciTech Connect

    Bluhm, Hendrik; Andersson, Klas J.; Araki, Tohru; Benzerara, Karim; Brown, Gordon E.; Dynes, Jay J.; Ghosal, Sutapa; Gilles, Mary K.; Hansen, Hans C.; Hemminger, J. C.; Hitchcock, Adam P.; Ketteler, Guido; Kilcoyne, Arthur L.; Kneedler, Eric M.; Lawrence, John R.; Leppard, Gary G.; Majzlam, Juraj; Mun, B. S.; Myneni, Satish C.; Nilsson, Anders R.; Ogasawara, Hirohito; Ogletree, D. F.; Pecher, Klaus H.; Salmeron, Miquel B.; Shuh, David K.; Tonner, Brian; Tyliszczak, Tolek; Warwick, Tony; Yoon, T. H.

    2006-02-01

    We present examples of the application of synchrotron-based spectroscopies and microscopies to environmentally-relevant samples. The experiments were performed at the Molecular Environmental Science beamline (11.0.2) at the Advanced Light Source, Lawrence Berkeley National Laboratory. Examples range from the study of water monolayers on Pt(111) single crystal surfaces using X-ray emission spectroscopy and the examination of alkali halide solution/water vapor interfaces using ambient pressure photoemission spectroscopy, to the investigation of actinides, river-water biofilms, Al-containing colloids and mineral-bacteria suspensions using scanning transmission X-ray spectromicroscopy. The results of our experiments show that spectroscopy and microscopy in the soft X-ray energy range are excellent tools for the investigation of environmentally relevant samples under realistic conditions, i.e. with water or water vapor present at ambient temperature.

  12. Environmental assessment for the resiting, construction, and operation of the Environmental and Molecular Sciences Laboratory at the Hanford Site, Richland, Washington

    SciTech Connect

    Not Available

    1994-07-01

    This environmental assessment (EA) presents estimated environmental impacts from the resiting, construction, and operation of the US Department of Energy`s (DOE`s) Environmental and Molecular Sciences Laboratory (EMSL), which is proposed to be constructed and operated on land near the south boundary of the Hanford Site near Richland, Washington. The EMSL, if constructed, would be a modern research facility in which experimental, theoretical, and computational techniques can be focused on environmental restoration problems, such as the chemical and transport behavior of complex mixtures of contaminants in the environment. The EMSL design includes approximately 18,500 square meters (200,000 square feet) of floor space on a 12-hectare (30-acre) site. The proposed new site is located within the city limits of Richland in north Richland, at the south end of DOE`s 300 Area, on land to be deeded to the US by the Battelle Memorial Institute. Approximately 200 persons are expected to be employed in the EMSL and approximately 60 visiting scientists may be working in the EMSL at any given time. State-of-the-art equipment is expected to be installed and used in the EMSL. Small amounts of hazardous substances (chemicals and radionuclides) are expected to be used in experimental work in the EMSL.

  13. Microbiology Learning and Education Online.

    PubMed

    Guarner, Jeannette; Niño, Silvia M

    2016-05-01

    The ubiquity of devices that connect to the Internet has exploded, allowing for easy dissemination of information. Many teachers from kindergarten to universities use the information obtained online or post material they want their students to access. Online media readily places articles, books, videos, and games at our fingertips. The public in general also gathers health information from the Internet. The following review will explore what has been published regarding microbiology education and learning online and the use of electronic media by microbiologists for scientific purposes. PMID:26935727

  14. Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level

    SciTech Connect

    Hettich, Robert {Bob} L

    2009-01-01

    The increase in sequencing capacity led to a new wave of metagenomic projects, enabling and setting the prerequisite for the application of environmental proteomics technologies. This review describes the current status of environmental proteomics. It describes sample preparation as well as the two major technologies applied within this field: two-dimensional electrophoresis-based environmental proteomics and liquid chromatography-mass spectrometry-based environmental proteomics. It also highlights current publications and describes major scientific findings. The review closes with a discussion of critical improvements in the area of integrating experimental mass spectrometry technologies with bioinformatics as well as improved sample handling.

  15. Child toy safety: An interdisciplinary approach to unravel the microbiological hazard posed by soap bubbles.

    PubMed

    Amoruso, Irene; Bertoncello, Chiara; Caravello, Gianumberto; Giaccone, Valerio; Baldovin, Tatjana

    2015-11-01

    In 2012 some children developed sepsis after playing together with a soap bubble toy. Microbiological testing revealed heavy contamination of the soap solution, which reasonably represented the vehicle of infection. We investigated the issue with a multidisciplinary approach: review of toy safety legislation; microbiological testing of additional samples; query of the RAPEX database for non-compliant soap bubbles; identification of major manufacturing districts. Microbiological contamination of industrial soap bubbles was widespread. Sixty-three notifications of batches contaminated by environmental microorganisms and opportunistic pathogens had been reported. The Chinese had a virtual monopoly of the soap bubble market. We identified two main manufacturing districts in Guangdong Province, both notable for degradation of their water resources. The use of untreated water for the industrial production of soap bubbles may explain the bacterial contamination. Existing legislation provides an unsatisfactory approach for managing microbiological hazards in sensitive toy categories and for identifying responsible parties in import and export of the products. PMID:26424202

  16. Microbiology on Space Station Freedom

    NASA Technical Reports Server (NTRS)

    Pierson, Duane L. (Editor); Mcginnis, Michael R. (Editor); Mishra, S. K. (Editor); Wogan, Christine F. (Editor)

    1991-01-01

    This panel discussion convened in Houston, Texas, at the Lunar and Planetary Institute, on November 6 to 8, 1989, to review NASA's plans for microbiology on Space Station Freedom. A panel of distinguished scientists reviewed, validated, and recommended revisions to NASA's proposed acceptability standards for air, water, and internal surfaces on board Freedom. Also reviewed were the proposed microbiology capabilities and monitoring plan, disinfection procedures, waste management, and clinical issues. In the opinion of this advisory panel, ensuring the health of the Freedom's crews requires a strong goal-oriented research effort to determine the potential effects of microorganisms on the crewmembers and on the physical environment of the station. Because there are very few data addressing the fundamental question of how microgravity influences microbial function, the panel recommended establishing a ground-based microbial model of Freedom, with subsequent evaluation using in-flight shuttle data. Sampling techniques and standards will be affected by both technological advances in microgravity-compatible instrumentation, and by changes in the microbial population over the life of the station.

  17. Laboratory Design for Microbiological Safety

    PubMed Central

    Phillips, G. Briggs; Runkle, Robert S.

    1967-01-01

    Of the large amount of funds spent each year in this country on construction and remodeling of biomedical research facilities, a significant portion is directed to laboratories handling infectious microorganisms. This paper is intended for the scientific administrators, architects, and engineers concerned with the design of new microbiological facilities. It develops and explains the concept of primary and secondary barriers for the containment of microorganisms. The basic objectives of a microbiological research laboratory, (i) protection of the experimenter and staff, (ii) protection of the surrounding community, and (iii) maintenance of experimental validity, are defined. In the design of a new infectious-disease research laboratory, early identification should be made of the five functional zones of the facility and their relation to each other. The following five zones and design criteria applicable to each are discussed: clean and transition, research area, animal holding and research area, laboratory support, engineering support. The magnitude of equipment and design criteria which are necessary to integrate these five zones into an efficient and safe facility are delineated. Images Fig. 1 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 11 Fig. 12 Fig. 13 Fig. 14 Fig. 15 Fig. 16 Fig. 17 Fig. 18 Fig. 19 PMID:4961771

  18. Comparative quantification of Campylobacter jejuni from environmental samples using traditional and molecular biological techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Campylobacter jejuni (C. jejuni) is one of the most common causes of gastroenteritis in the world. Given the potential risks to human, animal and environmental health the development and optimization of methods to quantify this important pathogen in environmental samples is essential. Two of the mos...

  19. Molecular mapping of two environmentally sensitive male-sterile mutants in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In soybean [Glycine max (L.) Merr.], manual cross-pollination to produce large quantities of hybrid seed is difficult and time consuming. Identification of an environmentally stable male-sterility system could make hybrid seed production commercially valuable. In soybean, two environmentally sensi...

  20. Environmental Research Division: fundamental molecular physics and chemistry. Annual report, January-December 1983. Part I

    SciTech Connect

    Not Available

    1985-03-01

    Research progress is reported in the following areas: (1) photoionization of radicals or excited states; (2) molecular spectroscopy by resonant multiphoton ionization; (3) studies conducted with the synchrotron radiation facility at the National Bureau of Standards; (4) theoretical studies on molecular photoabsorption; (5) analysis of photoabsorption spectra of open-shell atoms; (6) the electron energy-loss spectra of molecules; and (7) cross sections and stopping powers. Items have been individually abstracted for the data base. (ACR)

  1. Rapid methods and automation in dairy microbiology.

    PubMed

    Vasavada, P C

    1993-10-01

    The importance of microbiology to the dairy industry has been demonstrated by recent outbreaks of foodborne illness associated with consumption of milk and dairy products that had been contaminated with pathogenic organisms or toxins. Undesirable microorganisms constitute the primary hazard to safety, quality, and wholesomeness of milk and dairy foods. Consequently, increased emphasis has been placed on the microbiological analysis of milk and dairy products designed to evaluate quality and to ensure safety and regulatory compliance. The focus of dairy microbiology, however, remains largely on conventional methods: plate counts, most probable numbers, and dye reduction tests. These methods are slow, tedious, intensive in their requirements for material and labor, and often not suitable for assessing the quality and shelf-life of perishable dairy foods. With the exception of coliforms, Salmonella, and Staphylococcus aureus, isolation and characterization of various organisms occurring in milk and milk products are seldom a part of the routine microbiological analysis in the dairy industry. Recent emphasis on the programs based on HACCP (Hazard Analysis and Critical Control Points) for total quality management in the dairy industry and increased demand for microbiological surveillance of products, process, and environment have led to increased interest in rapid methods and automation in microbiology. Several methods for rapid detection, isolation, enumeration, and characterization of microorganisms are being adapted by the dairy industry. This presentation reviews rapid methods and automation in microbiology for microbiological analysis of milk and dairy products. PMID:8227634

  2. Evaluation of the 3M™ Molecular Detection Assay (MDA) 2 - Salmonella for the Detection of Salmonella spp. in Select Foods and Environmental Surfaces: Collaborative Study, First Action 2016.01.

    PubMed

    Bird, Patrick; Flannery, Jonathan; Crowley, Erin; Agin, James R; Goins, David; Monteroso, Lisa

    2016-07-01

    The 3M™ Molecular Detection Assay (MDA) 2 - Salmonella uses real-time isothermal technology for the rapid and accurate detection of Salmonella spp. from enriched select food, feed, and food-process environmental samples. The 3M MDA 2 - Salmonella was evaluated in a multilaboratory collaborative study using an unpaired study design. The 3M MDA 2 - Salmonella was compared to the U.S. Food and Drug Administration Bacteriological Analytical Manual Chapter 5 reference method for the detection of Salmonella in creamy peanut butter, and to the U.S. Department of Agriculture, Food Safety and Inspection Service Microbiology Laboratory Guidebook Chapter 4.08 reference method "Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg and Catfish Products and Carcass and Environmental Samples" for the detection of Salmonella in raw ground beef (73% lean). Technicians from 16 laboratories located within the continental United States participated. Each matrix was evaluated at three levels of contamination: an uninoculated control level (0 CFU/test portion), a low inoculum level (0.2-2 CFU/test portion), and a high inoculum level (2-5 CFU/test portion). Statistical analysis was conducted according to the probability of detection (POD) statistical model. Results obtained for the low inoculum level test portions produced difference in collaborator POD values of 0.03 (95% confidence interval, -0.10 to 0.16) for raw ground beef and 0.06 (95% confidence interval, -0.06 to 0.18) for creamy peanut butter, indicating no statistically significant difference between the candidate and reference methods. PMID:27330049

  3. Microbiological Food Safety Surveillance in China

    PubMed Central

    Pei, Xiaoyan; Li, Ning; Guo, Yunchang; Liu, Xiumei; Yan, Lin; Li, Ying; Yang, Shuran; Hu, Jing; Zhu, Jianghui; Yang, Dajin

    2015-01-01

    Microbiological food safety surveillance is a system that collects data regarding food contamination by foodborne pathogens, parasites, viruses, and other harmful microbiological factors. It helps to understand the spectrum of food safety, timely detect food safety hazards, and provide relevant data for food safety supervision, risk assessment, and standards-setting. The study discusses the microbiological surveillance of food safety in China, and introduces the policies and history of the national microbiological surveillance system. In addition, the function and duties of different organizations and institutions are provided in this work, as well as the generation and content of the surveillance plan, quality control, database, and achievement of the microbiological surveillance of food safety in China. PMID:26343705

  4. Microbiological monitoring in geothermal plants

    NASA Astrophysics Data System (ADS)

    Alawi, M.; Lerm, S.; Vetter, A.; Vieth, A.; Seibt, A.; Wolfgramm, M.; Würdemann, H.

    2009-12-01

    In times of increasing relevance of alternative energy resources the utilization of geothermal energy and subsurface energy storage gains importance and arouses increasing interest of scientists. The research project “AquiScreen” investigates the operational reliability of geothermally used groundwater systems under microbial, geochemical, mineralogical and petrological aspects. Microbiological analyses based on fluid and solid phases of geothermal systems are conducted to evaluate the impact of microbial populations on these systems. The presentation focuses on first results obtained from microbiological monitoring of geothermal plants located in two different regions of Germany: the North German Basin and the Molasse Basin in the southern part characterized by different salinities and temperatures. Fluid and filter samples taken during regular plant operation were investigated using genetic fingerprinting based on PCR-amplified 16S rRNA genes to characterize the microbial biocenosis of the geothermal aquifer. Sequencing of dominant bands of the fingerprints and the subsequent comparison to 16S rRNA genes from public databases enables a correlation to metabolic classes and provides information about the biochemical processes in the deep biosphere. The genetic profiles revealed significant differences in microbiological community structures of geothermal aquifers investigated. Phylogenetic analyses indicate broad metabolical diversity adapted to the specific conditions in the aquifers. Additionally a high amount of so far uncultivated microorganisms was detected indicating very specific indigenous biocenosis. However, in all geothermal plants bacteria were detected despite of fluid temperatures from 45° to 120°C. The identified microorganisms are closely related to thermophilic and hyperthermophilic species detectable in hot wells and hot springs, like Thermus scotoductus and Thermodesulfovibrio yellowstonii, respectively. Halophilic species were detected in

  5. atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples

    PubMed Central

    2013-01-01

    Background The environment is the likely source of many pathogenic mycobacterial species but detection of mycobacteria by bacteriological tools is generally difficult and time-consuming. Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an in silico search for proteins exclusive to Mycobacterium spp. genomes in order to design sensitive and specific molecular targets. Results Among the 3989 predicted proteins from M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples. Conclusions The results indicate that this real-time PCR method targeting the atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples. PMID:24299240

  6. Microbiology and treatment of acute apical abscesses.

    PubMed

    Siqueira, José F; Rôças, Isabela N

    2013-04-01

    Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease. PMID:23554416

  7. Microbiology and Treatment of Acute Apical Abscesses

    PubMed Central

    Rôças, Isabela N.

    2013-01-01

    SUMMARY Acute apical abscess is the most common form of dental abscess and is caused by infection of the root canal of the tooth. It is usually localized intraorally, but in some cases the apical abscess may spread and result in severe complications or even mortality. The reasons why dental root canal infections can become symptomatic and evolve to severe spreading and sometimes life-threatening abscesses remain elusive. Studies using culture and advanced molecular microbiology methods for microbial identification in apical abscesses have demonstrated a multispecies community conspicuously dominated by anaerobic bacteria. Species/phylotypes commonly found in these infections belong to the genera Fusobacterium, Parvimonas, Prevotella, Porphyromonas, Dialister, Streptococcus, and Treponema. Advances in DNA sequencing technologies and computational biology have substantially enhanced the knowledge of the microbiota associated with acute apical abscesses and shed some light on the etiopathogeny of this disease. Species richness and abundance and the resulting network of interactions among community members may affect the collective pathogenicity and contribute to the development of acute infections. Disease modifiers, including transient or permanent host-related factors, may also influence the development and severity of acute abscesses. This review focuses on the current evidence about the etiology and treatment of acute apical abscesses and how the process is influenced by host-related factors and proposes future directions in research, diagnosis, and therapeutic approaches to deal with this disease. PMID:23554416

  8. Lessons learned and unlearned in periodontal microbiology

    PubMed Central

    Teles, Ricardo; Teles, Flavia; Frias-Lopez, Jorge; Paster, Bruce; Haffajee, Anne

    2013-01-01

    Periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation initiated by specific subgingival species. In the past few decades, efforts to understand the microbiota of periodontal diseases have led to an exponential increase in information about biofilms associated with periodontal health and disease. In fact, the oral microbiota is one of the best characterized microbiomes that colonize the human body. Despite this increased knowledge, one has to ask if our fundamental concepts of the etiology and pathogenesis of periodontal diseases have really changed. In this chapter we will review how our comprehension of the structure and function of the subgingival microbiota evolved over the years in search of lessons learned and unlearned in periodontal microbiology. More specifically, this review focuses on: 1) how the data obtained through molecular techniques has impacted our knowledge of the etiology of periodontal infections; 2) the potential role of viruses in the etiopathogenesis of periodontal diseases; 3) how concepts of microbial ecology have expanded our understanding of host microbial interactions that might lead to periodontal diseases; 4) the role of inflammation in the pathogenesis of periodontal diseases; and 5) the impact of these evolving concepts on treatment and preventive approaches to periodontal infections. We will conclude by reviewing how novel systems biology approaches promise to unravel new details of the pathogenesis of periodontal diseases and, hopefully, lead to a better understanding of periodontal disease mechanisms. PMID:23574465

  9. A study of the effects of end-cap molecular species on environmental characteristics of polimidesulfones

    NASA Technical Reports Server (NTRS)

    Singh, J. J.; St.clair, T. L.; Walker, S.

    1984-01-01

    To improve the environmental stability and mechanical properties of polyimidesulfone (PISO2), it was decided to investigate the effects of various types of end caps on its thermo-mechanical and related properties. It was noted that end caps are effective in reducing the environmental damage susceptibility of PISO2 samples, apparently due to their ability to react with free end groups which are believed to be moisture pickup sites. Phthalic anydride, aniline and aminobenzophenone were the end caps used in this study.

  10. Cellular and Molecular Investigations of the Adhesion and Mechanics of Listeria monocytogenes Lineages’ I and II Environmental and Epidemic Strains

    PubMed Central

    Eskhan, Asma O.; Abu-Lail, Nehal I.

    2013-01-01

    Atomic force microscopy (AFM) was used to probe the mechanical and adherence properties of eight L. monocytogenes’ strains representative of the species’ two phylogenetic lineages I and II. From a functional perspective, lineage’ I strains were characterized by lower overall adhesion forces and higher specific and nonspecific forces compared to lineage’ II strains. From a structural perspective, lineage’ II strains were characterized by higher Young’s moduli and longer and stiffer biopolymers compared to lineage’ I strains. Both lineages’ I and II strains were similar in their grafting densities. Finally, our results indicated that epidemic and environmental strains of L. monocytogenes and irrespective of their lineage group were characterized by similar Young’s moduli of elasticties and adhesion forces at the cellular level. However, at the molecular level, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser and more flexible biopolymers compared to environmental strains. PMID:23261349

  11. Cellular and molecular investigations of the adhesion and mechanics of Listeria monocytogenes lineages' I and II environmental and epidemic strains.

    PubMed

    Eskhan, Asma O; Abu-Lail, Nehal I

    2013-03-15

    Atomic force microscopy (AFM) was used to probe the mechanical and adherence properties of eight Listeria monocytogenes' strains representative of the species' two phylogenetic lineages I and II. From a functional perspective, lineage' I strains were characterized by lower overall adhesion forces and higher specific and nonspecific forces compared to lineage' II strains. From a structural perspective, lineage' II strains were characterized by higher Young's moduli and longer and stiffer biopolymers compared to lineage' I strains. Both lineages' I and II strains were similar in their grafting densities. Finally, our results indicated that epidemic and environmental strains of L. monocytogenes and irrespective of their lineage group were characterized by similar Young's moduli of elasticities and adhesion forces at the cellular level. However, at the molecular level, epidemic strains were characterized by higher specific and nonspecific forces, shorter, denser, and more flexible biopolymers compared to environmental strains. PMID:23261349

  12. Expert Systems in Clinical Microbiology

    PubMed Central

    Winstanley, Trevor; Courvalin, Patrice

    2011-01-01

    Summary: This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the “big three”: Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically. PMID:21734247

  13. Microbiologic assay of space hardware.

    NASA Technical Reports Server (NTRS)

    Favero, M. S.

    1971-01-01

    Review of the procedures used in the microbiological examination of space hardware. The general procedure for enumerating aerobic and anaerobic microorganisms and spores is outlined. Culture media and temperature-time cycles used for incubation are reviewed, along with assay systems designed for the enumeration of aerobic and anaerobic spores. The special problems which are discussed are involved in the precise and accurate enumeration of microorganisms on surfaces and in the neutralization of viable organisms buried inside solid materials that could be released to a planet's surface if the solid should be fractured. Special attention is given to sampling procedures including also the indirect techniques of surface assays of space hardware such as those using detachable or fallout strips. Some data on comparative levels of microbial contamination on lunar and planetary spacecraft are presented.

  14. Dental abscess: A microbiological review

    PubMed Central

    Shweta; Prakash, S Krishna

    2013-01-01

    Dental abscess is a frequently occurring infectious process known to the health practice. The fate of the infection depends on the virulence of the bacteria, host resistance factors, and regional anatomy. Serious consequences arising from the spread of a dental abscess lead to significant morbidity and mortality. Acute dental abscess is polymicrobial, comprising of strict anaerobes, such as anaerobic cocci, Prevotella, Fusobacterium species, and facultative anaerobes, such as viridans group streptococci and the Streptococcus anginosus group. Numerous novel, uncultivable and fastidious organisms have been identified as potential pathogens with the use of non-culture techniques. The majority of localized dental abscesses respond to surgical treatment while the use of antimicrobials is limited to severe spreading infections. There is a need for good-quality clinical trials of sufficient size to identify the ideal treatment. The microbiology of the acute dentoalveolar abscess and its treatment in the light of improved culture and diagnostic methods are reviewed. PMID:24348613

  15. The microbiology of terrestrial ecosystems

    SciTech Connect

    Richards, B.N.

    1987-01-01

    Emphasizing the role of soil organisms, especially fungi and bacteria, in maintaining productive and stable ecosystems, this book addresses the imbalance found in most ecological texts, which often neglect microorganisms. It stresses the inter-relationship between soil microbes and plants in functional activities such as the capture and transfer of energy and the circulation of chemical elements in ecological systems. It begins with a review of basic concepts followed by a description of the soil as a living entity, including its physical and chemical characteristics, and the life forms found within it. Organic matter mineralization is treated in the context if energy flow and carbon turnover in the biosphere. Also covered are mineral cycling, the microbiology of the rhizosphere, mycorrhiza, root nodule symbiosis, and the cycling of nutrients in the soil-plant-atmosphere system.

  16. Expert systems in clinical microbiology.

    PubMed

    Winstanley, Trevor; Courvalin, Patrice

    2011-07-01

    This review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). It considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. A variety of noncommercial systems is described, and the central role played by the EUCAST is stressed. The need for expert rules in the environment of reset EUCAST breakpoints is also questioned. Commercial automated systems with on-board expert systems are considered, with emphasis being placed on the "big three": Vitek 2, BD Phoenix, and MicroScan. By necessity and in places, the review becomes a general review of automated system performances for the detection of specific resistance mechanisms rather than focusing solely on expert systems. Published performance evaluations of each system are drawn together and commented on critically. PMID:21734247

  17. Photosynthesis, environmental change, and plant adaptation: Research topics in plant molecular ecology. Summary report of a workshop

    SciTech Connect

    1995-07-01

    As we approach the 21st Century, it is becoming increasingly clear that human activities, primarily related to energy extraction and use, will lead to marked environmental changes at the local, regional, and global levels. The realized and the potential photosynthetic performance of plants is determined by a combination of intrinsic genetic information and extrinsic environmental factors, especially climate. It is essential that the effects of environmental changes on the photosynthetic competence of individual species, communities, and ecosystems be accurately assessed. From October 24 to 26, 1993, a group of scientists specializing in various aspects of plant science met to discuss how our predictive capabilities could be improved by developing a more rational, mechanistic approach to relating photosynthetic processes to environmental factors. A consensus emerged that achieving this goal requires multidisciplinary research efforts that combine tools and techniques of genetics, molecular biology, biophysics, biochemistry, and physiology to understand the principles, mechanisms, and limitations of evolutional adaptation and physiological acclimation of photosynthetic processes. Many of these basic tools and techniques, often developed in other fields of science, already are available but have not been applied in a coherent, coordinated fashion to ecological research. The efforts of this research program are related to the broader efforts to develop more realistic prognostic models to forecast climate change that include photosynthetic responses and feedbacks at the regional and ecosystem levels.

  18. [Predictive microbiology and risk assessment].

    PubMed

    Hildebrandt, G; Kleer, J

    2004-05-01

    Predictive microbiology (predictive modelling PM), in spite of its limits and short-comings, may often contribute to a reduction of the problems arising when HACCP systems are established or microbiological risk assessment is done. Having identified the agents which constitute a risk and the contamination rate and density in the raw material, the influences of production steps and storage on these microorganisms have to be examined. Finally, there should be an exposure assessment, i.e. an estimate of the contamination density in the final product at the time of consumption. Should the exposure assessment together with data from dose response assessments reveal a potential for intake of inacceptable numbers of organisms, the risk identified has to be characterized. As a consequence, risk management should result in a modification of the composition of the product and/or of the production process so that the risk does not surpass an acceptable limit. For this approach it is indispensable to have product- and process-specific information on the multiplication of pathogens prior to heat treatment, on reduction of their density by thermal treatment and on growth or dying of organisms having survived heat treatment or penetrated into the product after heat treatment as post-process contaminant. Commonly, challenge tests are conducted to provide such information. But they are time consuming and, as their results are only valid for the specific product tested and the conditions prevailing during the experiment, the have to be repeated if there is any modification of intrinsic or extrinsic factors. At least partially, the PM may replace the challenge tests. The efficiency of the models is rated particularly high if they are used already at the stage of product development when the question has to be answered whether a planned recipe or process of production are already save or have to be modified to become save. PMID:15233338

  19. Advanced continuous cultivation methods for systems microbiology.

    PubMed

    Adamberg, Kaarel; Valgepea, Kaspar; Vilu, Raivo

    2015-09-01

    Increasing the throughput of systems biology-based experimental characterization of in silico-designed strains has great potential for accelerating the development of cell factories. For this, analysis of metabolism in the steady state is essential as only this enables the unequivocal definition of the physiological state of cells, which is needed for the complete description and in silico reconstruction of their phenotypes. In this review, we show that for a systems microbiology approach, high-resolution characterization of metabolism in the steady state--growth space analysis (GSA)--can be achieved by using advanced continuous cultivation methods termed changestats. In changestats, an environmental parameter is continuously changed at a constant rate within one experiment whilst maintaining cells in the physiological steady state similar to chemostats. This increases the resolution and throughput of GSA compared with chemostats, and, moreover, enables following of the dynamics of metabolism and detection of metabolic switch-points and optimal growth conditions. We also describe the concept, challenge and necessary criteria of the systematic analysis of steady-state metabolism. Finally, we propose that such systematic characterization of the steady-state growth space of cells using changestats has value not only for fundamental studies of metabolism, but also for systems biology-based metabolic engineering of cell factories. PMID:26220303

  20. Public Health Microbiology of Shiga Toxin-Producing Escherichia coli.

    PubMed

    Caprioli, Alfredo; Scavia, Gaia; Morabito, Stefano

    2014-12-01

    Shiga toxin-producing Escherichia coli (STEC) strains are the only pathogenic group of E. coli that has a definite zoonotic origin, with ruminants and, in particular, cattle being recognized as the major reservoir. Most human STEC infections are food borne, but the routes of transmission include direct contact with animals and a variety of environment-related exposures. Therefore, STEC public health microbiology spans the fields of medical, veterinary, food, water, and environmental microbiology, requiring a "One Health" perspective and laboratory scientists with the ability to work effectively across disciplines. Public health microbiology laboratories play a central role in the surveillance of STEC infections, as well as in the preparedness for responding to outbreaks and in providing scientific evidence for the implementation of prevention and control measures. This article reviews (i) how the integration of surveillance of STEC infections and monitoring of these pathogens in animal reservoirs and potential food vehicles may contribute to their control; (ii) the role of reference laboratories, in both the public health and veterinary and food sectors; and (iii) the public health perspectives, including those related to regulatory issues in both the European Union and the United States. PMID:26104435

  1. Microbiological and Geochemical Characterization of the Deep Subsurface Environment: Kumano Mud Volcano, Nankai Trough, Japan

    NASA Astrophysics Data System (ADS)

    Case, D. H.; Ijiri, A.; Morono, Y.; Orphan, V. J.; Inagaki, F.

    2013-12-01

    Submarine mud volcanoes play an important environmental role by delivering deep-sourced fluids, elements, and hydrocarbons to the seafloor. These fluxes in turn support chemosynthetic benthic communities. However, due to difficulty in accessing the deep biosphere most mud volcano samples only represent the top one to several meters below seafloor (mbsf) obtainable by remotely operated vehicle (ROV) or gravity cores. Thus, the geochemical and microbiological conditions, as well as vertical homogeneity, deep within mud volcanoes remains poorly constrained. In 2012, using the deep-sea drilling vessel Chikyu, we drilled one of the most active submarine mud volcanoes in the Kumano forearc basin of the Nankai Trough, off the Kii Peninsula of Japan (33°67.581'N, 136°56.8085'E: 1,986.7 m in water depth). Cores were obtained down to 200 mbsf. Cell counts indicate the presence of microorganisms at relatively low abundance (less than 105 cells/cm3) throughout the cored depth. Molecular analyses reveal vertical heterogeneity in the microbial community composition, including specific depth horizons harboring putative methanogenic and methanotrophic phylotypes at >100 mbsf. Geochemical profiles indicate the potential for microbial activity and rate measurements with radiotracers revealed active homoacetogenesis rates that were 2-3 orders of magnitude higher than rates of homo- and acetoclastic methanogenesis. To assess active autotrophic, methanotrophic and heterotrophic populations, 13C- and 15N-amendment experiments with sediment samples collected from 15 and 115 mbsf were established and single cell stable isotope analyses with nanoSIMS are in progress. Our samples and analyses represent a unique observation of a subseafloor setting different from previously explored stratified sediments on continental margins and will allow further understanding of how submarine mud volcanoes contribute to geochemical and microbiological fluxes into the surface biosphere.

  2. The Response of Photosynthesis and Stomatal Conductance to Rising [CO2]: Molecular Mechanisms and Environmental Interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants directly sense and respond to elevated atmospheric carbon dioxide concentration ([CO2]) in two ways, decreased stomatal conductance (gs) and increased photosynthesis (A). First, this review summarizes the molecular and biochemical bases for these responses. Second, it examines how downstream ...

  3. Molecular Method for Bartonella Species Identification in Clinical and Environmental Samples▿

    PubMed Central

    García-Esteban, Coral; Gil, Horacio; Rodríguez-Vargas, Manuela; Gerrikagoitia, Xeider; Barandika, Jesse; Escudero, Raquel; Jado, Isabel; García-Amil, Cristina; Barral, Marta; García-Pérez, Ana L.; Bhide, Mangesh; Anda, Pedro

    2008-01-01

    A new, efficient molecular method for detection of Bartonella, based on the 16S-23S rRNA intergenic spacer and 16S rRNA amplification by multiplex PCR combined with reverse line blotting, was designed. This assay could simultaneously detect 20 different known species and other Bartonella species not described previously. PMID:18094134

  4. Microbiological Lessons Learned from the Space Shuttle

    NASA Technical Reports Server (NTRS)

    Pierson, Duane L.; Ott, C. Mark; Bruce, Rebekah; Castro, Victoria A.; Mehta, Satish K.

    2011-01-01

    After 30 years of being the centerpiece of NASA s human spacecraft, the Space Shuttle will retire. This highly successful program provided many valuable lessons for the International Space Station (ISS) and future spacecraft. Major microbiological risks to crewmembers include food, water, air, surfaces, payloads, animals, other crewmembers, and ground support personnel. Adverse effects of microorganisms are varied and can jeopardize crew health and safety, spacecraft systems, and mission objectives. Engineering practices and operational procedures can minimize the negative effects of microorganisms. To minimize problems associated with microorganisms, appropriate steps must begin in the design phase of new spacecraft or space habitats. Spacecraft design must include requirements to control accumulation of water including humidity, leaks, and condensate on surfaces. Materials used in habitable volumes must not contribute to microbial growth. Use of appropriate materials and the implementation of robust housekeeping that utilizes periodic cleaning and disinfection will prevent high levels of microbial growth on surfaces. Air filtration can ensure low levels of bioaerosols and particulates in the breathing air. The use of physical and chemical steps to disinfect drinking water coupled with filtration can provide safe drinking water. Thorough preflight examination of flight crews, consumables, and the environment can greatly reduce pathogens in spacecraft. The advances in knowledge of living and working onboard the Space Shuttle formed the foundation for environmental microbiology requirements and operations for the International Space Station (ISS) and future spacecraft. Research conducted during the Space Shuttle Program resulted in an improved understanding of the effects of spaceflight on human physiology, microbial properties, and specifically the host-microbe interactions. Host-microbe interactions are substantially affected by spaceflight. Astronaut immune

  5. Space Habitation and Microbiology: Status and Roadmap of Space Agencies

    NASA Technical Reports Server (NTRS)

    Ott, Mark; Pierson, Duane; Shirakawa, Masaki; Tanigaki, Fumiaki; Hida, Masamitsu; Yamazaki, Takashi; Shimazu, Toru; Ishioka, Noriaki

    2016-01-01

    The ubiquitous nature of microbiology is reflected in the diversity of microbiological research and operational efforts at NASA. For example, the impact of microorganisms on other planets and the protection of Earth from the potential of microbial life elsewhere is the responsibility of the Office of Planetary Protection (http://planetaryprotection.nasa.gov/ about). While the Office of Planetary Protection does not include forward or back contamination to or from a low Earth orbit, research platforms, such as the ISS, are being used to better understand the survival of microorganisms and corresponding contamination control in the extreme conditions of space (2, 4, 10). Another example is the NASA Center for Astrobiology, which focuses on the origin, evolution, distribution, and future of life in the universe (https:// astrobiology.nasa.gov/). The large focus on microbiology is within its human exploration operations. NASA has historically set microbiological requirements, including stringent monitoring regimes, to mitigate risks to the health and performance of astronauts. Microorganisms can have both positive and negative impacts on many aspects of human spaceflight, including the risk and prevention of infectious diseases, performance of Environmental Control and Life Support Systems (ECLSS), spaceflight foods, and vehicle design and integrity. Even though a great amount of information has been obtained, several key questions regarding the impact of microorganisms on human spaceflight still remain. Research into the uncertainties of risks that may affect crew health are the responsibility of the NASA Human Research Program (http://www.nasa.gov/exploration/human research/). The research that addresses our fundamental understanding of space life science and its translation for benefits to the general public on Earth is the responsibility of NASA Space Biology.

  6. Changing needs, opportunities and constraints for the 21st century microbiology laboratory.

    PubMed

    Van Eldere, J

    2005-04-01

    Clinical microbiologists and microbiology laboratories are experiencing changes due to evolving views on 'healthcare delivery' as an economic activity, due to changes in the medical environment and the demographics of the workforce, and technical evolution. Cost-effectiveness of laboratory procedures has been achieved through consolidation and integration of laboratories. Consolidation offers economy of scale and reduction in numbers of on-site staff, but also leads to separation of microbiologists from their clinical colleagues. Integration puts different laboratory disciplines under a single management, and leads to reorganisation of laboratories along common work-lines. Cost-savings combined with on-site availability of laboratories are achieved at the expense of a reduction in the influence of microbiologists in the daily running of the laboratory. Medically, there is growing emphasis on evidence-based diagnostics. Because of time-delays inherent in culturing, microbiology through rapid testing is mandatory. There is an increasing shortage in Europe and the USA of trained microbiology laboratory technicians and microbiologists. This reinforces the trend towards more automation and integration. Technological advances, particularly in molecular diagnostics, offer the possibility of rapid reporting and improvement of the impact of clinical microbiology on patient management. Molecular tests, however, fit perfectly the concept of an integrated laboratory and may further loosen the link between microbiologist and microbiology tests. The challenge for clinical microbiology will be to use new techniques to improve its cost-effectiveness and impact on infectious disease management. The future organisation of microbiology laboratories must support this but is itself of secondary importance. The training of future microbiologist must prepare them for this changing environment. PMID:15816102

  7. Automation in the clinical microbiology laboratory.

    PubMed

    Novak, Susan M; Marlowe, Elizabeth M

    2013-09-01

    Imagine a clinical microbiology laboratory where a patient's specimens are placed on a conveyor belt and sent on an automation line for processing and plating. Technologists need only log onto a computer to visualize the images of a culture and send to a mass spectrometer for identification. Once a pathogen is identified, the system knows to send the colony for susceptibility testing. This is the future of the clinical microbiology laboratory. This article outlines the operational and staffing challenges facing clinical microbiology laboratories and the evolution of automation that is shaping the way laboratory medicine will be practiced in the future. PMID:23931839

  8. Microbiological Spoilage of Acidified Specialty Products

    NASA Astrophysics Data System (ADS)

    Sperber, William H.

    Acidified specialty products or condiments are among the most microbiologically stable and safe food products. Often formulated, packaged, and distributed without heat treatments, they are microbiologically stable indefinitely at ambient temperatures in unopened containers. The packaged, acidified products are often intended for multiple uses, exposing them at the points of consumption to numerous opportunities for contamination with microorganisms. Nonetheless, they remain resistant to microbiological spoilage for many months, often under refrigerated conditions that are used to retard chemical reactions, flavor changes, and yeast growth.

  9. Molecular Modeling for Screening Environmental Chemicals for Estrogenicity: Use of the Toxicant-Target Approach

    EPA Science Inventory

    There is a paucity of relevant experimental information available for the evaluation of the potential health and environmental effects of many man made chemicals. Knowledge of the potential pathways for activity provides a rational basis for the extrapolations inherent in the pre...

  10. Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol.

    PubMed

    Santos, Nuno; Santos, Catarina; Valente, Teresa; Gortázar, Christian; Almeida, Virgílio; Correia-Neves, Margarida

    2015-01-01

    Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area. PMID:26561038

  11. Widespread Environmental Contamination with Mycobacterium tuberculosis Complex Revealed by a Molecular Detection Protocol

    PubMed Central

    Santos, Nuno; Santos, Catarina; Valente, Teresa; Gortázar, Christian; Almeida, Virgílio; Correia-Neves, Margarida

    2015-01-01

    Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70–0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area. PMID:26561038

  12. Functional Molecular Ecological Networks

    PubMed Central

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  13. Functional molecular ecological networks.

    PubMed

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on "species" richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO(2) enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO(2) and ambient CO(2) (aCO(2)) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO(2) and aCO(2), at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO(2) dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  14. Environmental Forensics: Molecular Insight into Oil Spill Weathering Helps Advance High Magnetic Field FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    McKenna, Amy

    2013-03-01

    The depletion of terrestrial global oil reserves has shifted oil exploration into offshore and ultra-deep water (> 5000 ft) oil reserves to meet global energy demands. Deep water reservoirs are currently in production in many parts of the world, including the Gulf of Mexico, but production is complicated by the water depth and thick salt caps that challenge reservoir characterization / production. The explosion aboard the Deepwater Horizon in April 2010 resulted in an estimated total release of ~5 million barrels (BP claims that they collected ~1M barrels, for a net release of 4 M) of light, sweet crude oil into the Gulf of Mexico and shifted attention toward the environmental risks associated with offshore oil production. The growing emphasis on deep water and ultra-deep water oil production poses a significant environmental threat, and increased regulations require that oil companies minimize environmental impact to prevent oil spills, and mitigate environmental damage when spills occur. Every oil spill is unique. The molecular transformations that occur to petroleum after contact with seawater depend on the physical and chemical properties of the spilled oil, environmental conditions, and deposition environment. Molecular-level knowledge of the composition, distribution, and total mass of released hydrocarbons is essential to disentangle photo- and bio-degradation, source identification, and long-term environmental impact of hydrocarbons released into the environment. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is unsurpassed in its ability to characterize complex mixtures at the level of elemental composition assignment. Only FT-ICR mass spectrometry can routinely achieve the required minimum resolving power necessary to elucidate molecular-level characterization of crude oil. Conversely, the spectral complexity of petroleum facilitates identification of systematic errors in the accumulation, transfer, excitation, and detection

  15. Conformational analysis of environmental agents: use of X-ray crystallographic data to determine molecular reactivity.

    PubMed Central

    Cody, V

    1985-01-01

    This paper explores the use of crystallographic techniques as an aid in understanding the molecular reactivities of a number of agents that are of concern to pharmacologists and toxicologists. The selected examples demonstrate the role of structural data in the determination of absolute configuration, configurational flexibility and active-site topology for a reactive species. For example, the role of absolute stereochemistry in understanding synthetic pyrethroid structure-activity relationships is shown from analysis of their crystal structures; conformational flexibility among DDT analogues, and the importance of conformational and electronic properties in phenylalkanoic acid herbicides are shown from systematic analysis of their crystal structures; and interpretation of active-site stereochemistry is made by study of computer modeling of enzyme inhibitors in the active sites of related protein crystal structures. Thus, the observed patterns in conformational flexibility and their resultant effects on substrate pharmacological profile can be interpreted in understanding the molecular level events that influence biological reactivity. PMID:3905372

  16. Microbiological profile of selected mucks

    NASA Astrophysics Data System (ADS)

    Dąbek-Szreniawska, M.; Wyczółkowski, A. I.

    2009-04-01

    INTRODUCTION Matyka-Sarzynska and Sokolowska (2000) emphasize that peats and peat soils comprise large areas of Poland. The creation of soil begins when the formation of swamp has ended. Gawlik (2000) states that the degree of influence of the mucky process of organic soils on the differentiations of the conditions of growth and development of plants is mainly connected with the changes of moisture-retentive properties of mucks which constitute the material for these soils, and the loss of their wetting capacities. The above-mentioned changes, which usually occur gradually and show a clear connection with the extent of dehydration and, at times, with its duration, intensify significantly when the soils are under cultivation. The mucky process of peat soils leads to transformations of their physical, chemical and biological properties. The main ingredient of peat soils is organic substance. The substance is maintained inside them by the protective activity of water. The process of land improvement reduces the humidity of the environment, and that Intensifies the pace of the activity of soil microorganisms which cause the decay of organic substance. The decay takes place in the direction of two parallel processes: mineralization and humification. All groups of chemical substances constituting peat undergo mineralization. Special attention should be called to the mineralization of carbon and nitrogen compounds, which constitute a large percentage of theorganic substance of the peat organic mass. Okruszko (1976) has examined scientificbases of the classification of peat soils depending on the intensity of the muck process. The aim of this publication was to conduct a microbiological characteristic of selected mucky material. METHODS AND MATERIALS Soil samples used in the experiments were acquired from the Leczynsko-Wlodawski Lake Region, a large area of which constitutes a part of the Poleski National Park, which is covered to a large extent with high peat bogs. It was

  17. Chemometric Methods and Theoretical Molecular Descriptors in Predictive QSAR Modeling of the Environmental Behavior of Organic Pollutants

    NASA Astrophysics Data System (ADS)

    Gramatica, Paola

    This chapter surveys the QSAR modeling approaches (developed by the author's research group) for the validated prediction of environmental properties of organic pollutants. Various chemometric methods, based on different theoretical molecular descriptors, have been applied: explorative techniques (such as PCA for ranking, SOM for similarity analysis), modeling approaches by multiple-linear regression (MLR, in particular OLS), and classification methods (mainly k-NN, CART, CP-ANN). The focus of this review is on the main topics of environmental chemistry and ecotoxicology, related to the physico-chemical properties, the reactivity, and biological activity of chemicals of high environmental concern. Thus, the review deals with atmospheric degradation reactions of VOCs by tropospheric oxidants, persistence and long-range transport of POPs, sorption behavior of pesticides (Koc and leaching), bioconcentration, toxicity (acute aquatic toxicity, mutagenicity of PAHs, estrogen binding activity for endocrine disruptors compounds (EDCs)), and finally persistent bioaccumulative and toxic (PBT) behavior for the screening and prioritization of organic pollutants. Common to all the proposed models is the attention paid to model validation for predictive ability (not only internal, but also external for chemicals not participating in the model development) and checking of the chemical domain of applicability. Adherence to such a policy, requested also by the OECD principles, ensures the production of reliable predicted data, useful also in the new European regulation of chemicals, REACH.

  18. Identification of molecular and physiological responses to chronic environmental challenge in an invasive species: the Pacific oyster, Crassostrea gigas

    PubMed Central

    Clark, Melody S; Thorne, Michael A S; Amaral, Ana; Vieira, Florbela; Batista, Frederico M; Reis, João; Power, Deborah M

    2013-01-01

    Understanding the environmental responses of an invasive species is critical in predicting how ecosystem composition may be transformed in the future, especially under climate change. In this study, Crassostrea gigas, a species well adapted to the highly variable intertidal environment, was exposed to the chronic environmental challenges of temperature (19 and 24°C) and pH (ambient seawater and a reduction of 0.4 pH units) in an extended 3-month laboratory-based study. Physiological parameters were measured (condition index, shell growth, respiration, excretion rates, O:N ratios, and ability to repair shell damage) alongside molecular analyses. Temperature was by far the most important stressor, as demonstrated by reduced condition indexes and shell growth at 24°C, with relatively little effect detected for pH. Transcriptional profiling using candidate genes and SOLiD sequencing of mantle tissue revealed that classical “stress” genes, previously reported to be upregulated under acute temperature challenges, were not significantly expressed in any of the treatments, emphasizing the different response between acute and longer term chronic stress. The transcriptional profiling also elaborated on the cellular responses underpinning the physiological results, including the identification of the PI3K/AKT/mTOR pathway as a potentially novel marker for chronic environmental challenge. This study represents a first attempt to understand the energetic consequences of cumulative thermal stress on the intertidal C. gigas which could significantly impact on coastal ecosystem biodiversity and function in the future. PMID:24223268

  19. Rapid effects of estrogens on behavior: environmental modulation and molecular mechanisms

    PubMed Central

    Laredo, Sarah A.; Landeros, Rosalina Villalon; Trainor, Brian C.

    2014-01-01

    Estradiol can modulate neural activity and behavior via both genomic and nongenomic mechanisms. Environmental cues have a major impact on the relative importance of these signaling pathways with significant consequences for behavior. First we consider how photoperiod modulates nongenomic estrogen signaling on behavior. Intriguingly, short days permit rapid effects of estrogens on aggression in both rodents and song sparrows. This highlights the importance of considering photoperiod as a variable in laboratory research. Next we review evidence for rapid effects of estradiol on ecologically-relevant behaviors including aggression, copulation, communication, and learning. We also address the impact of endocrine disruptors on estrogen signaling, such as those found in corncob bedding used in rodent research. Finally, we examine the biochemical mechanisms that may mediate rapid estrogen action on behavior in males and females. A common theme across these topics is that the effects of estrogens on social behaviors vary across different environmental conditions. PMID:24685383

  20. Microbiology in Schools Advisory Committee (MISAC)

    ERIC Educational Resources Information Center

    Bainbridge, B. W.

    1972-01-01

    Summarizes the work of the committee, lists its membership, and provides the addresses of (English) suppliers of microbiological equipment and (British) sources of microbial cultures, including bacteria, fungi, and freshwater plankton. (AL)

  1. Experiments with Writing to Teach Microbiology.

    ERIC Educational Resources Information Center

    Cannon, Robert E.

    1990-01-01

    Described are the experiences of one teacher with the teaching of writing in college level microbiology, virology, and immunology courses. Assignments, methods, evaluation, and student responses are discussed. (CW)

  2. Ecotoxicogenomic Approaches for Understanding Molecular Mechanisms of Environmental Chemical Toxicity Using Aquatic Invertebrate, Daphnia Model Organism

    PubMed Central

    Kim, Hyo Jeong; Koedrith, Preeyaporn; Seo, Young Rok

    2015-01-01

    Due to the rapid advent in genomics technologies and attention to ecological risk assessment, the term “ecotoxicogenomics” has recently emerged to describe integration of omics studies (i.e., transcriptomics, proteomics, metabolomics, and epigenomics) into ecotoxicological fields. Ecotoxicogenomics is defined as study of an entire set of genes or proteins expression in ecological organisms to provide insight on environmental toxicity, offering benefit in ecological risk assessment. Indeed, Daphnia is a model species to study aquatic environmental toxicity designated in the Organization for Economic Co-operation and Development’s toxicity test guideline and to investigate expression patterns using ecotoxicology-oriented genomics tools. Our main purpose is to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and relevant modes of toxicity in Daphnia magna. These approaches enable us to address adverse phenotypic outcomes linked to particular gene function(s) and mechanistic understanding of aquatic ecotoxicology as well as exploration of useful biomarkers. Furthermore, key challenges that currently face aquatic ecotoxicology (e.g., predicting toxicant responses among a broad spectrum of phytogenetic groups, predicting impact of temporal exposure on toxicant responses) necessitate the parallel use of other model organisms, both aquatic and terrestrial. By investigating gene expression profiling in an environmentally important organism, this provides viable support for the utility of ecotoxicogenomics. PMID:26035755

  3. Microbiology facilities aboard Space Station Freedom (SSF)

    NASA Technical Reports Server (NTRS)

    Cioletti, L. A.; Mishra, S. K.; Richard, Elizabeth E.; Taylor, R.

    1990-01-01

    A comprehensive microbiological facility is being designed for use on board Space Station Freedom (SSF). Its purpose will be to conduct microbial surveillance of the SSF environment and to examine clinical specimens. Air, water, and internal surfaces will be periodically monitored to satisfy requirements for a safe environment. Crew health will remain a principle objective for every mission. This paper will review the Microbiology Subsystem capabilities planned for SSF application.

  4. Microbiological consequences of indoor composting.

    PubMed

    Naegele, A; Reboux, G; Vacheyrou, M; Valot, B; Millon, L; Roussel, S

    2016-08-01

    Recycling of organic waste appeals to more and more people. The aim of this study was to evaluate the microbiological contamination around organic waste bins at three distances over a 12-month period. Contamination near the customary trash of control households was evaluated at the beginning to ensure that there is no recruitment bias. Air samples using the MAS 100 impactor were carried out in 38 dwellings that do household waste composting and in 10 dwellings of controls. Collection of particles by CIP 10 rotating cup sampler and dust samples collected by electrostatic dust collector cloths were acquired in dwellings that do household waste composting. Samples were analyzed by culture and by real-time quantitative PCR. Information about dwelling characteristics and inhabitant practices was obtained by a standardized questionnaire. The genera most often isolated were Penicillium, Aspergillus, Cladosporium and Streptomyces. Near the organic waste bins, bioaerosol samples showed an increase of Acarus siro (P = 0.001). Sedimented dust analyses highlighted an increase of A. siro, Wallemia sebi, Aspergillus versicolor, and Cladosporium sphaerospermum concentrations after a 12-month survey compared to the beginning. Composting favors microorganism development over time, but does not seem to have an effect on the bioaerosol levels and the surface microbiota beyond 0.5 m from the waste bin. PMID:26299932

  5. Microbiological assay using bioluminescent organism

    SciTech Connect

    Stiffey, A.V.

    1987-12-21

    This invention relates to testing processes for toxicity involving microorganisms and, more particularly, to testing processes for toxicity involving bioluminescent organisms. The present known method of testing oil-well drilling fluids for toxicity employs the mysid shrimp (Mysidopsis bahia) as the assay organism. The shrimp are difficult to raise and handle as laboratory assay organisms. This method is labor-intensive, because it requires a assay time of about 96 hours. Summary of the Invention: A microbiological assay in which the assay organism is the dinoflagellate, Pyrocystis lunula. A sample of a substance to be assayed is added to known numbers of the bioluminescent dinoflagellate and the mixture is agitated to subject the organisms to a shear stress causing them to emit light. The amount of light emitted is measured and compared with the amount of light emitted by a known non-toxic control mixture to determine if there is diminution or non-diminution of light emitted by the sample under test which is an indication of the presence or absence of toxicity, respectively. Accordingly, an object of the present invention is the provision of an improved method of testing substances for toxicity. A further object of the invention is the provision of an improved method of testing oil-well drilling fluids for toxicity using bioluminescent dinoflagellate (Pyrocystis lunula).

  6. [Diabetic foot infections: microbiological aspects].

    PubMed

    Noviello, Silvana; Esposito, Isabella; Pascale, Renato; Esposito, Silvano; Zeppa, Pio

    2012-01-01

    The diagnosis of wound infection is based on clinical signs and local and/or systemic inflammation. Therefore, the examination has a major role in the diagnosis of infected lesions of the foot. Once the clinical diagnosis of infection is made, the next step is to determine the etiology with the aim to undertake a rational and appropriate treatment. The most reliable method for assessing microbiological etiology is the specimen of material from infected lesion to perform a bacterioscopic examination and culture. The microorganisms involved in the etiology of diabetic foot depends on the type of injury and on specific patient features (antibiotic therapy, previous hospitalization). The most frequently detected pathogen is Staphylococcus aureus. Mild infections are mostly caused by Gram positive cocci, with a prevalence of S. aureus. Moderate infections are mostly supported by pyogenic Gram positive cocci, but also Gram-negative bacteria can be involved. In severe infections the etiology is polymicrobial. As regards the involvement of fungi in diabetic foot infections data are few and mostly conflicting. PMID:22982694

  7. 40 CFR 141.52 - Maximum contaminant level goals for microbiological contaminants.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Maximum contaminant level goals for microbiological contaminants. 141.52 Section 141.52 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Maximum Contaminant Level Goals and Maximum...

  8. 40 CFR 141.52 - Maximum contaminant level goals for microbiological contaminants.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Maximum contaminant level goals for microbiological contaminants. 141.52 Section 141.52 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Maximum Contaminant Level Goals and Maximum...

  9. 40 CFR 141.63 - Maximum contaminant levels (MCLs) for microbiological contaminants.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Maximum contaminant levels (MCLs) for microbiological contaminants. 141.63 Section 141.63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS National Primary Drinking Water Regulations:...

  10. 40 CFR 141.63 - Maximum contaminant levels (MCLs) for microbiological contaminants.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Maximum contaminant levels (MCLs) for microbiological contaminants. 141.63 Section 141.63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS National Primary Drinking Water Regulations:...

  11. 40 CFR 141.52 - Maximum contaminant level goals for microbiological contaminants.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 23 2014-07-01 2014-07-01 false Maximum contaminant level goals for microbiological contaminants. 141.52 Section 141.52 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Maximum Contaminant Level Goals and Maximum...

  12. 40 CFR 141.52 - Maximum contaminant level goals for microbiological contaminants.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 24 2013-07-01 2013-07-01 false Maximum contaminant level goals for microbiological contaminants. 141.52 Section 141.52 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Maximum Contaminant Level Goals and Maximum...

  13. 40 CFR 141.52 - Maximum contaminant level goals for microbiological contaminants.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 24 2012-07-01 2012-07-01 false Maximum contaminant level goals for microbiological contaminants. 141.52 Section 141.52 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Maximum Contaminant Level Goals and Maximum...

  14. Use of the Pathogen Modeling Program (PMP) and the Predictive Microbiology Information Portal (PMIP)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Predictive Microbiology Program,(PMP)is based on the fact that most bacterial behaviors are reproducible and can be quantified by characterizing the environmental factors that affect growth, survival, and inactivation using mathematical modeling. The contents of PMP, a collection of models, are ...

  15. One Small Step for the Gram Stain, One Giant Leap for Clinical Microbiology.

    PubMed

    Thomson, Richard B

    2016-06-01

    The Gram stain is one of the most commonly performed tests in the clinical microbiology laboratory, yet it is poorly controlled and lacks standardization. It was once the best rapid test in microbiology, but it is no longer trusted by many clinicians. The publication by Samuel et al. (J. Clin. Microbiol. 54:1442-1447, 2016, http://dx.doi.org/10.1128/JCM.03066-15) is a start for those who want to evaluate and improve Gram stain performance. In an age of emerging rapid molecular results, is the Gram stain still relevant? How should clinical microbiologists respond to the call to reduce Gram stain error rates? PMID:27008876

  16. Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution

    PubMed Central

    Skinner, Michael K.

    2015-01-01

    Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution. PMID:25917417

  17. Biochemical and molecular changes at the cellular level in response to exposure to environmental estrogen-like chemicals

    SciTech Connect

    Roy, D.; Palangat, M.; Chen, Chiao-Wen

    1997-01-01

    Estrogen-like chemical are unique because the estrogenic property of these compounds allows them to act like sex hormones. Whether weak or strong, the estrogenic response of a chemical, if not overcome, will add extra estrogenic burden to the system. At elevated doses, natural estrogens and environmental estrogen-like chemicals are known to produce adverse effects. The source of extra or elevated concentration of estrogen could be either endogenous or exogenous. The potential of exposure for humans and animals to environmental estrogen-like chemicals is high. Only a limited number of estrogen-like compounds, such as diethylstibestrol (DES), bisphenol A, nonylphenol, polychlorinated biphenyls (PCBs), and dichlorodiphenyltrichloroethane (DDT), have been used to assess the biochemical and molecular changes at the cellular level. This article is focused mainly on DES-related observations. In addition to estrogenic effects, environmental estrogen-like chemical produce multiple and multitype genetic and/or nongenetic hits. Exposure of Syrian hamsters to stilbene estrogen (DES) produces several changes in the nuclei of target organ for carcinogenesis (kidney). Exposure of Noble rats to DES also produces several changes in the mammary gland. Some other estrogenic compounds may also follow a similar pattern of effects to DES, because these compounds alter cell cycle kinetics, produce telomeric associations, and produce chromosomal aberrations. It should be noted that a particular or multitype hit(s) will depend upon the nature of the environmental estrogen-like chemical. The role of individual attack leading to a particular change is not clear at this stage. Consequences of these multitypes of attack on the nuclei of cells could be (1) nuclear toxicity/cell death; (2) repair of all the hits and then acting as normal cells; or (3) sustaining most of the hits and acting as unstable cells. 180 refs., 4 figs., 1 tab.

  18. Molecular Approaches to Studying Denitrification

    NASA Astrophysics Data System (ADS)

    Voytek, M. A.

    2001-05-01

    Denitrification is carried out by a diverse array of microbes, mainly as an alternative mode of respiration that allows the organisms to respire using oxidized N compounds instead of oxygen. A common approach in biogeochemistry to the study of the regulation of denitrification is to assess activity by mass balance of substrates and products or direct rate measurements and has intrinsically assumed resource regulation of denitrification. Reported rates can vary significantly even among ecosystems characterized by similar environmental conditions, thus indicating that direct control by abiotic factors often is not sufficient to predict denitrification rates accurately in natural environments. Alternatively, a microbiological approach would proceed with the identification of the organisms responsible and an evaluation of the effect of environmental factors on the biochemical pathways involved. Traditional studies have relied on culturing techniques, such as most probable number enrichments, and have failed to assess the role of the predominately uncultivable members of the microbial community. A combination of biogeochemical measurements and the assessment of the microbial community is necessary and becoming increasingly possible with the development and application of molecular techniques. In order to understand how the composition and physiological behavior of the microbial community affects denitrification rates, we use a suite of molecular techniques developed for phylogenetic and metabolic characterization of denitrifying communities. Molecular tools available for quantifying denitrifying bacteria and assessing their diversity and activity are summarized. Their application is illustrated with examples from marine and freshwater environments. Emerging techniques and their application to ground water studies will be discussed.

  19. Magnetic separation techniques in diagnostic microbiology.

    PubMed Central

    Olsvik, O; Popovic, T; Skjerve, E; Cudjoe, K S; Hornes, E; Ugelstad, J; Uhlén, M

    1994-01-01

    The principles of magnetic separation aided by antibodies or other specific binding molecules have been used for isolation of specific viable whole organisms, antigens, or nucleic acids. Whereas growth on selective media may be helpful in isolation of a certain bacterial species, immunomagnetic separation (IMS) technology can isolate strains possessing specific and characteristic surface antigens. Further separation, cultivation, and identification of the isolate can be performed by traditional biochemical, immunologic, or molecular methods. PCR can be used for amplification and identification of genes of diagnostic importance for a target organism. The combination of IMS and PCR reduces the assay time to several hours while increasing both specificity and sensitivity. Use of streptavidin-coated magnetic beads for separation of amplified DNA fragments, containing both biotin and a signal molecule, has allowed for the conversion of the traditional PCR into an easy-to-read microtiter plate format. The bead-bound PCR amplicons can also easily be sequenced in an automated DNA sequencer. The latter technique makes it possible to obtain sequence data of 300 to 600 bases from 20 to 30 strains, starting with clinical samples, within 12 to 24 h. Sequence data can be used for both diagnostic and epidemiologic purposes. IMS has been demonstrated to be a useful method in diagnostic microbiology. Most recent publications describe IMS as a method for enhancing the specificity and sensitivity of other detection systems, such as PCR, and providing considerable savings in time compared with traditional diagnostic systems. The relevance to clinical diagnosis has, however, not yet been fully established for all of these new test principles. In the case of PCR, for example, the presence of specific DNA in a food sample does not demonstrate the presence of a live organism capable of inducing a disease. However, all tests offering increased sensitivity and specificity of detection

  20. Molecular Detection of Leptospiral DNA in Environmental Water on St. Kitts

    PubMed Central

    Rawlins, Julienne; Portanova, Alexandra; Zuckerman, Ilana; Loftis, Amanda; Ceccato, Pietro; Willingham, Arve Lee; Verma, Ashutosh

    2014-01-01

    Leptospirosis is an important waterborne zoonotic disease caused by pathogenic Leptospira. The pathogen is maintained in a population due to chronic colonization and shedding from renal tubules of domestic and wild animals. Humans and other animals become infected when they come in contact with urine from infected animals, either directly or through urine-contaminated surface water. In this study, we screened environmental water on the island of St. Kitts by using a TaqMan based real time quantitative polymerase chain reaction (qPCR) targeting a pathogen specific leptospiral gene, lipl32. Our results indicate that around one-fifth of tested water sources have detectable leptospiral DNA. PMID:25105546

  1. Application of molecular endpoints in early life stage salmonid environmental biomonitoring.

    PubMed

    Marlatt, Vicki L; Sherrard, Ryan; Kennedy, Chris J; Elphick, James R; Martyniuk, Christopher J

    2016-04-01

    Molecular endpoints can enhance existing whole animal bioassays by more fully characterizing the biological impacts of aquatic pollutants. Laboratory and field studies were used to examine the utility of adopting molecular endpoints for a well-developed in situ early life stage (eyed embryo to onset of swim-up fry) salmonid bioassay to improve diagnostic assessments of water quality in the field. Coastal cutthroat trout (Oncorhynchus clarki clarki) were exposed in the laboratory to the model metal (zinc, 40μg/L) and the polycyclic aromatic hydrocarbon (pyrene, 100μg/L) in water to examine the resulting early life stage salmonid responses. In situ field exposures and bioassays were conducted in parallel to evaluate the water quality of three urban streams in British Columbia (two sites with anthropogenic inputs and one reference site). The endpoints measured in swim-up fry included survival, deformities, growth (weight and length), vitellogenin (vtg) and metallothionein (Mt) protein levels, and hepatic gene expression (e.g., metallothioneins [mta and mtb], endocrine biomarkers [vtg and estrogen receptors, esr] and xenobiotic-metabolizing enzymes [cytochrome P450 1A3, cyp1a3 and glutathione transferases, gstk]). No effects were observed in the zinc treatment, however exposure of swim-up fry to pyrene resulted in decreased survival, deformities and increased estrogen receptor alpha (er1) mRNA levels. In the field exposures, xenobiotic-metabolizing enzymes (cyp1a3, gstk) and zinc transporter (zntBigM103) mRNA were significantly increased in swim-up fry deployed at the sites with more anthropogenic inputs compared to the reference site. Cluster analysis revealed that gene expression profiles in individuals from the streams receiving anthropogenic inputs were more similar to each other than to the reference site. Collectively, the results obtained in this study suggest that molecular endpoints may be useful, and potentially more sensitive, indicators of site

  2. Environmental Changes in MoTe2 Excitonic Dynamics by Defects-Activated Molecular Interaction.

    PubMed

    Chen, Bin; Sahin, Hasan; Suslu, Aslihan; Ding, Laura; Bertoni, Mariana I; Peeters, F M; Tongay, Sefaattin

    2015-05-26

    Monolayers of group VI transition metal dichalcogenides possess direct gaps in the visible spectrum with the exception of MoTe2, where its gap is suitably located in the infrared region but its stability is of particular interest, as tellurium compounds are acutely sensitive to oxygen exposure. Here, our environmental (time-dependent) measurements reveal two distinct effects on MoTe2 monolayers: For weakly luminescent monolayers, photoluminescence signal and optical contrast disappear, as if they are decomposed, but yet remain intact as evidenced by AFM and Raman measurements. In contrast, strongly luminescent monolayers retain their optical contrast for a prolonged amount of time, while their PL peak blue-shifts and PL intensity saturates to slightly lower values. Our X-ray photoelectron spectroscopy measurements and DFT calculations suggest that the presence of defects and functionalization of these defect sites with O2 molecules strongly dictate their material properties and aging response by changing the excitonic dynamics due to deep or shallow states that are created within the optical band gap. Presented results not only shed light on environmental effects on fundamental material properties and excitonic dynamics of MoTe2 monolayers but also highlight striking material transformation for metastable 2D systems such as WTe2, silicone, and phosphorene. PMID:25868985

  3. Evolution of microbiological analytical methods for dairy industry needs.

    PubMed

    Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

    2014-01-01

    Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry's needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards. PMID:24570675

  4. Evolution of microbiological analytical methods for dairy industry needs

    PubMed Central

    Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

    2014-01-01

    Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards. PMID:24570675

  5. [The new tools of microbiological diagnosis of tuberculosis].

    PubMed

    Guillet-Caruba, C; Martinez, V; Doucet-Populaire, F

    2014-12-01

    This review focuses on the role of new tools in the "modern" microbiological diagnosis of tuberculosis. Traditional techniques of microscopy and culture remain essential to diagnostic certainty, but some innovations replace daily the older techniques such as the identification of Mycobacterium tuberculosis complex by immunochromatography or mass spectrometry MALDI-TOF type from positive cultures, or susceptibility testing in liquid medium. New tools that use molecular techniques have become important. They all have in common to optimize the fight against tuberculosis by reducing diagnostic delay. They also allow rapid detection of drug resistance. However, the techniques of gene amplification directly from clinical samples are still less sensitive than culture. Bacteriological diagnosis of tuberculosis disease therefore still relies on the complementarities of different phenotypic and molecular techniques. PMID:25112804

  6. Molecular modeling of interactions in electronic nose sensors for environmental monitoring

    NASA Technical Reports Server (NTRS)

    Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Yen, S. -P. S.; Zhou, H.; Manatt, K.

    2002-01-01

    We report a study aimed at understanding analyte interactions with sensors made from polymer-carbon black composite films. The sensors are used in an Electronic Nose (ENose) which is used for monitoring the breathing air quality in human habitats. The model mimics the experimental conditions of the composite film deposition and formation and was developed using molecular modeling and simulation tools. The Dreiding 2.21 Force Field was used for the polymer and analyte molecules while graphite parameters were assigned to the carbon black atoms. The polymer considered for this work is methyl vinyl ether / maleic acid copolymer. The target analytes include both inorganic (NH3) and organic (methanol) types of compound. Results indicate different composite-analyte interaction behavior.

  7. Environmental Catastrophes in the Earth's History Due to Solar Systems Encounters with Giant Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Pavlov, Alexander A.

    2011-01-01

    In its motion through the Milky Way galaxy, the solar system encounters an average density (>=330 H atoms/cubic cm) giant molecular cloud (GMC) approximately every 108 years, a dense (approx 2 x 103 H atoms/cubic cm) GMC every approx 109 years and will inevitably encounter them in the future. However, there have been no studies linking such events with severe (snowball) glaciations in Earth history. Here we show that dramatic climate change can be caused by interstellar dust accumulating in Earth's atmosphere during the solar system's immersion into a dense (approx ,2 x 103 H atoms/cubic cm) GMC. The stratospheric dust layer from such interstellar particles could provide enough radiative forcing to trigger the runaway ice-albedo feedback that results in global snowball glaciations. We also demonstrate that more frequent collisions with less dense GMCs could cause moderate ice ages.

  8. Genetic-molecular basis for a simple Drosophila melanogaster somatic system that detects environmental mutagens

    SciTech Connect

    Green, M.M.; Todo, T.; Ryo, H.; Fujikawa, K.

    1986-09-01

    We have developed a simple, objectively scorable test for the mutagenicity of chemical compounds which can be fed Drosophila melanogaster. The test depends upon the somatic reversion of the X chromosome, recessive eye color mutation, white-ivory (wi) to wild type (w+). Reversions are scored as clones of w+ facets in the wi eyes of eclosing adults. To increase the sensitivity, a tandem quadruplication containing four wi mutations was synthesized. Thus, in homozygous females eight wi mutations are potentially revertible. Six mutagenic compounds, all alkylating agents, all gave positive results at several concentrations tested. Molecular analysis demonstrates that the induced reversions, germinal and somatic, are associated with the loss of 2.9-kilobase DNA duplicated in the wi mutation.

  9. Microbiological Monitoring in Geothermal Plants

    NASA Astrophysics Data System (ADS)

    Alawi, M.; Lerm, S.; Linder, R.; Vetter, A.; Vieth-Hillebrand, A.; Miethling-Graff, R.; Seibt, A.; Wolfgramm, M.; Wuerdemann, H.

    2010-12-01

    In the scope of the research projects “AquiScreen” and “MiProTherm” we investigated geothermally used groundwater systems under microbial, geochemical, mineralogical and petrological aspects. On one side an enhanced process understanding of engineered geothermal systems is mandatory to optimize plant reliability and economy, on the other side this study provides insights into the microbiology of terrestrial thermal systems. Geothermal systems located in the North German Basin and the Molasse Basin were analyzed by sampling of fluids and solid phases. The investigated sites were characterized by different temperatures, salinities and potential microbial substrates. The microbial population was monitored by the use of genetic fingerprinting techniques and PCR-cloning based on PCR-amplified 16S rRNA and dissimilatory sulfite reductase (DSR) genes. DNA-sequences of fingerprints and cloned PCR-products were compared to public databases and correlated with metabolic classes to provide information about the biogeochemical processes. In all investigated geothermal plants, covering a temperature range from 5° to 120°C, microorganisms were found. Phylogenetic gene analyses indicate a broad diversity of microorganisms adapted to the specific conditions in the engineered system. Beside characterized bacteria like Thermus scotoductus, Siderooxidans lithoautotrophicus and the archaeon Methanothermobacter thermoautotrophicus a high number of so far uncultivated microorganisms was detected. As it is known that - in addition to abiotic factors - microbes like sulfate-reducing bacteria (SRB) are involved in the processes of corrosion and scaling in plant components, we identified SRB by specific analyses of DSR genes. The SRB detected are closely related to thermotolerant and thermophilic species of Desulfotomaculum, Thermodesulfovibrio, Desulfohalobium and Thermodesulfobacterium, respectively. Overall, the detection of microbes known to be involved in biocorrosion and the

  10. Multiparametric comparison of chromogenic-based culture methods used to assess the microbiological quality of drinking water and the mFC method combined with a molecular confirmation procedure.

    PubMed

    Maheux, Andrée F; Dion-Dupont, Vanessa; Bisson, Marc-Antoine; Bouchard, Sébastien; Jubinville, Éric; Nkuranga, Martine; Rodrigue, Lynda; Bergeron, Michel G; Rodriguez, Manuel J

    2015-03-01

    MI agar and Colilert(®), as well as mFC agar combined with an Escherichia coli-specific molecular assay (mFC + E. coli rtPCR), were compared in terms of their sensitivity, ease of use, time to result and affordability. The three methods yielded a positive E. coli signal for 11.5, 10.8, and 11.5% of the 968 well water samples tested, respectively. One hundred and thirty-six (136) samples gave blue colonies on mFC agar and required confirmation. E. coli-specific rtPCR showed false-positive results in 23.5% (32/136) of cases. In terms of ease of use, Colilert was the simplest method to use while the MI method provided ease of use comparable to all membrane filtration methods. However, the mFC + E. coli rtPCR assay required highly trained employees for confirmation purposes. In terms of affordability, and considering contamination rate of well water samples tested, the Colilert method and the mFC + E. coli rtPCR assay were at least five times more costly than the MI agar method. Overall, compared with the other two methods tested, the MI agar method offers the most advantages to assess drinking water quality. PMID:25719466

  11. Stereo-electronic, vibrational, and environmental contributions to polarizabilities of large molecular systems: a feasible anharmonic protocol

    PubMed Central

    Egidi, Franco; Giovannini, Tommaso; Piccardo, Matteo; Bloino, Julien; Cappelli, Chiara; Barone, Vincenzo

    2015-01-01

    Reliable computations of linear and non-linear optical properties of molecular systems in condensed phases require a proper account of stereo-electronic, vibrational, and environmental effects. In the framework of density functional theory, these effects can be accurately introduced using second-order vibrational perturbation theory in conjunction with polarizable continuum models. We illustrate the combination of an anharmonic description of the ground-state potential energy surface with solvation effects treated with the polarizable continuum model (PCM) in the calculation of the electronic, zero-point, and pure vibrational polarizabilities of selected systems. The description of the solvation environment is enriched by taking into account the dynamical aspects of the solute-solvent interactions through the inclusion of both electronic and vibrational non-equilbrium effects, as well as the direct effect of the solvent on the electric field that generates the molecular response (local field effect). This treatment yields accurate results which can be directly compared with experimental findings without the need of empirical corrections. PMID:26550004

  12. Intersex related gene expression profiles in clams Scrobicularia plana: Molecular markers and environmental application.

    PubMed

    Ciocan, Corina M; Cubero-Leon, Elena; Langston, William J; Pope, Nick; Cornelius, Keith; Hill, E M; Alvarez-Munoz, Diana; Indiveri, Paolo; Lerebours, Adelaide; Minier, Christophe; Rotchell, Jeanette M

    2015-06-30

    Intersex, the appearance of female characteristics in male gonads, has been identified in several aquatic species. It is a widespread phenomenon in populations of the bivalve, Scrobicularia plana, from the southwest coast of the U.K. Genes previously identified as differentially expressed (ferritin, testicular haploid expressed gene, THEG, proliferating cell nuclear antigen, PCNA; receptor activated protein kinase C, RACK; cytochrome B, CYB; and cytochrome c oxidase 1, COX1) in intersex clams relative to normal male clams, were selected for characterisation and an environmental survey of the Channel region. Transcripts were significantly differentially expressed at sites with varying intersex incidence and contaminant burdens. Significant correlations between specific gene expressions, key contaminants and sampling locations have been identified, though no single gene was associated with intersex incidence. The results highlight the difficulty in understanding the intersex phenomenon in molluscs where there is still a lack of knowledge on the control of normal reproduction. PMID:25746199

  13. Molecular diversity and distribution of marine fungi across 130 European environmental samples.

    PubMed

    Richards, Thomas A; Leonard, Guy; Mahé, Frédéric; Del Campo, Javier; Romac, Sarah; Jones, Meredith D M; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

    2015-11-22

    Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal 'OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments. PMID:26582030

  14. The Molecular Ecology of Guerrero Negro: Justifying the Need for Environmental Genomics

    NASA Technical Reports Server (NTRS)

    Smith, Jason M.; Green, Stefan J.; Moisander, Pia; Roberts, Kathryn J.; Francis, Chris; Prufert-Bebout, Leslie; Bebout, Brad M.

    2006-01-01

    The record of life on the only planet where it is known to exist is contained in the biogeochemical processes that organisms catalyze for their survival, in the compounds that they produce, and in their phylogenetic (evolutionary) relationships to each other. We manipulated sulfate and nutrient concentrations in intact microbial mats over periods of time up to a year. The objectives of the manipulations were: 1) characterize the diversity of process-associated functional genes; 2) understand environmental conditions leading to shifts in microbial guilds; 3) monitor/identify competitive responses of organisms sharing a metabolic niche. Characterization of functional genes associated with carbon (mcrA), nitrogen (nifH, nirK) and sulfur (dsrkB) cycling performed to date provided insight into the diversity and metabolic potential of the system; however, we only identified broad scale correlations between gene abundances and changes in mat physiology. For instance, increases in methane production by mats subjected to lowered sulfate and salinity concentrations were correlated with an observed increase in abundance of hydrogenotroph-like mcrA genes. However, due to low sequence similarity to any cultured isolates, phylogenetic associations only allow order level taxonomic commentary, preventing any associations being made on the cellular level. In each of the genes characterized from these experiments, a significant portion of sequences recovered show minimal phylogenetic affiliation to cultured organisms, preventing any understanding of inter-community dynamics and the functional capacities of these unknown organisms. Environmental genomics may provide insight into mat systems by allowing the correlation of functional genes with phylogenetic markers.

  15. Molecular diversity and distribution of marine fungi across 130 European environmental samples

    PubMed Central

    Richards, Thomas A.; Leonard, Guy; Mahé, Frédéric; del Campo, Javier; Romac, Sarah; Jones, Meredith D. M.; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

    2015-01-01

    Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal ‘OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments. PMID:26582030

  16. Effectiveness of visual inspection compared with non-microbiologic methods to determine the thoroughness of post-discharge cleaning

    PubMed Central

    2013-01-01

    Background Published data to date have provided a limited comparison between non-microbiologic methods—particularly visual inspection—and a microbiologic comparator to evaluate the effectiveness of environmental cleaning of patient rooms. We sought to compare the accuracy of visual inspection with other non-microbiologic methods of assessing the effectiveness of post-discharge cleaning (PDC). Methods Prospective evaluation to determine the effectiveness of PDC in comparison to a microbiologic comparator. Using a highly standardized methodology examining 15 high-touch surfaces, the effectiveness of PDC was evaluated by visual inspection, the removal of fluorescent marker (FM) placed prior to room occupancy, quantification of adenosine triphosphate (ATP) levels, and culture for aerobic colony counts (ACC). Results Twenty rooms including 293 surfaces were sampled in the study, including 290 surfaces sampled by all four methods. ACC demonstrated 72% of surfaces to be microbiologically clean. Visual inspection, FM, ATP demonstrated 57%, 49%, and 66% of surfaces to be clean. Using ACC as a microbiologic comparator, the sensitivity of visual inspection, FM, and ATP to detect a clean surface were 60%, 51%, and 70%, respectively; the specificity of visual inspection, FM, and ATP were 52%, 56%, and 44%. Conclusions In assessing the effectiveness of PDC, there was poor correlation between the two most frequently studied commercial methods and a microbiologic comparator. Visual inspection performed at least as well as commercial methods, directly addresses patient perception of cleanliness, and is economical to implement. PMID:24088298

  17. Molecular characterization of two glutathione peroxidase genes of Panax ginseng and their expression analysis against environmental stresses.

    PubMed

    Kim, Yu-Jin; Jang, Moon-Gi; Noh, Hae-Yong; Lee, Hye-Jin; Sukweenadhi, Johan; Kim, Jong-Hak; Kim, Se-Yeong; Kwon, Woo-Saeng; Yang, Deok-Chun

    2014-02-01

    Glutathione peroxidases (GPXs) are a group of enzymes that protect cells against oxidative damage generated by reactive oxygen species (ROS). GPX catalyzes the reduction of hydrogen peroxide (H2O2) or organic hydroperoxides to water or alcohols by reduced glutathione. The presence of GPXs in plants has been reported by several groups, but the roles of individual members of this family in a single plant species have not been studied. Two GPX cDNAs were isolated and characterized from the embryogenic callus of Panax ginseng. The two cDNAs had an open reading frame (ORF) of 723 and 681bp with a deduced amino acid sequence of 240 and 226 residues, respectively. The calculated molecular mass of the matured proteins are approximately 26.4kDa or 25.7kDa with a predicated isoelectric point of 9.16 or 6.11, respectively. The two PgGPXs were elevated strongly by salt stress and chilling stress in a ginseng seedling. In addition, the two PgGPXs showed different responses against biotic stress. The positive responses of PgGPX to the environmental stimuli suggested that ginseng GPX may help to protect against environmental stresses. PMID:24269671

  18. Environmental Impact of Steel Slag Reused as Aggregates in Road Manufacturing: Molecular Mechanisms of Chromium and Vanadium Release

    SciTech Connect

    Chaurand, P.; Borschneck, D.; Bottero, J. Y.; Proux, O.; Briois, V.; Salome, M.; Susini, J.; Ferrasse, J. H.; Rose, J

    2007-02-02

    The speciation of chromium (Cr) and vanadium (V), two potential pollutants, present as traces in a residue from steel-making operations (BOF slag) and their leaching behavior were studied to assess the environmental compatibility of this waste as a recycled material for road making. A multi techniques approach (XAS, XANES, micro-XANES, micro-XRF and micro-XRD) was required to assess the molecular mechanisms of Cr and V release. Leaching tests have shown that Cr is little released and moreover remains at its initial trivalent form, less toxic, even during leaching. One part of octahedral Cr(III) ions replaces structurally the octahedral Fe(III) in a dicalcium aluminoferrite phase and the other part is associated to a solid solution (Fe, Mn, Mg)O. Spatially resolved techniques allowed showing that Cr is tightly bound to a secondary phase formed during leaching which controls its solubility. V present in BOF slag is environmentally more critical because its release is relatively high and it is oxidized to its most toxic form (V(V)) during leaching. Micro-XRF coupled with chemometric analysis (SIMPLISMA) indicates that V is also associated to a dicalcium aluminoferrite.

  19. A review of environmental characteristics and effects of low-molecular weight organic acids in the surface ecosystem.

    PubMed

    Xiao, Min; Wu, Fengchang

    2014-05-01

    Low molecular weight organic acids (LMWOAs) are prevalent on the earth's surface. They are vital intermediate products during metabolic pathways of organic matter and participate in the tricarboxylic acid cycle during life activities. Photochemical reactions are pivotal for LMWOAs' origination and play a large role in determining their diversity and their ultimate fate. Within the long time that organic matter is preserved in sediments, it can be decomposed and converted to release organic and inorganic pollutants as well as C, N, and P nutrients, which are of potential ecological risk in causing secondary pollution to lake water. The sediment pool is a comprehensive and complex compartment closely associated with overlying water by various biochemical processes, during which LMWOAs play critical roles to transport and transform elements. This article elucidates geochemical behaviors of LMWOAs in the surface environment in details, taking natural water, soil, and aerosol as examples, focusing on reviewing research developments on sources and characteristics, migration and mineralization of LMWOAs and relevant environmental effects. Simultaneously, this review article depicts the categories and contents of LMWOAs or their contribution to DOC in environmental media, and evaluates their importance during organic matter early diagenesis. Through concluding and discussing the conversion mechanisms and influencing factors, the next research orientations on LMWOAs in lake ecosystems are determined, mainly concerning relationships with hydrochemical parameters and microorganisms, and interactions with pollutants. This will enrich the knowledge on organic matter degradation and related environmental effects, and help reconstruct a theoretical framework for organic compound succession and influencing factors, providing basic data for lake eutrophication and ecological risk assessment, conducive to better control over water pollution and proper management of water quality

  20. Sub-lethal coral stress: detecting molecular responses of coral populations to environmental conditions over space and time.

    PubMed

    Edge, S E; Shearer, T L; Morgan, M B; Snell, T W

    2013-03-15

    In order for sessile organisms to survive environmental fluctuations and exposures to pollutants, molecular mechanisms (i.e. stress responses) are elicited. Previously, detrimental effects of natural and anthropogenic stressors on coral health could not be ascertained until significant physiological responses resulted in visible signs of stress (e.g. tissue necrosis, bleaching). In this study, a focused anthozoan holobiont microarray was used to detect early and sub-lethal effects of spatial and temporal environmental changes on gene expression patterns in the scleractinian coral, Montastraea cavernosa, on south Florida reefs. Although all colonies appeared healthy (i.e. no visible tissue necrosis or bleaching), corals were differentially physiologically compensating for exposure to stressors that varied over time. Corals near the Port of Miami inlet experienced significant changes in expression of stress responsive and symbiont (zooxanthella)-specific genes after periods of heavy precipitation. In contrast, coral populations did not demonstrate stress responses during periods of increased water temperature (up to 29°C). Specific acute and long-term localized responses to other stressors were also evident. A correlation between stress response genes and symbiont-specific genes was also observed, possibly indicating early processes involved in the maintenance or disruption of the coral-zooxanthella symbiosis. This is the first study to reveal spatially- and temporally-related variation in gene expression in response to different stressors of in situ coral populations, and demonstrates that microarray technology can be used to detect specific sub-lethal physiological responses to specific environmental conditions that are not visually detectable. PMID:23291051

  1. Molecular epidemiology studies on occupational and environmental exposure to mutagens and carcinogens, 1997-1999.

    PubMed Central

    Srám, R J; Binková, B

    2000-01-01

    Molecular epidemiology is a new and evolving area of research, combining laboratory measurement of internal dose, biologically effective dose, biologic effects, and influence of individual susceptibility with epidemiologic methodologies. Biomarkers evaluated were selected according to basic scheme: biomarkers of exposure--metabolites in urine, DNA adducts, protein adducts, and Comet assay parameters; biomarkers of effect--chromosomal aberrations, sister chromatid exchanges, micronuclei, mutations in the hypoxanthine-guanine phosphoribosyltransferase gene, and the activation of oncogenes coding for p53 or p21 proteins as measured on protein levels; biomarkers of susceptibility--genetic polymorphisms of genes CYP1A1, GSTM1, GSTT1, NAT2. DNA adducts measured by 32P-postlabeling are the biomarker of choice for the evaluation of exposure to polycyclic aromatic hydrocarbons. Protein adducts are useful as a biomarker for exposure to tobacco smoke (4-aminobiphenyl) or to smaller molecules such as acrylonitrile or 1,3-butadiene. Of the biomarkers of effect, the most common are cytogenetic end points. Epidemiologic studies support the use of chromosomal breakage as a relevant biomarker of cancer risk. The use of the Comet assay and methods analyzing oxidative DNA damage needs reliable validation for human biomonitoring. Until now there have not been sufficient data to interpret the relationship between genotypes, biomarkers of exposure, and biomarkers of effect for assessing the risk of human exposure to mutagens and carcinogens. PMID:10698723

  2. Using Molecular Simulation to Develop New Materials for Energy and Environmental Applications

    NASA Astrophysics Data System (ADS)

    Maginn, Edward

    2012-02-01

    We face two enormous challenges in the coming decades. First, we must find ways to provide clean, affordable energy to an ever-growing population. Second, as underdeveloped countries advance, we must find ways to provide access to advanced technologies that enhance human wellbeing. What makes these two challenges even more daunting is that they both must be met using sustainable technologies; simply relying on old dirty technologies is not an option. In this talk, I will show how approaches rooted in chemical physics are being used to develop new materials that can be used to meet these challenges. In particular, I will give examples where molecular-based simulations are being used in three areas: 1) the discovery of new ionic liquid solvents for capturing CO2 produced from fossil fuel combustion; 2) the development of new refrigerants that have better performance and significantly lower global warming potentials than existing refrigerants; and 3) fundamental investigations of actinide ions in solution, with the objective of developing new separation processes for nuclear waste remediation and fuel reprocessing technologies.

  3. Environmental surveillance and molecular investigation of Legionella spp. in Apulia, in the years 2008-2011.

    PubMed

    Iatta, R; Cuna, T; Napoli, C; De Giglio, O; Montagna, M T

    2013-01-01

    Legionella spp. is considered an emerging microorganism involved in aquatic environments contamination and cause of Legionnaires' disease. The aims of the study are to evaluate the level of contamination of Legionella spp. in the water system of the largest Hospital of Apulia region during a 4-year surveillance and to establish, by molecular method, the presence of a predominant genotype of L. pn. sg 1. The results showed that Legionella spp. was present in 36% of water samples with Legionella pneumophila serogroup 1 (L. pn. sg 1) the most prevalent species and serogroup and the wards most contaminated are the high risk units. In addition, despite four main clones of L. pn. sg 1 were identified, a predominant genotype existed. In conclusion the study demonstrates the necessity for periodic evaluation on hospitals water system to assess the potential contamination of Legionella spp., performing decontamination in the presence of bacterial contamination, even low, in particular in high risk wards. Moreover, the switching of the disinfection methods may be suggested in order to prevent resistance phenomenon by some L. pn. sg 1 clones. PMID:24048182

  4. Environmental effects on molecular biomarkers expression in pancreatic and brain cancer

    NASA Astrophysics Data System (ADS)

    Mensah, Lawrence; Mallidi, Srivalleesha; Massodi, Iqbal; Anbil, Sriram; Mai, Zhiming; Hasan, Tayyaba

    2013-03-01

    A complete understanding of the biological mechanisms regulating devastating disease such as cancer remains elusive. Pancreatic and brain cancers are primary among the cancer types with poor prognosis. Molecular biomarkers have emerged as group of proteins that are preferentially overexpressed in cancers and with a key role in driving disease progression and resistance to chemotherapy. The epidermal growth factor receptor (EGFR), a cell proliferative biomarker is particularly highly expressed in most cancers including brain and pancreatic cancers. The ability of EGFR to sustain prolong cell proliferation is augmented by biomarkers such as Bax, Bcl-XL and Bcl-2, proteins regulating the apoptotic process. To better understand the role and effect of the microenvironment on these biomarkers in pancreatic cancer (PaCa); we analysed two pancreatic tumor lines (AsPc-1 and MiaPaCa-2) in 2D, 3D in-vitro cultures and in orthotopic tumors at different growth stages. We also investigated in patient derived glioblastoma (GBM) tumor cultures, the ability to utilize the EGFR expression to specifically deliver photosensitizer to the cells for photodynamic therapy. Overall, our results suggest that (1) microenvironment changes affect biomarker expression; thereby it is critical to understand these effects prior to designing combination therapies and (2) EGFR expression in tumor cells indeed could serve as a reliable and a robust biomarker that could be used to design targeted and image-guided photodynamic therapy.

  5. Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize

    PubMed Central

    Hekkala, Evon R.; Platt, Steven G.; Thorbjarnarson, John B.; Rainwater, Thomas R.; Tessler, Michael; Cunningham, Seth W.; Twomey, Christopher; Amato, George

    2015-01-01

    The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet’s crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research. PMID:26473062

  6. Atomic and molecular physics of plasma-based environmental technologies for abatement of volatile organic compounds

    SciTech Connect

    Penetrante, B.M.; Hsiao, M.C.; Bardsley, J.N.; Merritt, B.T.; Vogtlin, G.E.; Kuthi, A.; Burkhart, C.P.; Bayless, J.R.

    1996-08-01

    Non-thermal plasma techniques represent a new generation of air emission control technology that potentially could treat large-volume emissions containing dilute concentrations of volatile organic compounds (VOCs). In order to apply non-thermal plasmas in an industrial scale, it is important to establish the electrical power requirements and byproducts of the process. There is a need for reliable data concerning the primary decomposition mechanisms and subsequent chemical kinetics associated with non-thermal processing of VOCs. There are many basic atomic and molecular physics issues that are essential in evaluating the economic performance of non- thermal plasma reactors. These studies are important in understanding how the input electrical power is dissipated in the plasma and how efficiently it is converted to the production of the plasma species (radicals, ions, or electrons) responsible for the decomposition of the VOCs. This paper will present results from the basic experimental and theoretical studies aimed at identifying the reaction mechanisms responsible for the primary decomposition of various types of VOCs.

  7. Integrating molecular, phenotypic and environmental data to elucidate patterns of crocodile hybridization in Belize.

    PubMed

    Hekkala, Evon R; Platt, Steven G; Thorbjarnarson, John B; Rainwater, Thomas R; Tessler, Michael; Cunningham, Seth W; Twomey, Christopher; Amato, George

    2015-09-01

    The genus Crocodylus comprises 12 currently recognized species, many of which can be difficult to differentiate phenotypically. Interspecific hybridization among crocodiles is known to occur in captivity and has been documented between some species in the wild. The identification of hybrid individuals is of importance for management and monitoring of crocodilians, many of which are Convention on International Trade in Endangered Species (CITES) listed. In this study, both mitochondrial and nuclear DNA markers were evaluated for their use in confirming a suspected hybrid zone between American crocodile (Crocodylus acutus) and Morelet's crocodile (Crocodylus moreletii) populations in southern Belize where individuals and nests exhibiting atypical phenotypic features had previously been observed. Patterns observed in both phenotypic and molecular data indicate possible behavioural and ecological characteristics associated with hybridization events. The results of the combined analyses found that the majority of suspected hybrid samples represent crosses between female C. acutus and male C. moreletii. Phenotypic data could statistically identify hybrids, although morphological overlap between hybrids and C. moreletii reduced reliability of identification based solely on field characters. Ecologically, C. acutus was exclusively found in saline waters, whereas hybrids and C. moreletii were largely absent in these conditions. A hypothesized correlation between unidirectional hybridization and destruction of C. acutus breeding habitats warrants additional research. PMID:26473062

  8. Microbiological water examination during laboratory courses generates new knowledge for students, scientists and the government.

    PubMed

    Svanevik, Cecilie Smith; Lunestad, Bjørn Tore

    2015-10-01

    Contaminated water is globally the main vehicle for microbial pathogens in most regions. Teaching future microbiologist and employees in the food industry on the importance of hygienically satisfactory water, microbiological analyses and how to ensure good water quality and safety is highly relevant. This paper presents a complete experimental design for water analyses as a tool to teach students the methods and other key elements in microbiology, including food safety, environmental dissemination and survival of microorganisms, laboratory practices, water legislation and critical evaluation of results. All results from the last 10 classes (2006-2015) in a university course on seafood microbiology have been compiled and are presented here. Questionnaires used with former students reveal that the laboratory course is highly appreciated, and that many students remember important aspects of the water analyses, even after several years. The questionnaire results were consistent with our perception that some students find calculation of dilutions difficult to comprehend. PMID:26337153

  9. Bioremediation: environmental clean-up through pathway engineering.

    PubMed

    Singh, Shailendra; Kang, Seung Hyun; Mulchandani, Ashok; Chen, Wilfred

    2008-10-01

    Given the immense risk posed by widespread environmental pollution by inorganic and organic chemicals, novel methods of decontamination and clean-up are required. Owing to the relatively high cost and the non-specificity of conventional techniques, bioremediation is a promising alternative technology for pollutant clean-up. Advances in bioremediation harness molecular, genetic, microbiology, and protein engineering tools and rely on identification of novel metal-sequestering peptides, rational and irrational pathway engineering, and enzyme design. Recent advances have been made for enhanced inorganic chemical remediation and organic chemical degradation using various pathway-engineering approaches and these are discussed in this review. PMID:18760355

  10. Molecular ecological responses of dinoflagellate, Karenia mikimotoi to environmental nitrate stress.

    PubMed

    Lei, Qiang-Yong; Lü, Song-Hui

    2011-12-01

    Karenia mikimotoi is one of the most important harmful algal species in the Chinese coastal waters, and which produce hemolytic toxins and ichthyotoxins, resulting in devastating economic losses. Previous studies demonstrated that the increase of nitrate concentration could promote the growth and reproduction of K. mikimotoi. However, the intrinsic mechanisms regarding the effects of nitrate on the K. mikimotoi photosynthesis, nucleic acid replication and differential protein expression remain to be elucidated. Our study demonstrated that nitrate stress inhibited growth of K. mikimotoi (p<0.01). Algal chlorophyll fluorescence intensity varied slightly while algal cell cycle succession was significantly retarded by nitrate stress (p<0.05). Sixteen proteins were detected only in nitrate-limited cultures which related to nitrate transport, signal transduction, amino acid metabolism, DNA repair and hemolysin manufacture. Eleven proteins were detected only in nitrate-replete sample and were related to photorespiration, reproduction and growth, assistance of protein modification, cytoskeleton stability and signal transduction. Based on analysis of differential proteomic functional annotations, we hypothesized a proteomic response mechanism of K. mikimotoi to environmental nitrate stress. PMID:22019194

  11. Effects of potential environmental interferents on kinesin-powered molecular shuttles

    NASA Astrophysics Data System (ADS)

    Bachand, Marlene; Bachand, George D.

    2012-05-01

    Biomolecular motor-powered active transport represents an alternate means for analyte processing in nanoscale biosensors and bioanalytical devices. For example, a prototype ``smart dust'' biosensor has recently been reported in which the motor protein kinesin processes antibody-functionalized microtubules (MTs) to capture and separate optically tagged protein analytes. A potential limitation of this technology, however, involves the inhibition of transport function by interfering compounds that may be present in raw samples. Here we characterized the response of kinesin-MT transport to a range of potential interferents including solvents, acids, oxidizers, and environmental contaminants. The results of kinesin motility assays suggest that, among the tested interferents, only acetic acid and sodium hypochlorite adversely affected MT transport, primarily due to depolymerization of MT filaments. While negative effects were not observed for the remaining compounds tested, enhancement in motility was observed in the presence of acetone, antifreeze, and organic matter. Overall, the data suggest that kinesin-MT transport is resilient against a variety of common interferents, but primarily susceptible to failure due to significant changes in pH or the presence of an oxidizer.

  12. Molecular taxonomy of scopulariopsis-like fungi with description of new clinical and environmental species.

    PubMed

    Jagielski, Tomasz; Sandoval-Denis, Marcelo; Yu, Jin; Yao, Limin; Bakuła, Zofia; Kalita, Joanna; Skóra, Magdalena; Krzyściak, Paweł; de Hoog, G Sybren; Guarro, Josep; Gené, Josepa

    2016-04-01

    The taxonomy of scopulariopsis-like fungi, comprising numerous human opportunistic species, has recently been reassessed with delineation of the genera Microascus, Pithoascus, Pseudoscopulariopsis, and Scopulariopsis, using morphological data and multilocus sequence analysis based on four loci (ITS, LSU, EF-1α, and TUB). In this study, the same genetic markers were used to investigate a set of clinical and environmental isolates, morphologically identified as Microascus and Scopulariopsis spp. The ingroups of the concatenated phylogenetic tree resolved 41 species clades, with isolates distributed in four main lineages corresponding to the genera Microascus, Pithoascus, Scopulariopsis, and newly established genus Fuscoannellis, typified by Scopulariopsis carbonaria. The new species Microascus chinensis, Microascus onychoides, Microascus pseudolongirostris, Pithoascus lunatus, and Scopulariopsis macurae were described. Microascus trigonosporus var. terreus and Scopulariopsis alboflavescens were found different from M. trigonosporus and Scopulariopsis brevicaulis, respectively. All the species identified in the study, except Fuscoannellis carbonaria and S. macurae, originated from clinical samples, suggesting their potential role in human disease. The use of a four marker combination was demonstrated an efficient and reliable approach to infer phylogenetic relationships among the scopulariopsis-like fungi. Yet, the only genetic marker able to discriminate all species was EF-1α, therefore proposed as a secondary barcode for the identification of these fungi. PMID:27020159

  13. Molecular detection of enterotoxins in environmental strains of Aeromonas hydrophila and Aeromonas jandaei.

    PubMed

    Balsalobre, L C; Dropa, M; Matté, G R; Matté, M H

    2009-12-01

    Aeromonas species are widely distributed in aquatic environments and recent studies include the genus in the emergent pathogens group because of its frequent association with local and systemic infections in immunocompetent humans. Aiming to search for virulence genes in environmental strains of Aeromonas hydrophila and Aeromonas jandaei, we designed specific primers to detect act/hlyA/aer complex and alt genes. Primers described elsewhere were used to detect ast. Eighty-seven strains previously identified using phenotypic and genotypic tests as A. hydrophila (41) and A. jandaei (46) were analysed for the presence of the virulence genes using PCR. DNA fragments of expected size were purified and directly sequenced. Among the 41 strains of A. hydrophila 70.7% (29), 97.6% (40) and 26.8% (11) possessed act/hlyA/aer complex, ast and alt genes, respectively. Among the 46 strains of A. jandaei, 4.4% (2), 0% (0) and 32.6% (15) were positive for act/hly A/aer complex, ast and alt genes, respectively. Sequencing allowed for the confirmation of amplified products using BLAST. The present work proposes a specific and rapid diagnostic method to detect the main virulence determinants of Aeromonas, a genus potentially pathogenic to humans. PMID:19590136

  14. Cost analysis in a clinical microbiology laboratory.

    PubMed

    Brezmes, M F; Ochoa, C; Eiros, J M

    2002-08-01

    The use of models for business management and cost control in public hospitals has led to a need for microbiology laboratories to know the real cost of the different products they offer. For this reason, a catalogue of microbiological products was prepared, and the costs (direct and indirect) for each product were analysed, along with estimated profitability. All tests performed in the microbiology laboratory of the "Virgen de la Concha" Hospital in Zamora over a 2-year period (73192 tests) were studied. The microbiological product catalogue was designed using homogeneity criteria with respect to procedures used, workloads and costs. For each product, the direct personnel costs (estimated from workloads following the method of the College of American Pathologists, 1992 version), the indirect personnel costs, the direct and indirect material costs and the portion of costs corresponding to the remaining laboratory costs (capital and structural costs) were calculated. The average product cost was 16.05 euros. The average cost of a urine culture (considered, for purposes of this study, as a relative value unit) reached 13.59 euros, with a significant difference observed between positive and negative cultures (negative urine culture, 10.72 euros; positive culture, 29.65 euros). Significant heterogeneity exists, both in the costs of different products and especially in the cost per positive test. The application of a detailed methodology of cost analysis facilitates the calculation of the real cost of microbiological products. This information provides a basic tool for establishing clinical management strategies. PMID:12226688

  15. Microbiology of water and fluids for hemodialysis.

    PubMed

    Nystrand, Rolf

    2008-05-01

    In hemodialysis, huge amounts of water are used for diluting the concentrates to produce dialysis fluid. The water is produced on site by reverse osmosis units. The chemical and microbiological quality of the water is essential for dialysis patients. Reverse osmosis units produce water of acceptable chemical quality that can be kept throughout the water system. The microbiological water quality, on the other hand, does not depend on the reverse osmosis unit but on the maintenance of the whole water system. All over the world, dialysis units take water samples and send them to laboratories for cultivation and endotoxin tests. Depending on the method of microbiological analysis, the water may be judged to be very good even if in reality it is much worse and outside of standard recommendations. When standardizing the methods with adequate cultivation of water samples, the accuracy of the tests will be better, and as a result, dialysis units can use their resources for keeping the water systems in good shape, i.e. disinfect preventively and frequently and use less effort in collecting samples. This will benefit patients, who will receive a high-quality dialysis fluid, thus eliminating the effects of microbiological impacts such as increased levels of inflammation markers (e.g. C-reactive protein). In the situation of performing hemodiafiltration by producing the substitution fluid "on-line", it is even more important to have a sensitive method of microbiological verification to follow-up the hygienic quality. PMID:18490224

  16. Molecular characterization of Salmonella enterica serovar Saintpaul isolated from imported seafood, pepper, environmental and clinical samples.

    PubMed

    Akiyama, Tatsuya; Khan, Ashraf A; Cheng, Chorng-Ming; Stefanova, Rossina

    2011-09-01

    A total of 39 Salmonella enterica serovar Saintpaul strains from imported seafood, pepper and from environmental and clinical samples were analyzed for the presence of virulence genes, antibiotic resistance, plasmid and plasmid replicon types. Pulsed-field gel electrophoresis (PFGE) fingerprinting using the XbaI restriction enzyme and plasmid profiling were performed to assess genetic diversity. None of the isolates showed resistance to ampicillin, chloramphenicol, gentamicin, kanamycin, streptomycin, sulfisoxazole, and tetracycline. Seventeen virulence genes were screened for by PCR. All strains were positive for 14 genes (spiA, sifA, invA, spaN, sopE, sipB, iroN, msgA, pagC, orgA, prgH, lpfC, sitC, and tolC) and negative for three genes (spvB, pefA, and cdtB). Twelve strains, including six from clinical samples and six from seafood, carried one or more plasmids. Large plasmids, sized greater than 50 kb were detected in one clinical and three food isolates. One plasmid was able to be typed as IncI1 by PCR-based replicon typing. There were 25 distinct PFGE-XbaI patterns, clustered to two groups. Cluster A, with 68.5% similarity mainly consists of clinical isolates, while Cluster C, with 67.6% similarity, mainly consisted of shrimp isolates from India. Our findings indicated the genetic diversity of S. Saintpaul in clinical samples, imported seafood, and the environment and that this serotype possesses several virulent genes and plasmids which can cause salmonellosis. PMID:21645810

  17. Cellular and molecular mechanisms of immunomodulation in the brain through environmental enrichment

    PubMed Central

    Singhal, Gaurav; Jaehne, Emily J.; Corrigan, Frances; Baune, Bernhard T.

    2014-01-01

    Recent studies on environmental enrichment (EE) have shown cytokines, cellular immune components [e.g., T lymphocytes, natural killer (NK) cells], and glial cells in causal relationship to EE in bringing out changes to neurobiology and behavior. The purpose of this review is to evaluate these neuroimmune mechanisms associated with neurobiological and behavioral changes in response to different EE methods. We systematically reviewed common research databases. After applying all inclusion and exclusion criteria, 328 articles remained for this review. Physical exercise (PE), a form of EE, elicits anti-inflammatory and neuromodulatory effects through interaction with several immune pathways including interleukin (IL)-6 secretion from muscle fibers, reduced expression of Toll-like receptors on monocytes and macrophages, reduced secretion of adipokines, modulation of hippocampal T cells, priming of microglia, and upregulation of mitogen-activated protein kinase phosphatase-1 in central nervous system. In contrast, immunomodulatory roles of other enrichment methods are not studied extensively. Nonetheless, studies showing reduction in the expression of IL-1β and tumor necrosis factor-α in response to enrichment with novel objects and accessories suggest anti-inflammatory effects of novel environment. Likewise, social enrichment, though considered a necessity for healthy behavior, results in immunosuppression in socially defeated animals. This has been attributed to reduction in T lymphocytes, NK cells and IL-10 in subordinate animals. EE through sensory stimuli has been investigated to a lesser extent and the effect on immune factors has not been evaluated yet. Discovery of this multidimensional relationship between immune system, brain functioning, and EE has paved a way toward formulating environ-immuno therapies for treating psychiatric illnesses with minimal use of pharmacotherapy. While the immunomodulatory role of PE has been evaluated extensively, more research

  18. Molecular ecological network analyses

    PubMed Central

    2012-01-01

    ), which is open-accessible now (http://ieg2.ou.edu/MENA). Conclusions The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology. PMID:22646978

  19. Evaluating short-term changes in recreational water quality during a hydrograph event using a combination of microbial tracers, environmental microbiology, microbial source tracking and hydrological techniques: a case study in Southwest Wales, UK.

    PubMed

    Wyer, Mark D; Kay, David; Watkins, John; Davies, Cheryl; Kay, Chris; Thomas, Rod; Porter, Jonathan; Stapleton, Carl M; Moore, Heather

    2010-09-01

    Quantitative assessment of multiple sources to short-term variations in recreational water quality, as indexed by faecal indicator organism (FIO) concentrations, is becoming increasingly important with adoption of modern water quality standards and catchment-based water quality management requirements (e.g. the EU Water Framework Directive, Article 11 'Programmes of Measures' and the US Clean Water Act, 'Total Maximum Daily Loads'). This paper describes a study combining microbial tracers, intensive FIO measurement, open channel hydrology and molecular microbial source tracking (MST) to enhance understanding of recreational water quality at Amroth in southwest Wales, UK. Microbial tracers were released from four stream inputs during a moderate hydrograph event. Tracers from two local streams impacted simultaneously with a period of maximum FIO concentrations at the near-shore compliance monitoring site. Connection between these inputs and this site were rapid (9-33 min). Water quality impairment from a more remote stream input followed, 12.85 h after tracer release, sustaining FIO concentrations above desired compliance levels. MST analysis showed dominance of ruminant Bacteroidales genetic markers, associated with agricultural pollution. This integration of tracers and MST offers additional information on the movement and individual sources causing water quality impairment. PMID:20630556

  20. Molecular Marker Approach on Characterizing and Quantifying Charcoal in Environmental Media

    NASA Astrophysics Data System (ADS)

    Kuo, L.; Herbert, B. E.; Louchouarn, P.

    2006-12-01

    Black carbon (BC) is widely distributed in natural environments including soils, sediments, freshwater, seawater and the atmosphere. It is produced mostly from the incomplete combustion of fossil fuels and vegetation. In recent years, increasing attention has been given to BC due to its potential influence in many biogeochemical processes. In the environment, BC exists as a continuum ranging from partly charred plant materials, charcoal residues to highly condensed soot and graphite particles. The heterogeneous nature of black carbon means that BC is always operationally-defined, highlighting the need for standard methods that support data comparisons. Unlike soot and graphite that can be quantified with well-established methods, it is difficult to directly quantify charcoal in geologic media due to its chemical and physical heterogeneity. Most of the available charcoal quantification methods detect unknown fractions of the BC continuum. To specifically identify and quantify charcoal in soils and sediments, we adopted and validated an innovative molecular marker approach that quantifies levoglucosan, a pyrogenic derivative of cellulose, as a proxy of charcoal. Levoglucosan is source-specific, stable and is able to be detected at low concentrations using gas chromatograph-mass spectrometer (GC-MS). In the present study, two different plant species, honey mesquite and cordgrass, were selected as the raw materials to synthesize charcoals. The lab-synthesize charcoals were made under control conditions to eliminate the high heterogeneity often found in natural charcoals. The effects of two major combustion factors, temperature and duration, on the yield of levoglucosan were characterized in the lab-synthesize charcoals. Our results showed that significant levoglucosan production in the two types of charcoal was restricted to relatively low combustion temperatures (150-350 degree C). The combustion duration did not cause significant differences in the yield of

  1. Ultrasonic non invasive techniques for microbiological instrumentation

    NASA Astrophysics Data System (ADS)

    Elvira, L.; Sierra, C.; Galán, B.; Resa, P.

    2010-01-01

    Non invasive techniques based on ultrasounds have advantageous features to study, characterize and monitor microbiological and enzymatic reactions. These processes may change the sound speed, viscosity or particle distribution size of the medium where they take place, which makes possible their analysis using ultrasonic techniques. In this work, two different systems for the analysis of microbiological liquid media based on ultrasounds are presented. In first place, an industrial application based on an ultrasonic monitoring technique for microbiological growth detection in milk is shown. Such a system may improve the quality control strategies in food production factories, being able to decrease the time required to detect possible contaminations in packed products. Secondly, a study about the growing of the Escherichia coli DH5 α in different conditions is presented. It is shown that the use of ultrasonic non invasive characterization techniques in combination with other conventional measurements like optical density provides complementary information about the metabolism of these bacteria.

  2. Summary of research on microbiological processes

    SciTech Connect

    Winters, A.L.

    1992-09-01

    Storage of thermal energy in aquifers has obvious benefits of saving energy and decreasing the consumption of fossil fuels. However, aquifer thermal energy storage (ATES), which involves groundwater aquifers as the storage medium for heat or chill, impinges on the environment. A literature review of pertinent microbiology publications (Hicks and Stewart, 1988) identified the potential for the interaction of ATES systems and microbiological processes to create a source of infectious diseases and the potential for damage to the environment. In addition, the review identified a potential for microbiological processes to develop conditions that would interfere with the operation of an ATES system. As a result of this research effort, investigators from Finland, Germany, Switzerland, and the United States have examined several ATES systems in operation and have observed that the ATES systems studied do not contribute to infectious disease transmission, do not adversely affect the environment, and do not contribute significantly to biofouling or biocorrosion.

  3. [Current microbiological methods in the investigation of mycobacteria].

    PubMed

    Richter, E; Andres, S; Hillemann, D

    2015-05-01

    The rapid and reliable detection of tuberculosis is the main goal of microbiological analyses. This is not only of great value for an early diagnosis and early start of an adequate therapy, but also helps to stop transmission and spread of the disease. Prerequisites for successful detection of mycobacteria are careful selection of patient specimens, proper sampling and appropriate shipping. In addition to the classical microbiological methods such as staining for acid-fast bacteria and culture procedures, newer molecular methods are gaining greater importance (PCR; NAT). TB bacteria and resistance-associated mutations can be detected from the specimens directly, providing an early hint about resistant strains. In positive cultures, M. tuberculosis complex and nontuberculous mycobacteria must be discriminated from each other. Drug susceptibility testing (DST) of all first-line drugs has to be performed from one isolate of each patient and repeated if TB bacteria are still isolated after 2 months of therapy. DST of second-line drugs should follow in case of drug resistance or drug intolerance. PMID:25970121

  4. Three generations of experience and thought in microbiology and infection

    PubMed Central

    Goldner, Morris

    2003-01-01

    Views and comments were sought from Brian Lacey, who was professionally active from the 1930s to the 1970s, Alain Dublanchet, active from the 1960s to the 2000s, and Mark Pallen, active from the 1990s to 2000 and beyond. Professor Lacey was professor of microbiology at the Westminster Medical School, University of London, United Kingdom, for many years and is now retired. Docteur Dublanchet is the long time head of the laboratory of microbiology and virology at the Centre Hospitalier Intercommunal de Villeneuve-Saint-Georges in the greater Paris area. Professor Pallen is currently professor of bacterial genetics at the Medical School, University of Birmingham (United Kingdom); he is a keen enthusiast of genomic studies in the interest of molecular pathogenesis research. All three are medically qualified. Four questions were posed to each: What was the situation like in the infectious disease field when you first started your career? What do you feel have been the most important accomplishments with regard to problems of infectious disease during your period of activity? What do you foresee as the vital matters that still need to be addressed for countering infectious disease? Can infectious disease ever, practically, be eradicated and, if so, how would this be accomplished? PMID:18159476

  5. Molecularly imprinted polymer-coated hollow fiber membrane for the microextraction of triazines directly from environmental waters.

    PubMed

    Barahona, Francisco; Díaz-Álvarez, Myriam; Turiel, Esther; Martín-Esteban, Antonio

    2016-04-15

    In this work, novel molecularly imprinted polymer-coated hollow fibers (MIP-HFs) have been prepared and evaluated for the development of a micro-solid phase extraction method for the analysis of triazines in aqueous samples using high performance liquid chromatography and UV detection. The proposed extraction method combines liquid-liquid microextraction and molecular imprinting technology. In brief, a thin film of toluene is immobilised in the pores of the obtained MIP-HF. Afterwards, the conditioned MIP-HF is immersed in the water sample. Under stirring for a certain time, the target analytes are liquid-liquid extracted from the sample to the immobilised toluene and then these diffuse to the specific binding sites of the MIP. The effect of various experimental parameters as time and stirring-rate and salting-out effect among others, were studied for the establishment of optimum rebinding conditions. Recoveries for seven triazines tested in 100mL pure water samples spiked with 15 μg L(-1) of each triazine were within 0.8-6.9%, with a relative standard deviation (RSD)<10% (n=3). The detection limits (LODs) were within 0.05-0.1 μg L(-1), depending upon the triazine. The proposed methodology was successfully applied to extract the triazines from spiked tap and river water samples at μg L(-1) concentration level. The mircroextraction procedure with the developed MIP-HFs overcomes the typical low performance and lack of selective recognition of MIPs in aqueous media, allowing the determination of triazines in environmental waters at expected real concentration levels. PMID:26994922

  6. ENVIROSUITE: USING STATE-OF-THE-ART SYNCHROTRON TECHNIQUES TO UNDERSTAND ENVIRONMENTAL REMEDIATION SCIENCE ISSUES AT THE MOLECULAR LEVEL.

    SciTech Connect

    FITTS,J.P.; KALB,P.D.; FRANCIS,A.J.; FUHRMANN,M.; DODGE,C.J.; GILLOW,J.B.

    2004-03-01

    Although DOE's Environmental Management program has made steady progress in cleaning up environmental legacies throughout the DOE complex, there are still significant remediation issues that remain to be solved. For example, DOE faces difficult challenges related to potential mobilization of radionuclides (e.g., actinides) and other hazardous contaminants in soils, removal and final treatment of high-level waste and residuals from leaking tanks, and the long-term stewardship of remediated sites and engineered disposal facilities, to name just a few. In some cases, new technologies and technology applications will be required based on current engineering expertise. In others, however, basic scientific research is needed to understand the mechanisms of how contaminants behave under specific conditions and how they interact with the environment, from which new engineering solutions can emerge. At Brookhaven National Laboratory (BNL) and Stony Brook University, scientists have teamed to use state-of-the-art synchrotron techniques to help understand the basic interactions of contaminants in the environment. Much of this work is conducted at the BNL National Synchrotron Light Source (NSLS), which is a user facility that provides high energy X-ray and ultraviolet photon beams to facilitate the examination of contaminants and materials at the molecular level. These studies allow us to determine how chemical speciation and structure control important parameters such as solubility, which in turn drive critical performance characteristics such as leaching. In one study for example, we are examining the effects of microbial activity on actinide contaminants under conditions anticipated at the Waste Isolation Pilot Plant. One possible outcome of this research is the identification of specific microbes that can trap uranium or other contaminants within the intracellular structure and help mitigate mobility. In another study, we are exploring the interaction of contaminants with

  7. Successful Application of Active Learning Techniques to Introductory Microbiology.

    ERIC Educational Resources Information Center

    Hoffman, Elizabeth A.

    2001-01-01

    Points out the low student achievement in microbiology courses and presents an active learning method applied in an introductory microbiology course which features daily quizzes, cooperative learning activities, and group projects. (Contains 30 references.) (YDS)

  8. Recent advances in the study of microbiologically influenced corrosion

    SciTech Connect

    Little, B.; Wagner, P.

    1993-12-31

    The study of microbiologically influenced corrosion (MIC) has progressed from phenomenological case histories to a mature interdisciplinary science including electrochemical, metallurgical, surface analytical, microbiological, biotechnological and biophysical techniques. With gene probes and microelectrodes it is now possible to measure interfacial dissolved oxygen, dissolved sulfide and pH and to further determine the microbial species responsible for the localized chemistry. Biofilms can be tailored to contain consortia of specific microorganisms and naturally occurring biofilms can be dissected into cellular and extracellular constituents. Scanning vibrating electrodes can be used to map the distribution of anodes and cathodes so that localized corrosion can be correlated with the location of microorganisms. The development of environmental scanning electron, atomic force, and laser confocal microscopy makes it possible to image cells on surfaces and to accurately determine the spatial relationship between microorganisms and corrosion. Transport of nutrients through biofilms is being modeled using techniques including optical density measurements to precisely locate the water/biofilm interface and nuclear magnetic resonance imaging to visualize flow characteristics near surfaces colonized with microorganisms. The ways in which these new techniques can be used to understand fundamental mechanisms and to discriminate critical issues of MIC will be discussed.

  9. [Microbiological diagnosis of viral hepatitis].

    PubMed

    Alonso, Roberto; Aguilera, Antonio; Córdoba, Juan; Fuertes, Antonio

    2015-11-01

    Liver inflammation or hepatitis has many different causes, both infectious and non-infectious. Among the former, viral infection is responsible for at least half of all hepatitis worldwide. Different viruses have been described with primary tropism for liver tissue. These microorganisms have been successively named with letters of the alphabet: A, B, C, D, E and G. The aim of this paper is to review this heterogeneous group of viruses in its most basic aspects, including clinical implications, treatment, main control, and prophylactic measures and, of special interest, diagnostic approaches, both serological and molecular, which are used for their detection, quantification and characterization. PMID:25742731

  10. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

    PubMed Central

    Flynn, Jullien M; Brown, Emily A; Chain, Frédéric J J; MacIsaac, Hugh J; Cristescu, Melania E

    2015-01-01

    Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive. PMID:26078860

  11. The PdBI arcsecond whirlpool survey (PAWS): Environmental dependence of giant molecular cloud properties in M51

    SciTech Connect

    Colombo, Dario; Hughes, Annie; Schinnerer, Eva; Meidt, Sharon E.; Leroy, Adam K.; Pety, Jérôme; Dumas, Gaëlle; Schuster, Karl F.; Dobbs, Clare L.; García-Burillo, Santiago; Thompson, Todd A.; Kramer, Carsten

    2014-03-20

    Using data from the PdBI Arcsecond Whirlpool Survey (PAWS), we have generated the largest extragalactic giant molecular cloud (GMC) catalog to date, containing 1507 individual objects. GMCs in the inner M51 disk account for only 54% of the total {sup 12}CO(1-0) luminosity of the survey, but on average they exhibit physical properties similar to Galactic GMCs. We do not find a strong correlation between the GMC size and velocity dispersion, and a simple virial analysis suggests that ∼30% of GMCs in M51 are unbound. We have analyzed the GMC properties within seven dynamically motivated galactic environments, finding that GMCs in the spiral arms and in the central region are brighter and have higher velocity dispersions than inter-arm clouds. Globally, the GMC mass distribution does not follow a simple power-law shape. Instead, we find that the shape of the mass distribution varies with galactic environment: the distribution is steeper in inter-arm region than in the spiral arms, and exhibits a sharp truncation at high masses for the nuclear bar region. We propose that the observed environmental variations in the GMC properties and mass distributions are a consequence of the combined action of large-scale dynamical processes and feedback from high-mass star formation. We describe some challenges of using existing GMC identification techniques for decomposing the {sup 12}CO(1-0) emission in molecule-rich environments, such as M51's inner disk.

  12. Decoherence of many-spin systems in NMR: From molecular characterization to an environmentally induced quantum dynamical phase transition

    NASA Astrophysics Data System (ADS)

    Alvarez, Gonzalo A.

    2007-05-01

    The control of open quantum systems has a fundamental relevance for fields ranging from quantum information processing to nanotechnology. Typically, the system whose coherent dynamics one wants to manipulate, interacts with an environment that smoothly degrades its quantum dynamics. Thus, a precise understanding of the inner mechanisms of this process, called "decoherence", is critical to develop strategies to control the quantum dynamics. In this thesis we solved the generalized Liouville-von Neumann quantum master equation to obtain the dynamics of many-spin systems interacting with a spin bath. We also solve the spin dynamics within the Keldysh formalism. Both methods lead to identical solutions and together gave us the possibility to obtain numerous physical predictions that contrast well with Nuclear Magnetic Resonance experiments. We applied these tools for molecular characterizations, development of new numerical methodologies and the control of quantum dynamics in experimental implementations. But, more important, these results contributed to fundamental physical interpretations of how quantum dynamics behaves in open systems. In particular, we found a manifestation of an environmentally induced quantum dynamical phase transition.

  13. Molecular Biogeochemistry: Bridging Impressionism and Surrealism

    NASA Astrophysics Data System (ADS)

    Pearson, A.

    2009-12-01

    The history of environmental change is preserved over long time-scales in the structures and stable isotopic composition of biomarker lipids. To date, the connections between species diversity, biosynthetic diversity, and total lipid diversity remain poorly understood; yet understanding these relationships is a necessary prerequisite to accurate interpretation of paleoclimatic and paleoecological signals. Methods drawn from molecular microbiology provide one avenue to bridge this knowledge gap. A model system for studying such relationships is the distribution of microbial terpenoid lipids known as hopanoids. The primary enzyme for synthesis of hopanoids is squalene-hopene cyclase (SHC), and the phylogenetic relationships between most known SHCs and their corresponding species are congruent. The environmental diversity of hopanoid lipid structures, however, includes biosynthetic steps which may depend both on environmental growth conditions and on rates of biotic and abiotic degradation. Statistical methods for relating compound distributions to phylogenetic diversity are needed to provide insight into the dominant controlling factor(s). They may reveal whether sedimentary lipid profiles primarily reflect environmental conditions or microbial community composition. Together the molecular and geochemical data can help to paint the big picture.

  14. A Cartoon History of Soil Microbiology.

    ERIC Educational Resources Information Center

    Coyne, M. S.

    1996-01-01

    Describes the use of cartoons in presenting a historical perspective of soil microbiology that makes this information more entertaining to introductory students. Presents basic historical facts and major accomplishments of the pioneering soil microbiologists in a factual but tongue-in-cheek survey. (Author/JRH)

  15. Predictive microbiology in food packaging applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Predictive microbiology including growth, inactivation, surface transfer (or cross-contamination), and survival, plays important roles in understanding microbial food safety. Growth models may involve the growth potential of a specified pathogen under different stresses, e.g., temperature, pH, wate...

  16. Predictive Microbiology and Food Safety Applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mathematical modeling is the science of systematic study of recurrent events or phenomena. When models are properly developed, their applications may save costs and time. For microbial food safety research and applications, predictive microbiology models may be developed based on the fact that most ...

  17. Microbiology and Safety of Table Eggs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter describes the microbiology of table eggs, effects of processing, regulatory influences, relative risk of egg-borne disease, and the role of retail and consumer practices in outbreaks. Effects of washing, refrigeration, and facility sanitation in US commercial facilities will be describe...

  18. Applications for predictive microbiology to food packaging

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Predictive microbiology has been used for several years in the food industry to predict microbial growth, inactivation and survival. Predictive models provide a useful tool in risk assessment, HACCP set-up and GMP for the food industry to enhance microbial food safety. This report introduces the c...

  19. The Microbiology of Counterflow Scalding Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For most of the thousands of years that humans have used scalding to make it easier to remove feathers from birds, no one knew about the microbiological implications of scalding. The hot water in scald tanks kills many bacteria, but scalding multiple birds in the same tank gives surviving bacteria ...

  20. A Selected Bibliography on Microbiological Laboratory Design.

    ERIC Educational Resources Information Center

    Laboratory Design Notes, 1967

    1967-01-01

    Reference sources on microbiological laboratory design are cited. Subjects covered include--(1) policies and general requirements, (2) ventilated cabinets, (3) animal isolation equipment, (4) air handling, ventilation, and filtration, (5) germicidal ultraviolet irradiation, (6) aerosol test facilities, (7) process production of microorganisms, and…

  1. Defining the microbiological quality of dialysis fluid.

    PubMed

    Ledebo, I; Nystrand, R

    1999-01-01

    With increasing awareness about the degree and the potential impact of microbiological contamination in dialysis fluids, there is a desire to improve their microbiological quality. To achieve this goal, the origin of the microbiological contamination has to be identified. The water, the bicarbonate concentrate, and the fluid distribution system can be major contributors. Regular disinfection of the entire fluid path is necessary to prevent the formation of biofilm. The bicarbonate concentrate should be handled with special attention because it constitutes an excellent growth medium for microflora that may not be detected with regular assays. With a well maintained reverse osmosis (RO) system, frequent disinfection of the entire flow path, and microbiological awareness, it is possible to produce dialysis fluid that meets the most stringent standard (<10(2) colony forming units (CFU)/ml and <0.25 IU/ml of endotoxin). Adding a step of ultrafiltration just before the dialyzer can make the dialysis fluid ultrapure (<10(-1) CFU/ ml and <0.03 IU/ml). One additional step of controlled ultrafiltration provides sterile and pyrogen-free fluids (<10(-6) CFU/ml and <0.03 IU/ml) that can be used for infusion. PMID:9950177

  2. 21 CFR 866.2350 - Microbiological assay culture medium.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices §...

  3. 21 CFR 866.2350 - Microbiological assay culture medium.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices §...

  4. 21 CFR 866.2350 - Microbiological assay culture medium.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices §...

  5. 21 CFR 866.2350 - Microbiological assay culture medium.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices §...

  6. 21 CFR 866.2350 - Microbiological assay culture medium.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbiological assay culture medium. 866.2350 Section 866.2350 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices §...

  7. Using small molecules to study big questions in cellular microbiology.

    PubMed

    Ward, Gary E; Carey, Kimberly L; Westwood, Nicholas J

    2002-08-01

    High-throughput screening of small molecules is used extensively in pharmaceutical settings for the purpose of drug discovery. In the case of antimicrobials, this involves the identification of small molecules that are significantly more toxic to the microbe than to the host. Only a small percentage of the small molecules identified in these screens have been studied in sufficient detail to explain the molecular basis of their antimicrobial effect. Rarer still are small molecule screens undertaken with the explicit goal of learning more about the biology of a particular microbe or the mechanism of its interaction with its host. Recent technological advances in small molecule synthesis and high-throughput screening have made such mechanism-directed small molecule approaches a powerful and accessible experimental option. In this article, we provide an overview of the methods and technical requirements and we discuss the potential of small molecule approaches to address important and often otherwise experimentally intractable problems in cellular microbiology. PMID:12174082

  8. Recent Advances in Petroleum Microbiology

    PubMed Central

    Van Hamme, Jonathan D.; Singh, Ajay; Ward, Owen P.

    2003-01-01

    Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times (<60 s) are being used effectively. Microbes are being injected into partially spent petroleum reservoirs to enhance oil recovery. However, these microbial processes have not exhibited consistent and effective performance, primarily because of our inability to control conditions in the subsurface environment. Microbes may be exploited to break stable oilfield emulsions to produce pipeline quality oil. There is interest in replacing physical oil desulfurization processes with biodesulfurization methods through promotion of selective sulfur removal without degradation of associated carbon moieties. However, since microbes require an environment containing some water, a two-phase oil-water system must be established to optimize contact between the microbes and the hydrocarbon, and such an emulsion is not easily created with viscous crude oil. This challenge may be circumvented by application of the technology to more refined gasoline and diesel substrates, where aqueous-hydrocarbon emulsions are more easily generated. Molecular approaches are being used to broaden the substrate specificity and increase the rates and

  9. [Validation and verfication of microbiology methods].

    PubMed

    Camaró-Sala, María Luisa; Martínez-García, Rosana; Olmos-Martínez, Piedad; Catalá-Cuenca, Vicente; Ocete-Mochón, María Dolores; Gimeno-Cardona, Concepción

    2015-01-01

    Clinical microbiologists should ensure, to the maximum level allowed by the scientific and technical development, the reliability of the results. This implies that, in addition to meeting the technical criteria to ensure their validity, they must be performed with a number of conditions that allows comparable results to be obtained, regardless of the laboratory that performs the test. In this sense, the use of recognized and accepted reference methodsis the most effective tool for these guarantees. The activities related to verification and validation of analytical methods has become very important, as there is continuous development, as well as updating techniques and increasingly complex analytical equipment, and an interest of professionals to ensure quality processes and results. The definitions of validation and verification are described, along with the different types of validation/verification, and the types of methods, and the level of validation necessary depending on the degree of standardization. The situations in which validation/verification is mandatory and/or recommended is discussed, including those particularly related to validation in Microbiology. It stresses the importance of promoting the use of reference strains as controls in Microbiology and the use of standard controls, as well as the importance of participation in External Quality Assessment programs to demonstrate technical competence. The emphasis is on how to calculate some of the parameters required for validation/verification, such as the accuracy and precision. The development of these concepts can be found in the microbiological process SEIMC number 48: «Validation and verification of microbiological methods» www.seimc.org/protocols/microbiology. PMID:24958671

  10. A New Paradigm for Mentored Undergraduate Research in Molecular Microbiology

    ERIC Educational Resources Information Center

    Carson, Susan

    2007-01-01

    Science educators agree that an undergraduate research experience is critical for students who are considering graduate school or research careers. The process of researching a topic in the primary literature, designing experiments, implementing those experiments, and analyzing the results is essential in developing the analytical skills necessary…

  11. Cellular microbiology and molecular ecology of Legionella–amoeba interaction

    PubMed Central

    Richards, Ashley M.; Von Dwingelo, Juanita E.; Price, Christopher T.; Abu Kwaik, Yousef

    2013-01-01

    Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer. PMID:23535283

  12. The role of biomineralization in microbiologically influenced corrosion

    NASA Technical Reports Server (NTRS)

    Little, B.; Wagner, P.; Hart, K.; Ray, R.; Lavoie, D.; Nealson, K.; Aguilar, C.

    1998-01-01

    Synthetic iron oxides (goethite, alpha-FeO.OH; hematite, Fe2O3; and ferrihydrite, Fe(OH)3) were used as model compounds to simulate the mineralogy of surface films on carbon steel. Dissolution of these oxides exposed to pure cultures of the metal-reducing bacterium, Shewanella putrefaciens, was followed by direct atomic absorption spectroscopy measurement of ferrous iron coupled with microscopic analyses using confocal laser scanning and environmental scanning electron microscopies. During an 8-day exposure the organism colonized mineral surfaces and reduced solid ferric oxides to soluble ferrous ions. Elemental composition, as monitored by energy dispersive x-ray spectroscopy, indicated mineral replacement reactions with both ferrihydrite and goethite as iron reduction occurred. When carbon steel electrodes were exposed to S. putrefaciens, microbiologically influenced corrosion was demonstrated electrochemically and microscopically.

  13. Selective mixed-bed solid phase extraction of atrazine herbicide from environmental water samples using molecularly imprinted polymer.

    PubMed

    Zarejousheghani, Mashaalah; Fiedler, Petra; Möder, Monika; Borsdorf, Helko

    2014-11-01

    A novel approach for the selective extraction of organic target compounds from water samples has been developed using a mixed-bed solid phase extraction (mixed-bed SPE) technique. The molecularly imprinted polymer (MIP) particles are embedded in a network of silica gel to form a stable uniform porous bed. The capabilities of this method are demonstrated using atrazine as a model compound. In comparison to conventional molecularly imprinted-solid phase extraction (MISPE), the proposed mixed-bed MISPE method in combination with gas chromatography-mass spectrometry (GC-MS) analysis enables more reproducible and efficient extraction performance. After optimization of operational parameters (polymerization conditions, bed matrix ingredients, polymer to silica gel ratio, pH of the sample solution, breakthrough volume plus washing and elution conditions), improved LODs (1.34 µg L(-1) in comparison to 2.25 µg L(-1) obtained using MISPE) and limits of quantification (4.5 µg L(-1) for mixed-bed MISPE and 7.5 µg L(-1) for MISPE) were observed for the analysis of atrazine. Furthermore, the relative standard deviations (RSDs) for atrazine at concentrations between 5 and 200 µg L(-1) ranged between 1.8% and 6.3% compared to MISPE (3.5-12.1%). Additionally, the column-to-column reproducibility for the mixed-bed MISPE was significantly improved to 16.1%, compared with 53% that was observed for MISPE. Due to the reduced bed-mass sorbent and at optimized conditions, the total amount of organic solvents required for conditioning, washing and elution steps reduced from more than 25 mL for conventional MISPE to less than 2 mL for mixed-bed MISPE. Besides reduced organic solvent consumption, total sample preparation time of the mixed-bed MISPE method relative to the conventional MISPE was reduced from more than 20 min to less than 10 min. The amount of organic solvent required for complete elution diminished from 3 mL (conventional MISPE) to less than 0.4 mL with the mixed

  14. Microbiological and 16S rRNA analysis of sulphite-reducing clostridia from river sediments in central Italy

    PubMed Central

    Marcheggiani, Stefania; Iaconelli, Marcello; D'angelo, Annamaria; Pierdominici, Elio; La Rosa, Giuseppina; Muscillo, Michele; Equestre, Michele; Mancini, Laura

    2008-01-01

    Background Microbiological indicators are commonly used in the assessment of public health risks associated with fecal contamination of freshwater ecosystems. Sediments are a reservoir of microorganisms, and can thus provide information on past pollution events, not obtainable through the testing of surface water. Moreover, pathogens present in sediment may represent future threats to human health. Clostridium perfringens, a typical colonizer of sediments, has been suggested as an alternative indicator of fecal pollution. In order to be suitable for such purpose, the microorganism should be widely distributed in contaminated environments. The objective of this study was thus to determine the composition of the anaerobic community in sediment samples of the lower Tiber basin, in central Italy, through a combined approach involving granulometric analysis of sediment samples, as well as a microbiological and molecular (16S rRNA) analysis of strains. Results Granulometry showed a similar, clayey sediment composition, in most sampling sites. The microbiological method, employing, an adaptation of the standard method, proved to be effective in isolating anaerobic bacteria from the environmental matrix for the purpose of genetic analysis. Eighty-three strains of bacteria were isolated and the partial 16S rRNA gene sequenced. While biochemical analysis detected only C. perfringens strains, phylogenetic analysis indicated the presence of three clusters: C. perfringens, C. bifermentans and B. cereus, comprising eight taxa. C. perfringens, the commonest in almost all sediment sampling sites, was present in all sites, and in both seasons (seasonal sampling was carried out only along the Tiber and Aniene rivers). None of the described genetic profiles showed complete similarity with GenBank sequences. Conclusion The study underlines the value of C. perfringens as an alternative microbial indicator of fecal contamination in river sediments. This is supported by the bacterium

  15. [Microbiology laboratory as a base of information sending].

    PubMed

    Komori, Toshiaki; Fujita, Naohisa; Hirose, Yuri; Kimura, Takeshi; Kyotani, Noriko; Kurahashi, Satoko; Yamada, Yukiji; Ushiyama, Masaji; Yasumoto, Towa; Yuasa, Soh-ichi

    2007-10-01

    The goal of our microbiology laboratory is to provide an accurate microbiological result and a useful information for every healthcare workers (HCWs). For this purpose, we were trying to do several activities, such as improving the work-flow of microbiology testings, starting 365-day-open microbiology tests, providing some training courses of microbiology and sending many useful informations about infectious diseases and infection control. Before these activities, we needed another 5 microbiology technicians beside 3 technicians and had started the program to educate them. We have successfully finished it and enabled all plans begin in April, 2005. Since then we are open for 365 days and also sending HCWs many newsletters for performing effective microbiological testings via the intra-network system and having lectures for both doctors and nurses, especially for new resident doctors at the orientation. We had also the training course for certified infection control nurses and accepted two technicians from Africa, who came to study a basic microbiology via JICA. These activities have enabled every technician not only to report and analyze microbiological test result effectively but also to improve writing and presentation skills. Through these activities all technicians have realized that accurate and rapid information from a microbiology laboratory is a key to treat patients with infectious diseases and improve their prognosis. It is suggested that skill-up of technicians lead to report an accurate result in microbiology and at the same time improve the attitude for their job. PMID:18050672

  16. Microbiological safety and quality of Mozzarella cheese assessed by the microbiological survey method.

    PubMed

    Losito, Francesca; Arienzo, Alyexandra; Bottini, Giorgia; Priolisi, Francesca Romana; Mari, Alberto; Antonini, Giovanni

    2014-01-01

    Dairy products are characterized by reduced shelf life because they are an excellent growth medium for a wide range of microorganisms. For this reason, it is important to monitor the microbiological quality of dairy products and, in particular, the total viable count and concentration of Escherichia coli, as they are indicators of the hygienic state of these products. In addition, in dairy products such as Mozzarella cheese, it is important to monitor the concentration of lactic acid bacteria (LAB), as they are the major components of starter cultures used in cheese production, contributing to the taste and texture of fermented products and inhibiting food spoilage bacteria by producing growth-inhibiting substances. For these reasons, to ensure the quality and safety of their products, cheese makers should monitor frequently, during fresh cheese production, the concentration of LAB and spoilage bacteria. However, usually, small- to medium-size dairy factories do not have an internal microbiological laboratory and external laboratories of analysis are often too expensive and require several days for the results. Compared with traditional methods, the microbiological survey (MBS) method developed by Roma Tre University (Rome, Italy) allows faster and less-expensive microbiological analyses to be conducted wherever they are necessary, without the need for a microbiological laboratory or any instrumentation other than MBS vials and a thermostat. In this paper, we report the primary validation of the MBS method to monitor LAB concentration in Mozzarella cheese and the analysis, using the MBS method, of total viable count, E. coli, and LAB concentrations in the production line of Mozzarella cheese as well as during the shelf life of the product stored at 20°C. The results obtained indicate that the MBS method may be successfully used by small- to medium-size dairy factories that do not have an internal microbiological laboratory. Using the MBS method, these dairy

  17. Environmental Microbiology: Bacteria & Fungi on the Foods We Eat

    ERIC Educational Resources Information Center

    Segner, Suzanne; Scholthof, Karen-Beth G.

    2007-01-01

    The near daily news reports on food-borne diseases caused by contaminated produce, dairy, or meats suggests to the public that the safety of the U.S. food supply is in jeopardy. These reports, as well as a general distrust in federal agencies due in part to mad cow disease and toxigenic forms of "E. coli" in ground beef, have resulted in an…

  18. Project environmental microbiology as related to planetary quarantine

    NASA Technical Reports Server (NTRS)

    Pflug, I. J.

    1973-01-01

    The viability and dry heat resistance of indigenous microflora associated with small soil particles were investigated. An aluminum boat TDT CUP-TSA solid media system was developed for the analyses; a complete description of the technique is included. Data cited here were obtained using analyses of individual soil particles. Detailed particle viability profiles for dry heat effects were determined for Kennedy Space Center soil. At 110 C at least some particles retained viability through a heating period of between 8 and 16 hours. Single particles heated at 125 C for 80 minutes or longer did not show evidence of viability under test conditions. Preliminary aerobic, mesophilic plate counts of the 74-88 micron m soil fraction yielded mean values of 16.2 organisms per dark particle and 2.6 organisms per light particle. Heat treatment of particles in a dry atmosphere did not appear to increase the rate of inactivation for in situ soil particle microflora.

  19. Microbiological diagnosis of suppurative keratitis in Bangladesh.

    PubMed Central

    Williams, G; Billson, F; Husain, R; Howlader, S A; Islam, N; McClellan, K

    1987-01-01

    Experience in setting up an inexpensive microbiology laboratory in the Bangladesh National Society for the Blind Eye Hospital and Training Complex at Chittagong is presented, together with the results of a pilot study to identify organisms responsible in 33 consecutive cases of suppurative keratitis in the Chittagong area of Bangladesh. Of the 33 cases 21 were positively identified by means of Gram stain and/or culture. Two-thirds of the responsible organisms were bacteria, and one-third were fungi. The bacterial causes included Streptococcus pneumoniae and Pseudomonas aeruginosa. The fungi isolated were Aspergillus fumigatus, Aspergillus ochraceus, and Fusarium solani. Among the causes of failure to diagnose the organism was chronicity of infection and previous treatment. The value of the study in the planning of future treatment regimens, and the implications of setting up similar relatively cheap microbiology laboratory facilities in developing countries, are discussed. Images PMID:3555609

  20. Inflammation, suppuration, putrefaction, fermentation: Joseph Lister's microbiology

    PubMed Central

    Richardson, Ruth

    2013-01-01

    This paper focuses on Lister's inaugural lecture at King's College, London, in October 1877. As the new Professor of Clinical Surgery, Lister had much to report, including impressively high survival rates from complex operations previously regarded as foolhardy. Instead, he chose to address the processes of fermentation in wine, blood and milk. His reasons are not obvious to a modern audience, just as they probably were not to those who heard him in the Great Hall at King's. Having brought microbiological apparatus from his laboratory to the lecture theatre and presented proof of bacterial variety and specificity, Lister publicly demonstrated the creation of the first pure bacterial culture in the history of microbiology. It was an ingenious and well-thought-out strategy designed to generate a frame of mind among his new colleagues and future students, receptive to the causative role of bacteria in septic diseases. His timing was impeccable.

  1. [Microbiologic evaluation of instant soup concentrates].

    PubMed

    Wójcik-Stopczyńska, Barbara; Falkowski, Joachim; Jakubowska, Barbara

    2002-01-01

    The microbiological condition of instant soup powders purchased in retail network has been assessed. The study included 37 instant soups (8 types) manufactured by four Polish companies. The microbiological quality of a majority of soup powders fulfilled the requirements of the standard. No pathogenic bacteria (Salmonella, E. coli and Staphylococcus aureus) were detected, nor were there any spores of sulphitereducing anaerobic bacteria found. However, some samples of powders, mainly from one manufacturer, did have an excessive total number of bacteria (> 10(5) cfu/g) and a reduced (down to 0.01 g) level of coliform count. Aerobic bacteria occurring in powders were of vegetative and spore forms and exhibited the activity of amylo-, lipo- and proteolytic exoenzymes. The quantity of moulds did not exceed 100 cfu/g in a majority of samples. They were mainly represented by Penicillium sp., Aspergillus sp., Alternaria sp. and Cladosporium sp. PMID:12235671

  2. Microbiological decontamination of natural honey by irradiation

    NASA Astrophysics Data System (ADS)

    Migdał, W.; Owczarczyk, H. B.; K ȩdzia, B.; Hołderna-K ȩdzia, E.; Madajczyk, D.

    2000-03-01

    Degree of microbiological decontamination, organoleptic and physico-chemical properties of natural honeys were investigated after radiation treatment. Seven kinds of honeys were irradiated with the beams of 10 MeV electrons from a 10 kW linear accelerator "Elektronika 10-10" at the dose 10 kGy. It was shown, that after irradiation, the total count of aerobic and anaerobic bacteria and moulds decrease by 99%. The antibiotic value in investigated honeys increased in turn from 1.67 to 2.67 after irradiation. Such factors and parameters of investigated honeys as their consistency, content of water and saccharose, acidity, the diastase and 5-HMF values were not changed significantly after irradiation. Decontamination by irradiation is a process which allows us to obtain high microbiological purity of honeys. It is especially needed, when honeys are used in surgical treatment of injuries and in nutrition of babies with food deficiency.

  3. Microbiological contamination in counterfeit and unapproved drugs

    PubMed Central

    2014-01-01

    Background Counterfeit and unapproved medicines are inherently dangerous and can cause patient injury due to ineffectiveness, chemical or biological contamination, or wrong dosage. Growth of the counterfeit medical market in developed countries is mainly attributable to life-style drugs, which are used in the treatment of non-life-threatening and non-painful conditions, such as slimming pills, cosmetic-related pharmaceuticals, and drugs for sexual enhancement. One of the main tasks of health authorities is to identify the exact active pharmaceutical ingredients (APIs) in confiscated drugs, because wrong API compounds, wrong concentrations, and/or the presence of chemical contaminants are the main risks associated with counterfeit medicines. Serious danger may also arise from microbiological contamination. We therefore performed a market surveillance study focused on the microbial burden in counterfeit and unapproved medicines. Methods Counterfeit and unapproved medicines confiscated in Canada and Austria and controls from the legal market were examined for microbial contaminations according to the US and European pharmacopoeia guidelines. The microbiological load of illegal and legitimate samples was statistically compared with the Wilcoxon rank-sum test. Results Microbial cultivable contaminations in counterfeit and unapproved phosphodiesterase type 5 inhibitors were significantly higher than in products from the legal medicines market (p < 0.0001). Contamination levels exceeding the USP and EP limits were seen in 23% of the tested illegal samples in Canada. Additionally, microbiological contaminations above the pharmacopoeial limits were detected in an anabolic steroid and an herbal medicinal product in Austria (6% of illegal products tested). Conclusions Our results show that counterfeit and unapproved pharmaceuticals are not manufactured under the same hygienic conditions as legitimate products. The microbiological contamination of illegal medicinal

  4. Microbiological safety of household membrane water filter.

    PubMed

    Zhang, Yongli; Wang, Qing; Lou, Wei; Wang, Yuxin; Zhu, Xuan

    2013-04-01

    Waterborne pathogens outbreaks are major reasons of diarrhea disease worldwide. Detecting and monitoring emerging waterborne pathogens (EWPs) is important for drinking water microbiological safety. The microbiological safety of household water hollow fiber membrane filter which is the end of drinking water treatment process was studied with heterotrophic plate count (HPC) and real-time PCR method. The effect of the flow rate, idle time and washing fashion were investigated. Among the selected filters from three manufacturers, only the PVDF membrane water filter (Brand B) could achieve a good water purification criteria. Brand A was found a certain degree of EWPs in its effluent. The lowest bacteria-removing efficiency of the PVC membrane water filter was found Brand C. Our study showed that the microorganisms could reach up to 10(6) CFU ml(-1) and the 16s rDNA could reach up to 10(6) copies ml(-1) in the initial filtrate of Brand C. More species and amounts of EWPs were detected in the washing water. These results suggested that the popular household membrane filters might cause microbiological risks at certain circumstances such as the shock load of EWPs and leakage of the membranes in the case of abnormal source water or poor membrane filter quality. PMID:24620621

  5. Microbiology studies in the Space Shuttle

    NASA Technical Reports Server (NTRS)

    Taylor, G. R.

    1976-01-01

    Past space microbiology studies have evaluated three general areas: microbe detection in extraterrestrial materials; monitoring of autoflora and medically important species on crewmembers, equipment, and cabin air; and in vitro evaluations of isolated terrestrial species carried on manned and unmanned spaceflights. These areas are briefly reviewed to establish a basis for presenting probable experiment subjects applicable to the Space Shuttle era. Most extraterrestrial life detection studies involve visitations to other heavenly bodies. Although this is not applicable to the first series of Shuttle flights, attempts to capture meteors and spores in space could be important. Human pathogen and autoflora monitoring will become more important with increased variety among crewmembers. Inclusion of contaminated animal and plant specimens in the space lab will necessitate inflight evaluation of cross-contamination and infection potentials. The majority of Shuttle microbiology studies will doubtless fall into the third study area. Presence of a space lab will permit a whole range of experimentation under conditions similar to these experienced in earth-based laboratories. The recommendations of various study groups are analyzed, and probable inflight microbiological experiment areas are identified for the Life Sciences Shuttle Laboratory.

  6. Oral Microbiology: Past, Present and Future

    PubMed Central

    He, Xue-song; Shi, Wen-yuan

    2009-01-01

    Since the initial observations of oral bacteria within dental plaque by van Leeuwenhoek using his primitive microscopes in 1680, an event that is generally recognized as the advent of oral microbiological investigation, oral microbiology has gone through phases of “reductionism” and “holism”. From the small beginnings of the Miller and Black period, in which microbiologists followed Koch's postulates, took the reductionist approach to try to study the complex oral microbial community by analyzing individual species; to the modern era when oral researchers embrace “holism” or “system thinking”, adopt new concepts such as interspecies interaction, microbial community, biofilms, poly-microbial diseases, oral microbiological knowledge has burgeoned and our ability to identify the resident organisms in dental plaque and decipher the interactions between key components has rapidly increased, such knowledge has greatly changed our view of the oral microbial flora, provided invaluable insight into the etiology of dental and periodontal diseases, opened the door to new approaches and techniques for developing new therapeutic and preventive tools for combating oral poly-microbial diseases. PMID:20687296

  7. Use of U.S. Department of Agriculture - Pathogen Modeling Program and the Predictive Microbiology Information Portal

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The science of Predictive Microbiology is based on the assumption that bacterial behavior is reproducible, and that it can be quantified by characterizing the environmental factors that affect growth, survival, and inactivation. The U.S. Department of Agriculture (USDA), Agricultural Research Serv...

  8. Applying low-molecular weight supramolecular gelators in an environmental setting - self-assembled gels as smart materials for pollutant removal.

    PubMed

    Okesola, Babatunde O; Smith, David K

    2016-07-25

    This review explores supramolecular gels as materials for environmental remediation. These soft materials are formed by self-assembling low-molecular-weight building blocks, which can be programmed with molecular-scale information by simple organic synthesis. The resulting gels often have nanoscale 'solid-like' networks which are sample-spanning within a 'liquid-like' solvent phase. There is intimate contact between the solvent and the gel nanostructure, which has a very high effective surface area as a result of its dimensions. As such, these materials have the ability to bring a solid-like phase into contact with liquids in an environmental setting. Such materials can therefore remediate unwanted pollutants from the environment including: immobilisation of oil spills, removal of dyes, extraction of heavy metals or toxic anions, and the detection or removal of chemical weapons. Controlling the interactions between the gel nanofibres and pollutants can lead to selective uptake and extraction. Furthermore, if suitably designed, such materials can be recyclable and environmentally benign, while the responsive and tunable nature of the self-assembled network offers significant advantages over other materials solutions to problems caused by pollution in an environmental setting. PMID:27241027

  9. Short-term environmental enrichment is sufficient to counter stress-induced anxiety and associated structural and molecular plasticity in basolateral amygdala.

    PubMed

    Ashokan, Archana; Hegde, Akshaya; Mitra, Rupshi

    2016-07-01

    Moderate levels of anxiety enable individual animals to cope with stressors through avoidance, and could be an adaptive trait. However, repeated stress exacerbates anxiety to pathologically high levels. Dendritic remodeling in the basolateral amygdala is proposed to mediate potentiation of anxiety after stress. Similarly, modulation of brain-derived neurotrophic factor is thought to be important for the behavioral effects of stress. In the present study, we investigate if relatively short periods of environmental enrichment in adulthood can confer resilience against stress-induced anxiety and concomitant changes in neuronal arborisation and brain derived neurotrophic factor within basolateral amygdala. Two weeks of environmental enrichment countermanded the propensity of increased anxiety following chronic immobilization stress. Environmental enrichment concurrently reduced dendritic branching and spine density of projection neurons of the basolateral amygdala. Moreover, stress increased abundance of BDNF mRNA in the basolateral amygdala in agreement with the dendritic hypertrophy post-stress and role of BDNF in promoting dendritic arborisation. In contrast, environmental enrichment prevented stress-induced rise in the BDNF mRNA abundance. Gain in body weights and adrenal weights remained unaffected by exposure to environmental enrichment. These observations suggest that a short period of environmental enrichment can provide resilience against maladaptive effects of stress on hormonal, neuronal and molecular mediators of anxiogenesis. PMID:27128967

  10. The roots--a short history of industrial microbiology and biotechnology.

    PubMed

    Buchholz, Klaus; Collins, John

    2013-05-01

    Early biotechnology (BT) had its roots in fascinating discoveries, such as yeast as living matter being responsible for the fermentation of beer and wine. Serious controversies arose between vitalists and chemists, resulting in the reversal of theories and paradigms, but prompting continuing research and progress. Pasteur's work led to the establishment of the science of microbiology by developing pure monoculture in sterile medium, and together with the work of Robert Koch to the recognition that a single pathogenic organism is the causative agent for a particular disease. Pasteur also achieved innovations for industrial processes of high economic relevance, including beer, wine and alcohol. Several decades later Buchner, disproved the hypothesis that processes in living cells required a metaphysical 'vis vitalis' in addition to pure chemical laws. Enzymes were shown to be the chemical basis of bioconversions. Studies on the formation of products in microbial fermentations, resulted in the manufacture of citric acid, and chemical components required for explosives particularly in war time, acetone and butanol, and further products through fermentation. The requirements for penicillin during the Second World War lead to the industrial manufacture of penicillin, and to the era of antibiotics with further antibiotics, like streptomycin, becoming available. This was followed by a new class of high value-added products, mainly secondary metabolites, e.g. steroids obtained by biotransformation. By the mid-twentieth century, biotechnology was becoming an accepted specialty with courses being established in the life sciences departments of several universities. Starting in the 1970s and 1980s, BT gained the attention of governmental agencies in Germany, the UK, Japan, the USA, and others as a field of innovative potential and economic growth, leading to expansion of the field. Basic research in Biochemistry and Molecular Biology dramatically widened the field of life

  11. [Microbiological diagnosis of emerging bacterial pathogens: Anaplasma, Bartonella, Rickettsia, and Tropheryma whipplei].

    PubMed

    Blanco, José Ramón; Jado, Isabel; Marín, Mercedes; Sanfeliu, Isabel; Portillo, Aránzazu; Anda, Pedro; Pons, Immaculada; Oteo, José Antonio

    2008-11-01

    Ehrlichia/Anaplasma, Bartonella, Rickettsia and Tropheryma whipplei (formerly called whippelii) are fastidious bacterial organisms, considered the causative agents of potentially severe emerging and re-emerging diseases with repercussions on public health. The recent availability of advanced molecular biology and cell culture techniques has led to the implication of many of these species in human pathologies. These issues are extensively covered in number 27 of the SEIMC microbiological procedure: Diagnóstico microbiológico de las infecciones por patógenos bacterianos emergentes: Anaplasma, Bartonella, Rickettsia y Tropheryma whippelii (Microbiological diagnosis of Anaplasma, Bartonella, Rickettsia and Tropheryma whippelii infections) (2nd ed., 2007) (www.seimc.org/documentos/protocolos/microbiologia/). PMID:19100178

  12. Characterization of wami tilapia (Oreochromis urolepis hornorum) skin gelatin: microbiological, rheological and structural properties.

    PubMed

    Alfaro, Alexandre Da Trindade; Fonseca, Gustavo Graciano; Balbinot, Evellin; Prentice, Carlos

    2014-07-01

    Gelatin was extracted from the skin of tilapia (Oreochromis urolepis hornorum) and its microbiological, rheological and structural properties were characterized. The tilapia skin gelatin presented typical molecular weight distribution of type I collagen with contents of imino acids (proline + hydroxyproline) of 21.67%. Gel strength and viscosity values were 221 ± 5.68 g and 5.98 ± 0.34 cP, respectively, with the maturation time of 18 ± 1 h, and both parameters increased with the maturation time. Melting and gelling points of 25 degrees C and 21 degrees C, respectively, were obtained for tilapia skin gelatin. The gelatin presented microbiological standards in accordance with the Brazilian Legislation. PMID:23751549

  13. Symbiosis in the Soil: Citizen Microbiology in Middle and High School Classrooms †

    PubMed Central

    McKenney, Erin; Flythe, Taylar; Millis, Courtney; Stalls, Jennifer; Urban, Julie M.; Dunn, Robert R.; Stevens, Julia L.

    2016-01-01

    Microorganisms are vital to environmental health, yet their association with disease often overshadows these benefits. Building citizen-science activities around the positive role of microorganisms and an understanding of their ubiquity can begin to dispel misconceptions while simultaneously engaging the public in research. Here, we describe a citizen-science microbiology project geared toward implementation in middle and high school classrooms. Students culture environmental microorganisms and document microbial diversity of plant root systems compared with adjacent bulk soil. Results contribute data toward research on microbiome recruitment of weeds and other successful plants while addressing core topics in science education. PMID:27047592

  14. Symbiosis in the Soil: Citizen Microbiology in Middle and High School Classrooms.

    PubMed

    McKenney, Erin; Flythe, Taylar; Millis, Courtney; Stalls, Jennifer; Urban, Julie M; Dunn, Robert R; Stevens, Julia L

    2016-03-01

    Microorganisms are vital to environmental health, yet their association with disease often overshadows these benefits. Building citizen-science activities around the positive role of microorganisms and an understanding of their ubiquity can begin to dispel misconceptions while simultaneously engaging the public in research. Here, we describe a citizen-science microbiology project geared toward implementation in middle and high school classrooms. Students culture environmental microorganisms and document microbial diversity of plant root systems compared with adjacent bulk soil. Results contribute data toward research on microbiome recruitment of weeds and other successful plants while addressing core topics in science education. PMID:27047592

  15. Comparison of Molecular Methods and Traditional Plate Counting for Detecting Campylobacter Jejuni and Escherichia Coli from Environmental Samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The accurate detection of pathogenic bacteria from environmental samples is vital from both agricultural and human health perspectives. The goal of this study was to compare the detection of Campylobacter jejuni and Escherichia coli from environmental samples using quantitative real-time PCR (QRT-P...

  16. Development of a website for clinical microbiology in Brazil.

    PubMed

    Rossi, F; Andreazzi, D; Chao, L W

    2002-01-01

    The quality of Brazilian health services, including clinical microbiology laboratories, varies enormously. We established a Website to provide different professionals with up-to-date information and to create a virtual Brazilian microbiology community. The Website became operational in February 2000 and had 198,976 hits in the subsequent 20 months. There were 1031 user registrations in its virtual community. Different microbiology topics were discussed and three virtual training courses (representing about 300 printed pages of information) were given. The e-learning centre and the Brazilian virtual community created by this Website have facilitated distance learning, and have encouraged professional integration within Brazilian clinical microbiology. PMID:12217118

  17. Development of the morpholino gene knockdown technique in Fundulus heteroclitus: a tool for studying molecular mechanisms in an established environmental model

    PubMed Central

    Matson, Cole W.; Clark, Bryan W.; Jenny, Matthew J.; Fleming, Carrie R.; Hahn, Mark E.; Di Giulio, Richard T.

    2008-01-01

    A significant challenge in environmental toxicology is that many genetic and genomic tools available in laboratory models are not developed for commonly used environmental models. The Atlantic killifish (Fundulus heteroclitus) is one of the most studied teleost environmental models, yet few genetic or genomic tools have been developed for use in this species. The advancement of genetic and evolutionary toxicology will require that many of the tools developed in laboratory models be transferred into species more applicable to environmental toxicology. Antisense morpholino oligonucleotide (MO) gene knockdown technology has been widely utilized to study development in zebrafish and has been proven to be a powerful tool in toxicological investigations through direct manipulation of molecular pathways. To expand the utility of killifish as an environmental model, MO gene knockdown technology was adapted for use in Fundulus. Morpholino microinjection methods were altered to overcome the significant differences between these two species. Morpholino efficacy and functional duration were evaluated with molecular and phenotypic methods. A cytochrome P450-1A (CYP1A) MO was used to confirm effectiveness of the methodology. For CYP1A MO-injected embryos, a 70% reduction in CYP1A activity, a 86% reduction in total CYP1A protein, a significant increase in β-naphthoflavone-induced teratogenicity, and estimates of functional duration (50% reduction in activity 10 dpf, and 86% reduction in total protein 12 dpf) conclusively demonstrated that MO technologies can be used effectively in killifish and will likely be just as informative as they have been in zebrafish. PMID:18378331

  18. Microbiological Quality of Seafood Marketed in Taiwan.

    PubMed

    Wong, Hin-Chung; Jiang, Huai-Yu; Lin, Hsu-Yang; Wang, Yu-Ting

    2015-11-01

    Seafood is often associated with foodborne illnesses, and Vibrio parahaemolyticus is the most common pathogen implicated in outbreaks in Taiwan. In this study, the microbiological quality of 300 raw or mixed ready-to-eat (RTE) and other cooking-needed seafood samples was examined. The total aerobic and coliform counts of the RTE samples were significantly higher than those of other cooking-needed samples. On average, 55.8 and 29.7% of the RTE samples failed to meet the local microbiological standards for total aerobic (5 log CFU/g) and coliform (3 log most probable number [MPN] per g), counts respectively; the corresponding percentages for the RTE samples from Taipei City were 9.1 and 18.2%, respectively. The total aerobic and coliform counts in the RTE samples from supermarkets and chain restaurants were significantly lower than those from traditional restaurants. The Vibrio species were more frequently identified in the cooking-needed samples than in RTE samples. Low incidences of V. parahaemolyticus (1.4%), V. vulnificus (1.9%), and V. cholerae (0%) were detected in most RTE samples. High densities of V. parahaemolyticus and V. vulnificus (1,200 MPN/g) were detected in a few RTE samples, only one of which contained toxigenic (tdh(+)) V. parahaemolyticus. The results of this investigation reveal that better hygiene of seafood providers such as chain restaurants, supermarkets, and traditional restaurants in Taipei City would effectively improve the microbiological quality of the seafood. The results will facilitate the establishment of measures for controlling the risks associated with seafood in Taiwan. PMID:26555520

  19. Clinical and microbiological diagnosis of oral candidiasis

    PubMed Central

    Jiménez-Soriano, Yolanda

    2013-01-01

    Introduction: Candidiasis or oral candidiasis is the most frequent mucocutaneous mycosis of the oral cavity. It is produced by the genus Candida, which is found in the oral cavity of 53% of the general population as a common commensal organism. One hundred and fifty species have been isolated in the oral cavity, and 80% of the isolates correspond to Candida albicans, which can colonize the oral cavity alone or in combination with other species. Transformation from commensal organism to pathogen depends on the intervention of different predisposing factors that modify the microenvironment of the oral cavity and favor the appearance of opportunistic infection. The present study offers a literature review on the diagnosis of oral candidiasis, with the purpose of establishing when complementary microbiological techniques for the diagnosis of oral candidiasis should be used, and which techniques are most commonly employed in routine clinical practice in order to establish a definitive diagnosis. Materials and methods: A Medline-PubMed, Scopus and Cochrane search was made covering the last 10 years. Results: The diagnosis of oral candidiasis is fundamentally clinical. Microbiological techniques are used when the clinical diagnosis needs to be confirmed, for establishing a differential diagnosis with other diseases, and in cases characterized by resistance to antifungal drugs. Biopsies in turn are indicated in patients with hyperplastic candidiasis. Staining (10% KOH) and culture (Sabouraud dextrose agar) are the methods most commonly used for diagnosing primary candidiasis. Identification of the individual species of Candida is usually carried out with CHROMagar Candida®. For the diagnosis of invasive candidiasis, and in cases requiring differentiation between C. albicans and C. dubliniensis, use is made of immunological and genetic techniques such as ELISA and PCR. Key words:Clinical, oral candidiasis, microbiology. PMID:24455095

  20. Microbiological monitoring of endoscopes: 5-year review.

    PubMed

    Gillespie, Elizabeth E; Kotsanas, Despina; Stuart, Rhonda L

    2008-07-01

    Periodic microbiological monitoring of endoscopes is a recommendation of the Gastroenterological Society of Australia (GENSA). The aim of monitoring has been to provide quality assurance of the cleaning and disinfection of endoscopes; however, there is controversy regarding its frequency. This lack of consensus stimulated a review of the experience within our health service. At Southern Health, routine microbiological sampling has involved 4-weekly monitoring of bronchoscopes, duodenoscopes and automated flexible endoscope reprocessors (AFER), and 3-monthly monitoring of all other gastrointestinal endoscopes. Records of testing were reviewed from 1 January 2002 until 31 December 2006. A literature review was conducted, cost analysis performed and positive cultures investigated. There were 2374 screening tests performed during the 5-year period, including 287 AFER, 631 bronchoscopes for mycobacteria and 1456 endoscope bacterial screens. There were no positive results of the AFER or bronchoscopes for mycobacteria. Of the 1456 endoscopic bacterial samples, six were positive; however, retesting resulted in no growth. The overall cost of tests performed and cost in time for nursing staff to collect the samples was estimated at $AUD 100,400. Periodic monitoring of endoscopes is both time-consuming and costly. Our review demonstrates that AFER (Soluscope) perform well in cleaning endoscopes. Based on our 5-year experience, assurance of quality for endoscopic use could be achieved through process control as opposed to product control. Maintenance of endoscopes and AFER should be in accordance with the manufacturer's instructions and microbiological testing performed on commissioning, annually and following repair. Initial prompt manual leak testing and manual cleaning followed by mechanical leak testing, cleaning and disinfection should be the minimum standard in reprocessing of endoscopes. PMID:18086113

  1. Detection and control of microbiologically influenced corrosion

    SciTech Connect

    Licina, G.J. )

    1990-01-01

    The Sourcebook for Microbiologically Influenced Corrosion in Nuclear Power Plants (EPRI NP-5580) introduced many nuclear plant personnel to the mechanisms of MIC, provided a glossary of pertinent terms and a listing of organisms that have been associated with MIC, and gave examples of MIC from nuclear plant systems via fifteen case histories. Methods for the diagnosis, prevention, and control of existing MIC conditions were also provided. This report expands upon the background given in EPRI NP-5580 and provides updated information on field experience with various prevention, mitigation, repair, and replacement methods. Guidelines for replacement are also provided in the event that a MCI condition cannot been prevented or controlled.

  2. Cystic Fibrosis: Microbiology and Host Response.

    PubMed

    Zemanick, Edith T; Hoffman, Lucas R

    2016-08-01

    The earliest descriptions of lung disease in people with cystic fibrosis (CF) showed the involvement of 3 interacting pathophysiologic elements in CF airways: mucus obstruction, inflammation, and infection. Over the past 7 decades, our understanding of CF respiratory microbiology and inflammation has evolved with the introduction of new treatments, increased longevity, and increasingly sophisticated laboratory techniques. This article reviews the current understanding of infection and inflammation and their roles in CF lung disease. It also discusses how this constantly evolving information is used to inform current therapeutic strategies, measures and predictors of disease severity, and research priorities. PMID:27469179

  3. Microbiologically induced deterioration of concrete - A Review

    PubMed Central

    Wei, Shiping; Jiang, Zhenglong; Liu, Hao; Zhou, Dongsheng; Sanchez-Silva, Mauricio

    2013-01-01

    Microbiologically induced deterioration (MID) causes corrosion of concrete by producing acids (including organic and inorganic acids) that degrade concrete components and thus compromise the integrity of sewer pipelines and other structures, creating significant problems worldwide. Understanding of the fundamental corrosion process and the causal agents will help us develop an appropriate strategy to minimize the costs in repairs. This review presents how microorganisms induce the deterioration of concrete, including the organisms involved and their colonization and succession on concrete, the microbial deterioration mechanism, the approaches of studying MID and safeguards against concrete biodeterioration. In addition, the uninvestigated research area of MID is also proposed. PMID:24688488

  4. [Microbiology laboratory management: an (almost) pending matter].

    PubMed

    Aznar, Javier; Nogueira, José Miguel

    2010-10-01

    Many professionals from distinct disciplines work in health centers and consequently these workplaces should be considered as service companies, involving human, material and financial resources aimed at providing a service required by society. Hospitals are one of the most complex types of company, in which diverse goods and services are produced and consumed. Like the hospital as a whole, the various units and departments in which the hospital is divided, including the microbiology department, are sufficiently different to be called distinct, but related, branches of the same company, given that none can perform their function without the others. Viewing a hospital service as a branch of a large company (the hospital as a whole) allows its production, the resources used in this production, and its clients to be identified more clearly. The healthcare model based on clinical management units aims to constitute a new organizational model for public health systems in which health strategies are performed that allow innovation and decentralization of the healthcare network. Clinical management provides the framework for attending to the population's healthcare needs through a person-centered approach and involves all the professionals in any of the settings in which healthcare is provided. Among the aims of this model is to guarantee continuity of care, facilitate comprehensive health promotion and deliver daily healthcare effectively. The main instruments of clinical management are structured knowledge of the population's health needs, the use of the best scientific knowledge available, and a comprehensive and participatory practical model, together with assessment tools. Three possible clinical management models are proposed for the work of specialists in microbiology and parasitology: a) a microbiology clinical management unit; b) a biological diagnosis clinical management unit, and c) a multidisciplinary clinical management unit with cross-competencies with

  5. Issues in career progression in microbiology.

    PubMed

    Purser, L; Sheasby, L; Ward, L

    2004-12-01

    We are three highly motivated university graduates who are looking to begin careers in microbiology. We each attained a degree in a biological science discipline, one in biochemistry, one in microbial and cellular biology and one in biomedical sciences (the last gained in South Africa). However, the career obstacles we have so far encountered require us to be Olympic hurdlers. This article highlights the issues, and the advantages and disadvantages of the options open to us. We look at each career option in turn and describe the difficulties encountered. PMID:15779810

  6. Microbiological impact of three commercial laying hen housing systems.

    PubMed

    Jones, D R; Cox, N A; Guard, J; Fedorka-Cray, P J; Buhr, R J; Gast, R K; Abdo, Z; Rigsby, L L; Plumblee, J R; Karcher, D M; Robison, C I; Blatchford, R A; Makagon, M M

    2015-03-01

    Hen housing for commercial egg production continues to be a societal and regulatory concern. Controlled studies have examined various aspects of egg safety, but a comprehensive assessment of commercial hen housing systems in the US has not been conducted. The current study is part of a holistic, multidisciplinary comparison of the diverse aspects of commercial conventional cage, enriched colony cage, and cage-free aviary housing systems and focuses on environmental and egg microbiology. Environmental swabs and eggshell pools were collected from all housing systems during 4 production periods. Total aerobes and coliforms were enumerated, and the prevalence of Salmonella and Campylobacter spp. was determined. Environmental aerobic and coliform counts were highest for aviary drag swabs (7.5 and 4.0 log cfu/mL, respectively) and enriched colony cage scratch pad swabs (6.8 and 3.8 log cfu/mL, respectively). Aviary floor and system wire shell pools had the greatest levels of aerobic contamination for all eggshell pools (4.9 and 4.1 log cfu/mL, respectively). Hens from all housing systems were shedding Salmonella spp. (89-100% of manure belt scraper blade swabs). The dry belt litter removal processes for all housing systems appear to affect Campylobacter spp. detection (0-41% of manure belt scraper blade swabs) considering detection of Campylobacter spp. was much higher for other environmental samples. Aviary forage area drag swabs were 100% contaminated with Campylobacter spp., whereas enriched colony cage scratch pads had a 93% positive rate. There were no differences in pathogen detection in the shell pools from the 3 housing systems. Results indicate egg safety is enhanced when hens in alternative housing systems use nest boxes. Additionally, current outcomes indicate the use of scratch pads in hen housing systems needs to be more thoroughly investigated for effects on hen health and egg safety. PMID:25480737

  7. Microbiological impact of three commercial laying hen housing systems1

    PubMed Central

    Jones, D. R.; Cox, N. A.; Guard, J.; Fedorka-Cray, P. J.; Buhr, R. J.; Gast, R. K.; Abdo, Z.; Rigsby, L. L.; Plumblee, J. R.; Karcher, D. M.; Robison, C. I.; Blatchford, R. A.; Makagon, M. M.

    2014-01-01

    Hen housing for commercial egg production continues to be a societal and regulatory concern. Controlled studies have examined various aspects of egg safety, but a comprehensive assessment of commercial hen housing systems in the US has not been conducted. The current study is part of a holistic, multidisciplinary comparison of the diverse aspects of commercial conventional cage, enriched colony cage, and cage-free aviary housing systems and focuses on environmental and egg microbiology. Environmental swabs and eggshell pools were collected from all housing systems during 4 production periods. Total aerobes and coliforms were enumerated, and the prevalence of Salmonella and Campylobacter spp. was determined. Environmental aerobic and coliform counts were highest for aviary drag swabs (7.5 and 4.0 log cfu/mL, respectively) and enriched colony cage scratch pad swabs (6.8 and 3.8 log cfu/mL, respectively). Aviary floor and system wire shell pools had the greatest levels of aerobic contamination for all eggshell pools (4.9 and 4.1 log cfu/mL, respectively). Hens from all housing systems were shedding Salmonella spp. (89–100% of manure belt scraper blade swabs). The dry belt litter removal processes for all housing systems appear to affect Campylobacter spp. detection (0–41% of manure belt scraper blade swabs) considering detection of Campylobacter spp. was much higher for other environmental samples. Aviary forage area drag swabs were 100% contaminated with Campylobacter spp., whereas enriched colony cage scratch pads had a 93% positive rate. There were no differences in pathogen detection in the shell pools from the 3 housing systems. Results indicate egg safety is enhanced when hens in alternative housing systems use nest boxes. Additionally, current outcomes indicate the use of scratch pads in hen housing systems needs to be more thoroughly investigated for effects on hen health and egg safety. PMID:25480737

  8. Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

    USGS Publications Warehouse

    Harvey, J.B.J.; Hoy, M.S.; Rodriguez, R.J.

    2009-01-01

    Non-native marine species have been and continue to be introduced into Puget Sound via several vectors including ship's ballast water. Some non-native species become invasive and negatively impact native species or near shore habitats. We present a new methodology for the development and testing of taxon specific PCR primers designed to assess environmental samples of ocean water for the presence of native and non-native bivalves, crustaceans and algae. The intergenic spacer regions (IGS; ITS1, ITS2 and 5.8S) of the ribosomal DNA were sequenced for adult samples of each taxon studied. We used these data along with those available in Genbank to design taxon and group specific primers and tested their stringency against artificial populations of plasmid constructs containing the entire IGS region for each of the 25 taxa in our study, respectively. Taxon and group specific primer sets were then used to detect the presence or absence of native and non-native planktonic life-history stages (propagules) from environmental samples of ballast water and plankton tow net samples collected in Puget Sound. This methodology provides an inexpensive and efficient way to test the discriminatory ability of taxon specific oligonucleotides (PCR primers) before creating molecular probes or beacons for use in molecular ecological applications such as probe hybridizations or microarray analyses. This work addresses the current need to develop molecular tools capable of diagnosing the presence of planktonic life-history stages from non-native marine species (potential invaders) in ballast water and other environmental samples. ?? 2008 Elsevier B.V.

  9. Microscopic and microbiological investigations of Mississippian sylvite

    NASA Astrophysics Data System (ADS)

    Hoover, Richard B.; Pikuta, Elena V.

    2012-11-01

    Sylvite is a potassium chloride (KCl) mineral that was first discovered in 1832 in evaporite deposits in sedimentary basins of Mt. Vesuvius. Sylvite is colorless (grey or white) but it is often found in association with red deposits of halite and a variety of other minerals (e.g., hilgardite, volkovskite, trembathite and strontioginorite). We have conducted an Optical Microscopy and Microbiological study of freshly fractured interior material of core samples of Sylvite and Halite from the Penobsquis Mines of Kings County, New Brunswick. These samples are dated as Early Carboniferous period, and of Mississippian sub-period (Toumaisian stage 345-359 Myr) from the Upper Halite Member of the Windsor Group Evaporites. During this study, viable microorganisms were isolated in enrichment cultures that represent an ancient life of the deposits. Currently, in microbiology, there are several records of the isolation of viable bacterial cultures from the Permian salt crystals and oil. In this article, we present the preliminary results of the study of ancient anaerobic enrichment cultures isolated from Mississippian Sylvite and Halite samples. Therefore, this study extends by more than 50 million years the paleontological record of viable and culturable microorganisms preserved in ancient salt crystals.

  10. Progress in cultivation-independent phyllosphere microbiology.

    PubMed

    Müller, Thomas; Ruppel, Silke

    2014-01-01

    Most microorganisms of the phyllosphere are nonculturable in commonly used media and culture conditions, as are those in other natural environments. This review queries the reasons for their 'noncultivability' and assesses developments in phyllospere microbiology that have been achieved cultivation independently over the last 4 years. Analyses of total microbial communities have revealed a comprehensive microbial diversity. 16S rRNA gene amplicon sequencing and metagenomic sequencing were applied to investigate plant species, location and season as variables affecting the composition of these communities. In continuation to culture-based enzymatic and metabolic studies with individual isolates, metaproteogenomic approaches reveal a great potential to study the physiology of microbial communities in situ. Culture-independent microbiological technologies as well advances in plant genetics and biochemistry provide methodological preconditions for exploring the interactions between plants and their microbiome in the phyllosphere. Improving and combining cultivation and culture-independent techniques can contribute to a better understanding of the phyllosphere ecology. This is essential, for example, to avoid human-pathogenic bacteria in plant food. PMID:24003903

  11. Microbiologic spectrum of acute and chronic dacryocystitis

    PubMed Central

    Eshraghi, Bahram; Abdi, Parisa; Akbari, Mohammadreza; Fard, Masoud Aghsaei

    2014-01-01

    AIM To report the microbiological spectrum of acute and chronic dacrocystitis. METHODS Retrospective study on 100 patients who presented to the ophthalmic plastic clinic of a tertiary eye care center from May 2011 and April 2013 with acute and chronic dacryocystitis was reviewed for demographic and microbiological profile. The culture results and organisms isolated were recorded. RESULTS Sixty patients had acute onset and the remaining 40 patients had chronic onset dacryocystitis. The female to male ratio was 1.78. The mean age of patients was 44y. Gram-positive organisms were the most commonly isolated accounting for 54%, and the commonest species isolated was S. aureus in 26%. Percentage of gram positive cultures was higher in chronic dacryocystitis than acute ones (82% vs 48% of positive cultures; P=0.003). Also in culture positive acute dacryocystitis, gram negative species were found in 52% of eyes but only in 18% of chronic dacryocystitis. CONCLUSION Gram negative bacteria, culture negative samples, unusual and more virulent organisms are more common in acute dacryocystitis than chronic ones. The results of this study have significant bearing on the treatment of patients with dacrocystitis. PMID:25349808

  12. Progress in cultivation-independent phyllosphere microbiology

    PubMed Central

    Müller, Thomas; Ruppel, Silke

    2014-01-01

    Most microorganisms of the phyllosphere are nonculturable in commonly used media and culture conditions, as are those in other natural environments. This review queries the reasons for their ‘noncultivability’ and assesses developments in phyllospere microbiology that have been achieved cultivation independently over the last 4 years. Analyses of total microbial communities have revealed a comprehensive microbial diversity. 16S rRNA gene amplicon sequencing and metagenomic sequencing were applied to investigate plant species, location and season as variables affecting the composition of these communities. In continuation to culture-based enzymatic and metabolic studies with individual isolates, metaproteogenomic approaches reveal a great potential to study the physiology of microbial communities in situ. Culture-independent microbiological technologies as well advances in plant genetics and biochemistry provide methodological preconditions for exploring the interactions between plants and their microbiome in the phyllosphere. Improving and combining cultivation and culture-independent techniques can contribute to a better understanding of the phyllosphere ecology. This is essential, for example, to avoid human–pathogenic bacteria in plant food. PMID:24003903

  13. [Historical perspective of mass spectrometry in microbiology].

    PubMed

    Mingorance, Jesús; Regueiro, Benito; Muñoz-Bellido, Juan Luis

    2016-06-01

    La espectrometría de masas (EM) es una técnica de análisis que permite caracterizar muestras midiendo las masas (estrictamente las razones masa-carga) de las moléculas componentes. Cuenta con más de un siglo de historia y evolución tecnológica y a lo largo de los años ha ampliado su alcance desde los isótopos a moléculas pequeñas, moléculas orgánicas más complejas y, en las últimas décadas, macromoléculas (ácidos nucleicos y proteínas). La EM MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) es una variante que permite el análisis de mezclas complejas de proteínas y que se ha aplicado recientemente a la identificación de microorganismos en cultivo, convirtiéndose en una herramienta rápida y eficaz para el diagnóstico microbiológico que ha conseguido entrar en poco tiempo en la rutina de muchos servicios de microbiología clínica. El gran impacto que ha tenido está impulsando el desarrollo de nuevas aplicaciones en el campo de la microbiología clínica. PMID:27389286

  14. Microbiology of animal bite wound infections.

    PubMed

    Abrahamian, Fredrick M; Goldstein, Ellie J C

    2011-04-01

    The microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. Bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. Bacteria may also originate from the victim's own skin or the physical environment at the time of injury. Our review has focused on bite wound infections in humans from dogs, cats, and a variety of other animals such as monkeys, bears, pigs, ferrets, horses, sheep, Tasmanian devils, snakes, Komodo dragons, monitor lizards, iguanas, alligators/crocodiles, rats, guinea pigs, hamsters, prairie dogs, swans, and sharks. The medical literature in this area has been made up mostly of small case series or case reports. Very few studies have been systematic and are often limited to dog or cat bite injuries. Limitations of studies include a lack of established or inconsistent criteria for an infected wound and a failure to utilize optimal techniques in pathogen isolation, especially for anaerobic organisms. There is also a lack of an understanding of the pathogenic significance of all cultured organisms. Gathering information and conducting research in a more systematic and methodical fashion through an organized research network, including zoos, veterinary practices, and rural clinics and hospitals, are needed to better define the microbiology of animal bite wound infections in humans. PMID:21482724

  15. Lectins and their application to clinical microbiology.

    PubMed Central

    Slifkin, M; Doyle, R J

    1990-01-01

    Lectins are generally associated with plant or animal components, selectively bind carbohydrates, and interact with procaryotic and eucaryotic cells. Lectins have various specificities that are associated with their ability to interact with acetylaminocarbohydrates, aminocarbohydrates, sialic acids, hexoses, pentoses, and as other carbohydrates. Microbial surfaces generally contain many of the sugar residues that react with lectins. Lectins are presently used in the clinical laboratory to type blood cells and are used in a wide spectrum of applications, including, in part, as carriers of chemotherapeutic agents, as mitogens, for fractionation of animal cells, and for investigations of cellular surfaces. Numerous studies have shown that lectins can be used to identify rapidly certain microorganisms isolated from a clinical specimen or directly in a clinical specimen. Lectins have been demonstrated to be important diagnostic reagents in the major realms of clinical microbiology. Thus, they have been applied in bacteriology, mycology, mycobacteriology, and virology for the identification and/or differentiation of various microorganisms. Lectins have been used successfully as epidemiologic as well as taxonomic markers of specific microorganisms. Lectins provide the clinical microbiologist with cost-effective and potential diagnostic reagents. This review describes the applications of lectins in clinical microbiology. Images PMID:2200603

  16. Microbiology of Animal Bite Wound Infections

    PubMed Central

    Abrahamian, Fredrick M.; Goldstein, Ellie J. C.

    2011-01-01

    Summary: The microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. Bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. Bacteria may also originate from the victim's own skin or the physical environment at the time of injury. Our review has focused on bite wound infections in humans from dogs, cats, and a variety of other animals such as monkeys, bears, pigs, ferrets, horses, sheep, Tasmanian devils, snakes, Komodo dragons, monitor lizards, iguanas, alligators/crocodiles, rats, guinea pigs, hamsters, prairie dogs, swans, and sharks. The medical literature in this area has been made up mostly of small case series or case reports. Very few studies have been systematic and are often limited to dog or cat bite injuries. Limitations of studies include a lack of established or inconsistent criteria for an infected wound and a failure to utilize optimal techniques in pathogen isolation, especially for anaerobic organisms. There is also a lack of an understanding of the pathogenic significance of all cultured organisms. Gathering information and conducting research in a more systematic and methodical fashion through an organized research network, including zoos, veterinary practices, and rural clinics and hospitals, are needed to better define the microbiology of animal bite wound infections in humans. PMID:21482724

  17. Isolation by environmental distance in mobile marine species: molecular ecology of franciscana dolphins at their southern range.

    PubMed

    Mendez, Martin; Rosenbaum, Howard C; Subramaniam, Ajit; Yackulic, Charles; Bordino, Pablo

    2010-06-01

    The assessment of population structure is a valuable tool for studying the ecology of endangered species and drafting conservation strategies. As we enhance our understanding about the structuring of natural populations, it becomes important that we also understand the processes behind these patterns. However, there are few rigorous assessments of the influence of environmental factors on genetic patterns in mobile marine species. Given their dispersal capabilities and localized habitat preferences, coastal cetaceans are adequate study species for evaluating environmental effects on marine population structure. The franciscana dolphin, a rare coastal cetacean endemic to the Western South Atlantic, was studied to examine these issues. We analysed genetic data from the mitochondrial DNA and 12 microsatellite markers for 275 franciscana samples utilizing frequency-based, maximum-likelihood and Bayesian algorithms to assess population structure and migration patterns. This information was combined with 10 years of remote sensing environmental data (chlorophyll concentration, water turbidity and surface temperature). Our analyses show the occurrence of genetically isolated populations within Argentina, in areas that are environmentally distinct. Combined evidence of genetic and environmental structure suggests that isolation by distance and a process here termed isolation by environmental distance can explain the observed correlations. Our approach elucidated important ecological and conservation aspects of franciscana dolphins, and has the potential to increase our understanding of ecological processes influencing genetic patterns in other marine species. PMID:20465582

  18. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase

    SciTech Connect

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2008-02-01

    We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.

  19. 76 FR 48169 - Advancing Regulatory Science for Highly Multiplexed Microbiology/Medical Countermeasure Devices...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-08

    ... Microbiology/ Medical Countermeasure Devices; Public Meeting AGENCY: Food and Drug Administration, HHS. ACTION... following public meeting: ``Advancing Regulatory Science for Highly Multiplexed Microbiology/Medical... multiplexed microbiology/medical countermeasure (MCM) devices, their clinical application and public...

  20. Restructuring a General Microbiology Laboratory into an Investigative Experience.

    ERIC Educational Resources Information Center

    Deutch, Charles E.

    1994-01-01

    Describes an investigative laboratory sequence based upon the isolation and characterization of soil bacteria to aid microbiology teachers in providing students with activities that expose them to basic techniques of microbiology as well as demonstrates the scientific process and the experimental analysis of microorganisms. (ZWH)

  1. 21 CFR 211.113 - Control of microbiological contamination.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Control of microbiological contamination. 211.113... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures... contamination of drug products purporting to be sterile, shall be established and followed. Such...

  2. 21 CFR 211.113 - Control of microbiological contamination.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Control of microbiological contamination. 211.113... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures... contamination of drug products purporting to be sterile, shall be established and followed. Such...

  3. The next generation of microbiological testing of poultry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbiological testing of food products is a common practice of food processors to ensure compliance with food safety criteria. Sampling on its own is of limited value, but when applied regularly at different stages of the food chain, microbiology testing can be an integral part of a quality contr...

  4. Observations on Microbiology Laboratory Instruction for Allied Health Students.

    ERIC Educational Resources Information Center

    Benathen, Isaiah A.

    1993-01-01

    The purposes of this paper are (1) to demonstrate that medical microbiology laboratory exercises should be presented with a focus on medical applications, not just traditional microbiology and (2) that exercises devoted to differential diagnostic decision making can be used to enhance the problem solving of students. (PR)

  5. 21 CFR 211.113 - Control of microbiological contamination.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 4 2012-04-01 2012-04-01 false Control of microbiological contamination. 211.113... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures... contamination of drug products purporting to be sterile, shall be established and followed. Such...

  6. 21 CFR 211.113 - Control of microbiological contamination.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 4 2013-04-01 2013-04-01 false Control of microbiological contamination. 211.113... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures... contamination of drug products purporting to be sterile, shall be established and followed. Such...

  7. 21 CFR 211.113 - Control of microbiological contamination.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 4 2014-04-01 2014-04-01 false Control of microbiological contamination. 211.113... Process Controls § 211.113 Control of microbiological contamination. (a) Appropriate written procedures... contamination of drug products purporting to be sterile, shall be established and followed. Such...

  8. Environmental surveillance of human enteroviruses in Shandong Province, China, 2008 to 2012: serotypes, temporal fluctuation, and molecular epidemiology.

    PubMed

    Wang, Haiyan; Tao, Zexin; Li, Yan; Lin, Xiaojuan; Yoshida, Hiromu; Song, Lizhi; Zhang, Yong; Wang, Suting; Cui, Ning; Xu, Wenbo; Song, Yanyan; Xu, Aiqiang

    2014-08-01

    Environmental surveillance is an effective approach in investigating the circulation of polioviruses (PVs) and other human enteroviruses (EVs) in the population. The present report describes the results of environmental surveillance conducted in Shandong Province, China, from 2008 to 2012. A total of 129 sewage samples were collected, and 168 PVs and 1,007 nonpolio enteroviruses (NPEVs) were isolated. VP1 sequencing and typing were performed on all isolates. All PV strains were Sabin-like, with the numbers of VP1 substitutions ranging from 0 to 7. The NPEVs belonged to 19 serotypes, and echovirus 6 (E6), E11, coxsackievirus B3 (CVB3), E3, E12, and E7 were the six main serotypes, which accounted for 18.3%, 14.8%, 14.5%, 12.9%, 9.0%, and 5.7% of NPEVs isolated, respectively. Typical summer-fall peaks of NPEV were observed in the monthly distribution of isolation, and an epidemic pattern of annual circulation was revealed for the common serotypes. Phylogenetic analysis was performed on environmental CVB3 and E3 strains with global reference strains and local strains from aseptic meningitis patients. Shandong strains formed distinct clusters, and a close relationship was observed between local environmental and clinical strains. As an EV-specific case surveillance system is absent in China and many other countries, continuous environmental surveillance should be encouraged to investigate the temporal circulation and phylogeny of EVs in the population. PMID:24837389

  9. Environmental Surveillance of Human Enteroviruses in Shandong Province, China, 2008 to 2012: Serotypes, Temporal Fluctuation, and Molecular Epidemiology

    PubMed Central

    Wang, Haiyan; Tao, Zexin; Li, Yan; Lin, Xiaojuan; Yoshida, Hiromu; Song, Lizhi; Zhang, Yong; Wang, Suting; Cui, Ning; Xu, Wenbo

    2014-01-01

    Environmental surveillance is an effective approach in investigating the circulation of polioviruses (PVs) and other human enteroviruses (EVs) in the population. The present report describes the results of environmental surveillance conducted in Shandong Province, China, from 2008 to 2012. A total of 129 sewage samples were collected, and 168 PVs and 1,007 nonpolio enteroviruses (NPEVs) were isolated. VP1 sequencing and typing were performed on all isolates. All PV strains were Sabin-like, with the numbers of VP1 substitutions ranging from 0 to 7. The NPEVs belonged to 19 serotypes, and echovirus 6 (E6), E11, coxsackievirus B3 (CVB3), E3, E12, and E7 were the six main serotypes, which accounted for 18.3%, 14.8%, 14.5%, 12.9%, 9.0%, and 5.7% of NPEVs isolated, respectively. Typical summer-fall peaks of NPEV were observed in the monthly distribution of isolation, and an epidemic pattern of annual circulation was revealed for the common serotypes. Phylogenetic analysis was performed on environmental CVB3 and E3 strains with global reference strains and local strains from aseptic meningitis patients. Shandong strains formed distinct clusters, and a close relationship was observed between local environmental and clinical strains. As an EV-specific case surveillance system is absent in China and many other countries, continuous environmental surveillance should be encouraged to investigate the temporal circulation and phylogeny of EVs in the population. PMID:24837389

  10. There must be a prokaryote somewhere: microbiology's search for itself

    NASA Technical Reports Server (NTRS)

    Woese, C. R.

    1994-01-01

    While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.

  11. THE APPLICATION OF COMPUTATIONAL MOLECULAR METHODS TO UNDERSTAND THE HEALTH EFFECTS OF ENVIRONMENTAL CHEMICALS-POLYCYCLIC AROMATIC HYDROCARBONS

    EPA Science Inventory

    In evaluating the risk posed by chemicals introduced into the environment, information
    about their molecular mechanism of action provides a basis for extrapolating from the
    laboratory to the environment. Polycyclic aromatic hydrocarbons (PAH) are a large class
    of...

  12. The JCMT nearby galaxies legacy survey - X. Environmental effects on the molecular gas and star formation properties of spiral galaxies

    NASA Astrophysics Data System (ADS)

    Mok, Angus; Wilson, C. D.; Golding, J.; Warren, B. E.; Israel, F. P.; Serjeant, S.; Knapen, J. H.; Sánchez-Gallego, J. R.; Barmby, P.; Bendo, G. J.; Rosolowsky, E.; van der Werf, P.

    2016-03-01

    We present a study of the molecular gas properties in a sample of 98 H I - flux selected spiral galaxies within ˜25 Mpc, using the CO J = 3 - 2 line observed with the James Clerk Maxwell Telescope. We use the technique of survival analysis to incorporate galaxies with CO upper limits into our results. Comparing the group and Virgo samples, we find a larger mean H2 mass in the Virgo galaxies, despite their lower mean H I mass. This leads to a significantly higher H2 to H I ratio for Virgo galaxies. Combining our data with complementary Hα star formation rate measurements, Virgo galaxies have longer molecular gas depletion times compared to group galaxies, due to their higher H2 masses and lower star formation rates. We suggest that the longer depletion times may be a result of heating processes in the cluster environment or differences in the turbulent pressure. From the full sample, we find that the molecular gas depletion time has a positive correlation with the stellar mass, indicative of differences in the star formation process between low- and high-mass galaxies, and a negative correlation between the molecular gas depletion time and the specific star formation rate.

  13. Molecular Epidemiology of Stenotrophomonas maltophilia Isolated from Clinical Specimens from Patients with Cystic Fibrosis and Associated Environmental Samples

    PubMed Central

    Denton, Miles; Todd, Neil J.; Kerr, Kevin G.; Hawkey, Peter M.; Littlewood, James M.

    1998-01-01

    Stenotrophomonas maltophilia was isolated from the respiratory tracts of 41 (25%) of 163 children attending our pediatric cystic fibrosis unit between September 1993 and December 1995. The extents of S. maltophilia contamination of environmental sites frequented by these patients were investigated with a selective medium incorporating vancomycin, imipenem, and amphotericin B. Eighty-two isolates of S. maltophilia were cultured from 67 different environmental sites sampled between January and July 1996. The organism was widespread in the home environment, with 20 (36%) and 25 (42%) of sampled sites positive in the homes of colonized and noncolonized patients, respectively. In the nosocomial setting, it was isolated from 18 (32%) sites in the hospital ward and from 4 (17%) sites in the outpatient clinic area. The most common sites of contamination were sink drains, faucets, and other items frequently in contact with water. All environmental and clinical isolates were genotyped with enterobacterial repetitive intergenic consensus sequences as primers. A total of 33 of the 41 patients were colonized with unique strains, and four pairs of patients shared strains. Further characterization by pulsed-field gel electrophoresis after digestion with XbaI found that there was no evidence of patient-to-patient transmission; however, there was some evidence that a small number of patients may have acquired the organism from the hospital environment. Resampling of environmental sites in the hospital ward in January 1997 revealed evidence of genetic drift, complicating the accurate determination of environmental sources for clinical strains. The source of the majority of S. maltophilia strains colonizing the respiratory tracts of these patients with cystic fibrosis remained uncertain but may have represented multiple, independent acquisitions from a variety of environmental sites both within and outside the hospital. PMID:9650943

  14. Microbiological findings in prepubertal girls with vulvovaginitis.

    PubMed

    Sikanić-Dugić, Nives; Pustisek, Nives; Hirsl-Hećej, Vlasta; Lukić-Grlić, Amarela

    2009-01-01

    The aim of the study was to define the most common causes, symptoms and clinical features of vulvovaginitis in prepubertal girls, and to evaluate treatment success depending on the causative agent involved. The study included 115 girls aged 2-8 (mean 4.8) years, presenting with vulvovaginitis to the Outpatient Clinic for Pediatric and Adolescent Gynecology, Zagreb Children's Hospital, between September 2006 and July 2007. Medical history data were obtained from parents. Vaginal samples were collected for microbiological culture by using cotton-tipped swabs moistened with saline. All samples were referred to microbiology laboratory, where standard microbiological diagnostic procedures were performed. Selective and non-selective media were used. Of 115 study patients, 43 (37.4%) had received antibiotic therapy more than one month prior to their visit to the Clinic, mainly for upper respiratory tract infection. The most common presenting symptom was increased vaginal discharge usually noticed on the pants or diaper, found in 26 of 115 (22.6%) patients, followed by vulvar redness in 16 (13.9%), burning in seven (6.1%), itching in the vulvovaginal area in seven (6.1%), soreness in six (5.2%), odor in three (2.6%) patients, and two or more of these symptoms in another 50 (43.5%) patients. Fifty-nine of 115 children had normal clinical finding on gynecologic examination. Among the remaining 56 children, the most common finding was erythema observed in 19, vaginal discharge in ten, and a combination of discharge and erythema in 13 patients. Of 115 study patients, causative agents were isolated from vaginal culture in 38 (33%) cases. Of these, 21 grew group A beta hemolytic streptococcus, five patients Haemophilus influenzae, three Escherichia coli, two Enterococcus spp., and one each Staphylococcus aureus, Proteus mirabilis, and Streptococcus pneumoniae. Antibiotic therapy was administered in 31 of these 38 patients, except for those cases where intestinal bacteria and

  15. Current and Past Strategies for Bacterial Culture in Clinical Microbiology

    PubMed Central

    Lagier, Jean-Christophe; Edouard, Sophie; Pagnier, Isabelle; Mediannikov, Oleg; Drancourt, Michel

    2015-01-01

    SUMMARY A pure bacterial culture remains essential for the study of its virulence, its antibiotic susceptibility, and its genome sequence in order to facilitate the understanding and treatment of caused diseases. The first culture conditions empirically varied incubation time, nutrients, atmosphere, and temperature; culture was then gradually abandoned in favor of molecular methods. The rebirth of culture in clinical microbiology was prompted by microbiologists specializing in intracellular bacteria. The shell vial procedure allowed the culture of new species of Rickettsia. The design of axenic media for growing fastidious bacteria such as Tropheryma whipplei and Coxiella burnetii and the ability of amoebal coculture to discover new bacteria constituted major advances. Strong efforts associating optimized culture media, detection methods, and a microaerophilic atmosphere allowed a dramatic decrease of the time of Mycobacterium tuberculosis culture. The use of a new versatile medium allowed an extension of the repertoire of archaea. Finally, to optimize the culture of anaerobes in routine bacteriology laboratories, the addition of antioxidants in culture media under an aerobic atmosphere allowed the growth of strictly anaerobic species. Nevertheless, among usual bacterial pathogens, the development of axenic media for the culture of Treponema pallidum or Mycobacterium leprae remains an important challenge that the patience and innovations of cultivators will enable them to overcome. PMID:25567228

  16. [Microbiological Surveillance of Measles and Rubella in Spain. Laboratory Network].

    PubMed

    Echevarría, Juan Emilio; Fernández García, Aurora; de Ory, Fernando

    2015-01-01

    The Laboratory is a fundamental component on the surveillance of measles and rubella. Cases need to be properly confirmed to ensure an accurate estimation of the incidence. Strains should be genetically characterized to know the transmission pattern of these viruses and frequently, outbreaks and transmission chains can be totally discriminated only after that. Finally, the susceptibility of the population is estimated on the basis of sero-prevalence surveys. Detection of specific IgM response is the base of the laboratory diagnosis of these diseases. It should be completed with genomic detection by RT-PCR to reach an optimal efficiency, especially when sampling is performed early in the course of the disease. Genotyping is performed by genomic sequencing according to reference protocols of the WHO. Laboratory surveillance of measles and rubella in Spain is organized as a net of regional laboratories with different capabilities. The National Center of Microbiology as National Reference Laboratory (NRL), supports regional laboratories ensuring the availability of all required techniques in the whole country and watching for the quality of the results. The NRL is currently working in the implementation of new molecular techniques based on the analysis of genomic hypervariable regions for the strain characterization at sub-genotypic levels and use them in the surveillance. PMID:26580793

  17. The medically important aerobic actinomycetes: epidemiology and microbiology.

    PubMed Central

    McNeil, M M; Brown, J M

    1994-01-01

    The aerobic actinomycetes are soil-inhabiting microorganisms that occur worldwide. In 1888, Nocard first recognized the pathogenic potential of this group of microorganisms. Since then, several aerobic actinomycetes have been a major source of interest for the commercial drug industry and have proved to be extremely useful microorganisms for producing novel antimicrobial agents. They have also been well known as potential veterinary pathogens affecting many different animal species. The medically important aerobic actinomycetes may cause significant morbidity and mortality, in particular in highly susceptible severely immunocompromised patients, including transplant recipients and patients infected with human immunodeficiency virus. However, the diagnosis of these infections may be difficult, and effective antimicrobial therapy may be complicated by antimicrobial resistance. The taxonomy of these microorganisms has been problematic. In recent revisions of their classification, new pathogenic species have been recognized. The development of additional and more reliable diagnostic tests and of a standardized method for antimicrobial susceptibility testing and the application of molecular techniques for the diagnosis and subtyping of these microorganisms are needed to better diagnose and treat infected patients and to identify effective control measures for these unusual pathogens. We review the epidemiology and microbiology of the major medically important aerobic actinomycetes. Images PMID:7923055

  18. Turning the inside out: the microbiology of atopic dermatitis.

    PubMed

    Brüssow, Harald

    2016-07-01

    Allergy is on the rise worldwide. The hygiene hypothesis of atopic diseases linked microbes with atopic dermatitis (AD) both as drivers and modulators of skin pathology. The earlier literature favoured an inside-outside model of AD where an immunological abnormality compounded by a gut microbiota dysbiosis is the primary event. Probiotic intervention trials with lactobacilli and bifidobacteria as well as the application of bifidogenic oligosaccharide prebiotics showed indeed promising clinical results, but no consistent gut microbiota dysbiosis could be linked with AD. An alternative hypothesis known as outside-inside model of AD considers a genetic skin barrier effect compounded by a skin microbiota dysbiosis as primary pathogenic event. Cultivation microbiology has demonstrated strong skin colonization with superantigen-encoding Staphylococcus aureus in AD patients; microbiota and molecular microbiome analyses demonstrated that S. aureus abundance fluctuates and parallels clinical symptoms. In a mouse model, δ-toxin of S. aureus induced mast cell degranulation, leading to AD-like symptoms. Mutant mice developing AD symptoms showed increased skin colonization with S. aureus; antibiotic treatment alleviated the symptoms. Clinical trials showed that various treatments reducing S. aureus skin load also reduced AD symptoms, suggesting S. aureus as a potential critical driver of AD and a target for antimicrobial interventions other than antibiotics. PMID:26373255

  19. Fluorescence-based tools for single-cell approaches in food microbiology.

    PubMed

    Bridier, A; Hammes, F; Canette, A; Bouchez, T; Briandet, R

    2015-11-20

    The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now as an intrinsic and multi-origin feature of microbial populations and is a major determinant of their beneficial or detrimental functional properties. The understanding of the molecular and cellular mechanisms behind the behavior of bacteria in microbial communities requires therefore observations at the single-cell level in order to overcome "averaging" effects inherent to traditional global approaches. Recent advances in the development of fluorescence-based approaches dedicated to single-cell analysis provide the opportunity to study microbial communities with an unprecedented level of resolution and to obtain detailed insights on the cell structure, metabolism activity, multicellular behavior and bacterial interactions in complex communities. These methods are now increasingly applied in the field of food microbiology in different areas ranging from research laboratories to industry. In this perspective, we reviewed the main fluorescence-based tools used for single-cell approaches and their concrete applications with specific focus on food microbiology. PMID:26163933

  20. Development of a small-scale bioreactor method to monitor the molecular diversity and environmental impacts of bacterial biofilm communities from an acid mine drainage impacted creek.

    PubMed

    Cole, Michael; Wrubel, Joshua; Henegan, Patricia; Janzen, Christopher; Holt, Jack; Tobin, Tammy

    2011-10-01

    Shamokin Creek is a tributary of the Susquehanna River in central Pennsylvania that is heavily impacted by the acid mine drainage (AMD) caused by the oxidation of pyrite from the region's extensive anthracite coal mining industry. Recent studies have begun to characterize the microbial communities present in this and other AMD-impacted waters, but varying environmental conditions have complicated attempts to determine the ecological impacts of individual bacterial species within these communities. This study developed a small-scale biofilm reactor protocol that allowed us to simultaneously monitor the development of bacterial biofilm communities in AMD-impacted creek collected water using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, while assessing the impacts that the developing biofilms were having on water quality. Our analysis confirmed that the diversity and composition of these small in situ biofilm communities could be monitored using molecular methods, and indicated the possible presence of many taxa frequently found in AMD environments, including Sulfobacillus, Nitrospira, Desulfovibrio, Geobacter, and Leptothrix species. A significant increase in the total sulfate was observed in the bioreactor, and as most likely due to the accumulation of sulfur-oxidizing bacteria such as Sulfobacillus in the biofilms. This system will allow us to study the microbial ecology of Shamokin Creek through controlled experiments that will ultimately integrate microscopic, molecular, physiological and chemical analyses, and that can be utilized to develop more effective and cost-efficient environmental remediation techniques for AMD-impacted areas. PMID:21821067

  1. Environmental surveillance and molecular epidemiology of waterborne pathogen Legionella pneumophila in health-care facilities of Northeastern Greece: a 4-year survey.

    PubMed

    Alexandropoulou, Ioanna G; Ntougias, Spyridon; Konstantinidis, Theocharis G; Parasidis, Theodoros A; Panopoulou, Maria; Constantinidis, Theodoros C

    2015-05-01

    A 4-year proactive environmental surveillance of Legionella spp. in the water distribution and cooling systems of five health-care facilities was carried out as part of the strategy for the prevention of hospital-acquired Legionnaires' disease in Northeastern Greece. Legionella spp. were detected in 71 out of 458 collected samples. The majority of strains belonged to Legionella pneumophila serogroups 2-15 (75.0%), while all L. pneumophila serogroup 1 strains (23.6%) were isolated from a single hospital. The highest percentage of positive samples was found in distal sites (19.4%), while no Legionella strains were detected in cooling systems. Each hospital was colonized at least once with L. pneumophila, while remedial actions resulted in significant reduction of Legionella concentration. The molecular epidemiology of environmental L. pneumophila strains was also investigated using random amplified polymorphic DNA (RAPD) and multi-gene sequence-based analysis. Based on RAPD patterns, L. pneumophila serogroups 2-15 and serogroup 1 strains were classified into 24 and 9 operational taxonomic units (OTUs), respectively. Sequencing of housekeeping and diversifying pressure-related genes recommended by European Working Group for Legionella Infections (EWGLI) revealed not only a high intraspecies variability but also the circulation and persistence of one specific genotyping profile in the majority of hospitals. This study highlights the necessity for diachronic surveillance of Legionella in health-care facilities by adopting both cultural and molecular methods. PMID:25712880

  2. Status of the database on microorganism inactivation in environmental media (DIMEM)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inactivation of pathogenic and indicator microorganisms is the essential component of their environmental fate which needs to be considered in environmental microbiology models. Existing data from a large number of inactivation experiments are dispersed across numerous publications with varying avai...

  3. American Society for Microbiology resources in support of an evidence-based approach to teaching microbiology.

    PubMed

    Merkel, Susan M

    2016-08-01

    Numerous national reports have addressed the need for changing how science courses in higher education are taught, so that students develop a deeper understanding of critical concepts and the analytical and cognitive skills needed to address future challenges. This review presents some evidence-based approaches to curriculum development and teaching. Results from discipline-based education research indicate that it is critically important for educators to formulate learning goals, provide frequent and authentic assessments and actively engage students in their learning. Professional societies can play a role in helping to put these changes into practice. To this end, the American Society for Microbiology has developed a number of educational programs and resources, which are described here to encourage the implementation of student-centered learning in microbiology education. PMID:27412169

  4. The Microbiology of Perchlorate in the Environment

    NASA Astrophysics Data System (ADS)

    Coates, J. D.

    2007-12-01

    In the last decade perchlorate has been identified as an important groundwater component that poses potential health threat. Although primarily sourced anthropogenically, many recent studies have identified significant natural pools throughout the US and the natural mechanisms of its synthesis remain a mystery. As such, the true perchlorate concentrations naturally present in the environment are still unknown making its regulation problematic. Because of its solubility and non-reactivity the fate and transport of perchlorate in the environment is primarily a function of microbial activity. In the last seven years more than forty specialized perchlorate respiring organisms have been identified and characterized. These dissimilatory perchlorate reducing bacteria (DPRB) are metabolically diverse and environmental populations tend to be dominated by two primary genotypes, the Dechloromonas and the Azospira species. As such, the majority of our understanding of this metabolism is based on these organisms. These organisms are readily found in soil and sedimentary environments and often associate with the rhizosphere. Recent research has demonstrated an accumulation of these organisms along plant roots suggesting their catabolism of root exudates and molecular studies has demonstrated their existence as endophytic infections of the stem and leaves of actively growing Brachypodium grass plants although their exact role under these conditions is unknown. These microorganisms are generally not nutritionally fastidious and vitamin supplementation is unnecessary for growth although molybdenum is a required trace element for perchlorate reduction. The Dechloromonas and Azospira species generally grow optimally at pH values near neutrality in freshwater environments. Even so, recent field studies have shown that related deep-branching members of these genera often predominate in sites of adverse pH or salinity with some species being capable of growth and perchlorate respiration

  5. [Microbiology--laboratory examinations for bacterias].

    PubMed

    Hen, Renjun; Imafuku, Yuji; Yoshida, Hiroshi

    2002-11-01

    As it has been required to identify pathogenic microbes in shorter times, simple and rapid methods have been developed and used. Here, we summarized the present situation of rapid diagnostic testing in clinical microbiology in Japan, and also presented our results on PBP2' detection. The rapid test kits available in Japan for E. coli, Helicobacter pylori, Salmonella, Streptococcus and Staphylococcus aureus were described. Rapid examination methods are based mainly on immunologic reactions, which included slide agglutination using latex particle, immunochromatography and ELISA. Times required for the identification are 10 to 15 minutes. Moreover, rapid test kits employing PCR are also marketed. Further, we evaluated MRSA-LA "Seiken" which is a rapid detection kit for PBP2' produced by MRSA. The test was shown to be highly sensitive and specific. For the rapid identification of pathogenic microbes, simple and rapid test kits described here will be used more in clinical diagnosis. PMID:12491600

  6. [The microbiological diagnosis in severe infections].

    PubMed

    Piédrola Angulo, Gonzalo

    2010-01-01

    The microbiological diagnosis of infectious processes has been marked as any other laboratory test, two fundamental criteria: sensitivity and specificity of the results. But inserious infections in the hospital, once achieved the above criteria, it is claimed more and more third requirement: the speed at which the agent get the picture producer and antimicrobial susceptibility. In recent years there has been significant progress in this regard, which have always been behind the biochemical and hematological tests. Lately there ultrafast techniques such as mass spectrometry soft ionization, which can detect proteins of bacteria, fungi and yeasts, in a very short time. These techniques have some tangible gains in reducing hospitalization times, reduced health care costs per patient-oriented management and allow early and more effective antibiotics in areas such as ICU, pediatric ICU, Unit of Infectious and decreased waiting times in emergency patients. PMID:22263356

  7. A computer system for clinical microbiology.

    PubMed Central

    Williams, K N; Davidson, J M; Lynn, R; Rice, E; Phillips, I

    1978-01-01

    The Department of Clinical Microbiology at St Thomas' Hospital has been producing bacteriological reports on a computer for more than three years and is now producing some 2300 reports per week. The system is operated entirely by laboratory staff without special training, and involves the use of optical mark reader (OMR) forms as worksheets, automatic validation and release of most reports, the use of local terminals, and scrutiny of reports by pathologists using a visual display unit. The OMR worksheet records not only the final result but also most of the tests and observations made on the samples; it is the only working document used by technicians. One specialist clinic submits its laboratory requests on an OMR form, which is subsequently used to record the results. The reports are printed and also filed in the computer to produce analyses for hospital, laboratory, and clinical management. PMID:748389

  8. [Vinogradskiĭ and modern microbiology].

    PubMed

    Zavarzin, G A

    2006-01-01

    The 150th anniversary of the birth of Sergei N. Winogradsky is a special date for general microbiology. Apart from the discovery of chemosynthesis, the development of the elective method, the application of the direct method, and formulation of microbial ecology problems, Winogradsky, in his pioneering studies, addressed fundamental aspects of the naturalistic Weltanschauung from the position of a microbiologist who studies the role of microorganisms in nature. These problems are still important today. Expanding knowledge throws light on them from different angles of view and highlights them with varying degrees of completeness, but the problems remain beyond time. It may be useful for contemporary microbiologists to realize the extent to which they would recognize their own work in the system of questions and answers stated a hundred years ago. PMID:17091583

  9. Buccal microbiology analyzed by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    de Abreu, Geraldo Magno Alves; da Silva, Gislene Rodrigues; Khouri, Sônia; Favero, Priscila Pereira; Raniero, Leandro; Martin, Airton Abrahão

    2012-01-01

    Rapid microbiological identification and characterization are very important in dentistry and medicine. In addition to dental diseases, pathogens are directly linked to cases of endocarditis, premature delivery, low birth weight, and loss of organ transplants. Fourier Transform Infrared Spectroscopy (FTIR) was used to analyze oral pathogens Aggregatibacter actinomycetemcomitans ATCC 29523, Aggregatibacter actinomycetemcomitans-JP2, and Aggregatibacter actinomycetemcomitans which was clinically isolated from the human blood-CI. Significant spectra differences were found among each organism allowing the identification and characterization of each bacterial species. Vibrational modes in the regions of 3500-2800 cm-1, the 1484-1420 cm-1, and 1000-750 cm-1 were used in this differentiation. The identification and classification of each strain were performed by cluster analysis achieving 100% separation of strains. This study demonstrated that FTIR can be used to decrease the identification time, compared to the traditional methods, of fastidious buccal microorganisms associated with the etiology of the manifestation of periodontitis.

  10. Vaginitis: current microbiologic and clinical concepts.

    PubMed Central

    Hill, L V; Embil, J A

    1986-01-01

    Infectious vaginitis occurs when the normal vaginal flora is disrupted; it may arise when saprophytes overwhelm the host immune response, when pathogenic organisms are introduced into the vagina or when changes in substrate allow an imbalance of microorganisms to develop. Examples of these types of vaginitis include the presence of chronic fungal infection in women with an inadequate cellular immune response to the yeast, the introduction of trichomonads into vaginal epithelium that has a sufficient supply of glycogen, and the alteration in bacterial flora, normally dominated by Lactobacillus spp., and its metabolites that is characteristic of "nonspecific vaginitis". The authors review microbiologic and clinical aspects of the fungal, protozoal and bacterial infections, including the interactions of bacteria thought to produce nonspecific vaginitis, that are now recognized as causing vaginitis. Other causes of vaginitis are also discussed. PMID:3510698

  11. [Microbiological diagnosis of human immunodeficiency virus infection].

    PubMed

    Álvarez Estévez, Marta; Reina González, Gabriel; Aguilera Guirao, Antonio; Rodríguez Martín, Carmen; García García, Federico

    2015-10-01

    This document attempts to update the main tasks and roles of the Clinical Microbiology laboratory in HIV diagnosis and monitoring. The document is divided into three parts. The first deals with HIV diagnosis and how serological testing has changed in the last few years, aiming to improve diagnosis and to minimize missed opportunities for diagnosis. Technological improvements for HIV Viral Load are shown in the second part of the document, which also includes a detailed description of the clinical significance of low-level and very low-level viremia. Finally, the third part of the document deals with resistance to antiretroviral drugs, incorporating clinical indications for integrase and tropism testing, as well as the latest knowledge on minority variants. PMID:25444049

  12. Microbiological Spoilage of Fruits and Vegetables

    NASA Astrophysics Data System (ADS)

    Barth, Margaret; Hankinson, Thomas R.; Zhuang, Hong; Breidt, Frederick

    Consumption of fruit and vegetable products has dramatically increased in the United States by more than 30% during the past few decades. It is also estimated that about 20% of all fruits and vegetables produced is lost each year due to spoilage. The focus of this chapter is to provide a general background on microbiological spoilage of fruit and vegetable products that are organized in three categories: fresh whole fruits and vegetables, fresh-cut fruits and vegetables, and fermented or acidified vegetable products. This chapter will address characteristics of spoilage microorganisms associated with each of these fruit and vegetable categories including spoilage mechanisms, spoilage defects, prevention and control of spoilage, and methods for detecting spoilage microorganisms.

  13. Interfacing microbiology and biotechnology. Conference abstracts

    SciTech Connect

    Maupin, Julia A.

    2001-05-19

    The Interfacing Microbiology and Biotechnology Conference was attended by over 100 faculty, post-docs, students, and research scientists from the US, Europe, and Latin America. The conference successfully stimulated communication and the dissemination of knowledge among scientists involved in basic and applied research. The focus of the conference was on microbial physiology and genetics and included sessions on C1 metabolism, archaeal metabolism, proteases and chaperones, gene arrays, and metabolic engineering. The meeting provided the setting for in-depth discussions between scientists who are internationally recognized for their research in these fields. The following objectives were met: (1) The promotion of interaction and future collaborative projects among scientists involved in basic and applied research which incorporates microbial physiology, genetics, and biochemistry; (2) the facilitation of communication of new research findings through seminars, posters, and abstracts; (3 ) the stimulation of enthusiasm and education among participants including graduate and undergraduate students.

  14. New Approach for Setting a Management Criterion in Microbiological Monitoring Using Rapid Microbiological Methods.

    PubMed

    Miyashita, Noe; Tanaka, Makoto; Gotoda, Ryusuke

    2015-01-01

    The application of rapid microbiological methods (RMM) to bacterial monitoring in pharmaceutical manufacturing processes is now a key topic, since timely microbiological data are critical for product release, continuous process improvement and quality control. An automated, highly sensitive detection system has been developed which can measure the amount of ATP in a sample in 2 h with one hundredfold more sensitive than the conventional ATP method. One of the major subjects for adoption and implementation of RMM is how to set the criterion value for practical microbial control. This value was conventionally been set by experimental rule and indicated as the number of colonies counted after incubation in a particular medium. We have adopted a new approach to set a criterion value which enables assessment in whether the status of the object is normal or not. By setting this criterion value, it is possible to conduct the microbiological control with the intended probability of false-positive and false-negative. In this approach the probability distribution model of the measurement value of each object in a normal status has been established by performing repetitive measurement of each object. We have suggested and verified the probability distribution form of the ATP measurement value using measurement data of the standard bacterial solution of Staphylococcus aureus. The theoretical value of the model was in good agreement with the actual measured value. The results suggest it is possible to set an applicable management criterion value using this model and to conduct new microbiological monitoring using RMM. PMID:26521822

  15. Microbiological and histopathological aspects of canine pyometra

    PubMed Central

    Coggan, Jennifer Anne; Melville, Priscilla Anne; de Oliveira, Clair Motos; Faustino, Marcelo; Moreno, Andréa Micke; Benites, Nilson Roberti

    2008-01-01

    As pyometra is recognized as one of the main causes of disease and death in the bitch the purposes of this study were to evaluate microbiological and histopathological aspects of canine pyometra and to research the virulence factors of the E. coli isolates identifying possible risks to human health. The microbiological isolation from the intrauterine contents of 100 dogs with pyometra was carried out and the virulence factors in the E. coli strains were identified using PCR method. This study also consisted of the counting of microorganisms colonies forming units in samples of intrauterine content, tests of antimicrobial susceptibility of the E. coli isolates and the histological examination of the uterus. E. coli was the most prevalent microorganism isolated (76.6%) and 120 strains (79.5%) were positive for sfa, 86 (56.9%) were positive for cnf, 87 (57.6%) were positive for pap, 52 (34.4%) were positive for hly, 51 (33.8%) were positive for iuc and 5 (3.3%) were positive for afa genes. One observed more sensitivity of E. coli to norfloxacin, polimixin B, sulphazotrin, chloranfenicol and enrofloxacin. In 42% of the samples of uterine walls where microorganisms were isolated, the sizes of the areas of the inflammatory responses corresponded to 39–56%. Virulence factors were identified in 98.0% of the strains evaluated, demonstrating a high frequency of potentially pathogenic E. coli. It must be considered that dogs are animals that are living in close proximity to man for thousands of years and have an important role in the transmission of E. coli to other animals and to man. PMID:24031249

  16. Preparation of molecularly imprinted polymeric fibers using a single bifunctional monomer for the solid-phase microextraction of parabens from environmental solid samples.

    PubMed

    Díaz-Álvarez, Myriam; Smith, Stephen P; Spivak, David A; Martín-Esteban, Antonio

    2016-02-01

    In this study, molecularly imprinted polymer fibers for solid-phase microextraction have been prepared with a single bifunctional monomer, N,O-bismethacryloyl ethanolamine using the so-called "one monomer molecularly imprinted polymers" method, replacing the conventional combination of functional monomer and cross-linker to form high fidelity binding sites. For comparison, imprinted fibers were prepared following the conventional approach based on ethylene glycol dimethacrylate as cross-linker and methacrylic acid as monomer. The recognition performance of the new fibers was evaluated in the solid-phase microextraction of parabens, and from this study it was concluded that they provided superior performance over conventionally formulated fibers. Ultimately, real-world environmental testing on spiked solid samples was successful by the molecularly imprinted solid-phase microextraction of samples, and the relative recoveries obtained at enrichment levels of 10 ng/g of parabens were within 78-109% for soil and 83-109% for sediments with a relative standard deviation <15% (n = 3). PMID:26582435

  17. Molecular ecology of bacterial populations in environmental hazardous chemical control. Annual report, 15 January 1993-14 January 1994

    SciTech Connect

    Sayler, G.S.

    1994-01-14

    The major outcomes of the current work are: (1) Development of a new molecular strategy, mRNA extraction from soil, assesses the catabolic activity of soil bacteria in situ. (2) Quantitative the association between the biosensor bioluminescence response and the PAHs bioavailability present in the waste environment. (3) Demonstration the ability of NAH plasmid to mediate the initial biodegradation reactions in the catabolic pathway of fluorence. The current research work is focuses on developing new molecular diagnostics' method for measuring in situ PAH biodegradation activity and co-related the bioluminescence response, that produced by a naphthalene-lux reporter strain, to the bioavailability of different pollutants in the real environment. In addition, catabolism of a tricyclic aromatic hydrocarbon, fluorene, mediates by a NAH plasmid is also investigated.

  18. Microbiological study of the Murchison CM2 meteorite

    NASA Astrophysics Data System (ADS)

    Pikuta, Elena V.; Hoover, Richard B.

    2012-10-01

    In 1864, Louis Pasteur attempted to cultivate living microorganisms from pristine samples of the Orgueil CI1 carbonaceous meteorite. His results were negative and never published, but recorded it in his laboratory notebooks. At that time, only aerobic liquid or agar-based organic reach media were used, as his research on anaerobes had just started. In our laboratory the Murchison CM2 carbonaceous meteorite was selected to expand on these studies for microbiological study by cultivation on anaerobic mineral media. Since the surface could have been more easily contaminated, interior fragments of a sample of the Murchison meteorite were extracted and crushed under sterile conditions. The resulting powder was then mixed in anoxic medium and injected into Hungate tubes containing anaerobic media with various growth substrates at different pH and salinity and incubated at different temperatures. The goal of the experiments was to determine if living cells would grow from the material of freshly fractured interior fragments of the stone. If any growth occurred, work could then be carried out to assess the nature of the environmental contamination by observations of the culture growth (rates of speed and biodiversity); live/dead fluorescent staining to determine contamination level and DNA analysis to establish the microbial species present. In this paper we report the results of that study.

  19. Microbiological Analysis of Necrosols Collected from Urban Cemeteries in Poland.

    PubMed

    Całkosiński, Ireneusz; Płoneczka-Janeczko, Katarzyna; Ostapska, Magda; Dudek, Krzysztof; Gamian, Andrzej; Rypuła, Krzysztof

    2015-01-01

    Decomposition of organic matter is the primary function in the soil ecosystem, which involves bacteria and fungi. Soil microbial content depends on many factors, and secondary biological and chemical contaminations change and affect environmental feedback. Little work has been done to estimate the microbiological risk for cemetery employees and visitors. The potential risk of infection for people in the cemetery is primarily associated with injury and wound contamination during performing the work. The aim of this study was to analyze the microbiota of cemetery soil obtained from cemeteries and bacterial composition in selected soil layers encountered by gravediggers and cemetery caretakers. The most common bacterial pathogens were Enterococcus spp. (80.6%), Bacillus spp. (77.4%), and E. coli (45.1%). The fungi Penicillium spp. and Aspergillus spp. were isolated from 51% and 6.4% of samples, respectively. Other bacterial species were in the ground cemetery relatively sparse. Sampling depth was not correlated with bacterial growth (p > 0.05), but it was correlated with several differences in microbiota composition (superficial versus deep layer). PMID:26301242

  20. Microbiological Analysis of Necrosols Collected from Urban Cemeteries in Poland

    PubMed Central

    Całkosiński, Ireneusz; Płoneczka-Janeczko, Katarzyna; Ostapska, Magda; Dudek, Krzysztof; Gamian, Andrzej; Rypuła, Krzysztof

    2015-01-01

    Decomposition of organic matter is the primary function in the soil ecosystem, which involves bacteria and fungi. Soil microbial content depends on many factors, and secondary biological and chemical contaminations change and affect environmental feedback. Little work has been done to estimate the microbiological risk for cemetery employees and visitors. The potential risk of infection for people in the cemetery is primarily associated with injury and wound contamination during performing the work. The aim of this study was to analyze the microbiota of cemetery soil obtained from cemeteries and bacterial composition in selected soil layers encountered by gravediggers and cemetery caretakers. The most common bacterial pathogens were Enterococcus spp. (80.6%), Bacillus spp. (77.4%), and E. coli (45.1%). The fungi Penicillium spp. and Aspergillus spp. were isolated from 51% and 6.4% of samples, respectively. Other bacterial species were in the ground cemetery relatively sparse. Sampling depth was not correlated with bacterial growth (p > 0.05), but it was correlated with several differences in microbiota composition (superficial versus deep layer). PMID:26301242

  1. Molecular and environmental factors governing non-covalent bonding interactions and conformations of phosphorous functionalized γ-cyclodextrin hydrate systems.

    PubMed

    Ivanova, Bojidarka; Spiteller, Michael

    2016-06-01

    Recent strategies in molecular drugs-design shift efforts to nanomedicine. Large supra-molecular inclusion systems are implemented as therapeutics. The sophistication of design is based on major advances of cyclodextrins (CDs) as host molecules. They are friendly towards biological environment. CDs have good (bio)compatibility as well. CDs can form host-guest macromolecular systems incorporating small molecules with suitable shapes due to non-covalent interactions. Innovative strategies yield to polymeric nano-particles; micelles; linear polymers and/or CDs-functionalized dendrimeric nanostructures; nanofibers as well as hydrogels. Attractive are phosphorous containing (bio)matrerials, having high selectivity toward biological active molecules. The non-covalent interactions in aquatic CD-systems contribute to stability of host-guest systems under physiological conditions, determining conformational preferences of host-CD macromolecule and guest small molecular template. In this paper we have reported complementation application of mass spectrometric (MS) and quantum chemical analysis of phosphorous chemically substituted γ-cyclodextrin hydrates γ-CDPO/nH2O (n ∊ [0-14]), studying neutral and polynegatively charged molecules as an effort to describe realistic a representative scale of physiological conditions. The binding affinity and molecular conformations are discussed. The 250 neutral and charged systems (γ-CDPOHm/nH2O, n ∊ [10][0,14], m ∊ [0,15], γ-CDPOH-8/nH2O.8Na(+), and γ-CDPOH-16/nH2O.16Na(+)) in four main domains of non-covalent hydrogen bonding interactions are studied. PMID:26944657

  2. Molecular modeling of polymer composite interactions with analytes in electronic nose sensors for environmental monitoring in International Space Station

    NASA Technical Reports Server (NTRS)

    Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K.

    2002-01-01

    We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL Electronic Nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings (with no hydrogens). The Dreiding 2.21 force field is used for the polymer and solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4- vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic (ammonia) and organic (methanol, toluene, hydrazine) compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites.

  3. Ribosomal proteins as biomarkers for bacterial identification by mass spectrometry in the clinical microbiology laboratory

    PubMed Central

    Suarez, Stéphanie; Ferroni, Agnès; Lotz, Aurélie; Jolley, Keith A.; Guérin, Philippe; Leto, Julie; Dauphin, Brunhilde; Jamet, Anne; Maiden, Martin C.J.; Nassif, Xavier; Armengaud, Jean

    2014-01-01

    Whole-cell matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for identification of microorganisms that is increasingly used in microbiology laboratories. This identification is based on the comparison of the tested isolate mass spectrum with reference databases. Using Neisseria meningitidis as a model organism, we showed that in one of the available databases, the Andromas database, 10 of the 13 species-specific biomarkers correspond to ribosomal proteins. Remarkably, one biomarker, ribosomal protein L32, was subject to inter-strain variability. The analysis of the ribosomal protein patterns of 100 isolates for which whole genome sequences were available, confirmed the presence of inter-strain variability in the molecular weight of 29 ribosomal proteins, thus establishing a correlation between the sequence type (ST) and/or clonal complex (CC) of each strain and its ribosomal protein pattern. Since the molecular weight of three of the variable ribosomal proteins (L30, L31 and L32) was included in the spectral window observed by MALDI-TOF MS in clinical microbiology, i.e., 3640–12000 m/z, we were able by analyzing the molecular weight of these three ribosomal proteins to classify each strain in one of six subgroups, each of these subgroups corresponding to specific STs and/or CCs. Their detection by MALDI-TOF allows therefore a quick typing of N. meningitidis isolates. PMID:23916798

  4. Structuring Free-text Microbiology Culture Reports For Secondary Use

    PubMed Central

    Yim, Wen-wai; Evans, Heather L.; Yetisgen, Meliha

    2015-01-01

    Microbiology lab culture reports are a frequently used diagnostic tool for clinical providers. However, their incorporation into clinical surveillance applications and evidence-based medicine can be severely hindered by the free-text nature of these reports. In this work, we (1) created a microbiology culture template to structure free-text microbiology reports, (2) generated an annotated microbiology report corpus, and (3) built a microbiology information extraction system. Specifically, we combined rule-based, hybrid, and statistical techniques to extract microbiology entities and fill templates for structuring data. System performances were favorable, with entity f1-score 0.889 and relation f1-score 0.795. We plan to incorporate these extractions as features for our ongoing ventilator-associated pneumonia surveillance project, though this tool can be used as an upstream process in other applications. Our newly created corpus includes 1442 unique gram stain and culture microbiology reports generated from a cohort of 715 patients at the University of Washington Medical Facilities. PMID:26306288

  5. Microbiology of Ultrabasic Groundwaters of the Coast Range Ophiolite, California

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Cardace, D.; Hoehler, T. M.; McCollom, T. M.

    2013-12-01

    Upon exposure to water, ultramafic rocks characteristic of the Earth's mantle undergo a process known as serpentinization. These water-rock reactions lead to highly reducing conditions and some of the highest pH values reported in nature. In contrast to alkaline soda lakes, actively serpentinizing environments exposed on land are commonly associated with low salinity freshwaters, imparting unique challenges upon their resident microbial communities. These environments are especially prevalent along continental margins, and cover extensive portions of the west coast of North America. Most studies of serpentinizing environments have focused upon springs that emanate from fractures in the subsurface. Here, we present microbiological data from a series of groundwater wells associated with active serpentinization in the California Coast Range, an ophiolite complex near Lower Lake, California. Waters from ultrabasic wells had lower microbial cell concentrations and diversity than were found in moderate pH wells in the same area. Bacteria consistently made up a higher proportion of the microbial communities compared to Archaea as determined by qPCR. High pH wells were dominated by taxa within the Betaproteobacteria and Clostridia, whereas moderate pH wells predominantly contained common soil taxa related to Gammaproteobacteria and Bacilli. Multivariate statistical analyses incorporating key environmental parameters supported these observations and also highlighted correlations between the high-pH taxa and the abundance of hydrogen and methane gas. Similarly, colony forming units of alkaliphilic microorganisms were consistently 1-2 orders of magnitude higher in the ultrabasic wells and were taxonomically distinct from the moderate pH groundwaters. Together, these results show that distinct populations inhabit subsurface environments associated with active serpentinization, consistent with previous observations, and suggest that Betaproteobacteria and Clostridia probably

  6. Individual-based modelling: an essential tool for microbiology.

    PubMed

    Ferrer, Jordi; Prats, Clara; López, Daniel

    2008-04-01

    Micro-organisms play a central role in every ecosystem and in the global biomass cycle. They are strongly involved in many fields of human interest, from medicine to the food industry and waste control. Nevertheless, most micro-organisms remain almost unknown, and nearly 99% of them have not yet been successfully cultured in vitro. Therefore, new approaches and new tools must be developed in order to understand the collective behaviour of microbial communities in any natural or artificial setting. In particular, theoretical and practical methodologies to deal with such systems at a mesoscopic level of description (covering the range from 100 to 10(8) cells) are required. Individual-based modelling (IBM) has become a widely used tool for describing complex systems made up of autonomous entities, such as ecosystems and social networks. Individual-based models (IBMs) provide some advantages over the traditional whole-population models: (a) they are bottom-up approaches, so they describe the behaviour of a system as a whole by establishing procedural rules for the individuals and for their interactions, and thus allow more realistic assumptions for the model of the individuals than population models do; (b) they permit the introduction of randomness and individual variability, so they can reproduce the diversity found in real systems; and (c) they can account for individual adaptive behaviour to their environmental conditions, so the evolution of the whole system arises from the dynamics that govern individuals in their pursuit of optimal fitness. However, they also present some drawbacks: they lack the clarity of continuous models and may easily become rambling, which makes them difficult to analyse and communicate. All in all, IBMs supply a holistic description of microbial systems and their emerging properties. They are specifically appropriate to deal with microbial communities in non-steady states, and spatially explicit IBMs are particularly appropriate to study

  7. Molecular Epidemiology of Echoviruses 11 and 13, Based on an Environmental Surveillance Conducted in Toyama Prefecture, 2002-2003†

    PubMed Central

    Iwai, Masae; Yoshida, Hiromu; Matsuura, Kumiko; Fujimoto, Tsuguto; Shimizu, Hiroyuki; Takizawa, Takenori; Nagai, Yoshiyuki

    2006-01-01

    Nineteen echovirus 11 (E11) and 12 E13 isolates were isolated from three rivers in Toyama Prefecture, Japan, during an environmental surveillance conducted from April 2002 to March 2003. The nucleotide sequences of E13 isolates were closely related to those from patients with aseptic meningitis, with less than 1.3% divergence in the VP1 region of the viral capsid gene, and belonged to the same clade responsible for a worldwide outbreak that started in 2000. In contrast, E11 isolates were clustered into three genomic groups and were not closely related to echovirus strains isolated from patients. These results suggest that the combination of both virus isolation from environmental sources and phylogenetic analysis could be complementary assessment approaches to trace prevalent and minor circulating enteroviruses in the human population. PMID:16957267

  8. Molecular Detection of Candidatus Scalindua pacifica and Environmental Responses of Sediment Anammox Bacterial Community in the Bohai Sea, China

    PubMed Central

    Dang, Hongyue; Zhou, Haixia; Zhang, Zhinan; Yu, Zishan; Hua, Er; Liu, Xiaoshou; Jiao, Nianzhi

    2013-01-01

    The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named “Ca. Scalindua pacifica”. Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were

  9. A molecular approach for the rapid, selective and sensitive detection of Exophiala jeanselmei in environmental samples: development and performance assessment of a real-time PCR assay.

    PubMed

    Libert, X; Chasseur, C; Packeu, A; Bureau, F; Roosens, N H; De Keersmaecker, S J C

    2016-02-01

    Exophiala jeanselmei is an opportunistic pathogenic black yeast growing in humid environments such as water reservoirs of air-conditioning systems. Because this fungal contaminant could be vaporized into the air and subsequently cause health problems, its monitoring is recommended. Currently, this monitoring is based on culture and microscopic identification which are complex, sometimes ambiguous and time-demanding, i.e., up to 21 days. Therefore, molecular, culture-independent methods could be more advantageous for the monitoring of E. jeanselmei. In this study, we developed a SYBR®green real-time PCR assay based on the internal transcribed spacer 2 from the 18S ribosomal DNA complex for the specific detection of E. jeanselmei. The selectivity (100 %), PCR efficiency (95.5 %), dynamic range and repeatability of this qPCR assay were subsequently evaluated. The limit of detection for this qPCR assay was determined to be 1 copy of genomic DNA of E. jeanselmei. Finally, water samples collected from cooling reservoirs were analyzed using this qPCR assay to deliver a proof of concept for the molecular detection of E. jeanselmei in environmental samples. The results obtained by molecular analysis were compared with those of classical methods (i.e., culture and microscopic identification) used in routine analysis and were 100 % matching. This comparison demonstrated that this SYBR®green qPCR assay can be used as a molecular alternative for monitoring and routine investigation of samples contaminated by E. jeanselmei, while eliminating the need for culturing and thereby considerably decreasing the required analysis time to 2 days. PMID:26615400

  10. A 1-year Aspergillus terreus surveillance study at the University Hospital of Innsbruck: molecular typing of environmental and clinical isolates.

    PubMed

    Blum, G; Perkhofer, S; Grif, K; Mayr, A; Kropshofer, G; Nachbaur, D; Kafka-Ritsch, R; Dierich, M P; Lass-Flörl, C

    2008-12-01

    Aspergillus terreus appears to have become an increasingly frequent cause of opportunistic infections in the University Hospital of Innsbruck (UHI) and is of serious concern because of in vivo and in vitro resistance to amphotericin B. In order to determine the possible relationship between environmental contamination by A. terreus and the occurrence of invasive aspergillosis, a 1-year prospective study (2004-2005) was carried out in the UHI. Isolates obtained from air samples of various high-risk settings and those from surveillance cultures of proven and probable aspergillosis (EORTC/MSG criteria) were examined by genotyping. Within 1 year, 34 and 15 A. terreus isolates were collected from the environment and from patients, respectively. Genotypic analysis with rapid amplification of polymorphic DNA (RAPD) PCR and the combination of three different primers (R108, CII, P4) revealed 46 distinct genotypic profiles (types 1-46). No strain similarity was detected among and within the patients and environmental areas, indicating a great genomic diversity in A. terreus, which is common in the environment of Innsbruck and a source of invasive infections in immunosuppressed patients. Genotypical diversity was found in clinical and environmental A. terreus isolates. PMID:19076844

  11. Graphene coatings for protection against microbiologically induced corrosion

    NASA Astrophysics Data System (ADS)

    Krishnamurthy, Ajay

    Microbiologically induced corrosion (MIC) is a special form of electrochemical corrosion where micro-organisms affect the local environmental conditions at the metal-electrolyte interface by forming a stable biofilm. The biofilm introduces localized concentration cells, which accelerate the electrochemical corrosion rates. MIC has been found to affect many industrial systems such as sewage waste water pipes, heat exchangers, ships, underwater pipes etc. It has been traditionally eradicated by physical, biochemical and surface protection methods. The cleaning methods and the biocidal deliveries are required periodically and don't provide a permanent solution to the problem. Further, the use of biocides has been harshly criticized by environmentalists due to safety concerns associated with their usage. Surface based coatings have their own drawback of rapid degradation under harsh microbial environments. This has led to the exploration of thin, robust, inert, conformal passivation coatings for the protection of metallic surfaces from microbiologically induced corrosion. Graphene is a 2D arrangement of carbon atoms in a hexagonal honeycomb lattice. The carbon atoms are bonded to one another by sp2 hybridization and each layer of the carbon ring arrangement spans to a thickness of less than a nm. Due to its unique 2D arrangement of carbon atoms, graphene exhibits interesting in-plane and out of plane properties that have led to it being considered as the material for the future. Its excellent thermal, mechanical, electrical and optical properties are being explored in great depth to understand and realize potential applications in various technological realms. Early studies have shown the ability of bulk and monolayer graphene to protect metallic surfaces from air oxidation and solution based galvanic corrosion processes for short periods. However, the role of graphene in resisting MIC is yet to be determined, particularly over the long time spans characteristic of

  12. Rein and Zheng Elected to American Academy of Microbiology | Poster

    Cancer.gov

    By Nancy Parrish, Staff Writer Earlier this year, Alan Rein, Ph.D., and Zhi-Ming (Thomas) Zheng, M.D., Ph.D., were elected to fellowship in the American Academy of Microbiology, the honorific leadership group within the American Society for Microbiology (ASM). They were among 88 microbiologists who were elected to the academy “through a highly selective, peer-review process, based on their records of scientific achievement and original contributions that have advanced microbiology,” according to the society’s website.

  13. Biomedical Mass Spectrometry in Today's and Tomorrow's Clinical Microbiology Laboratories

    PubMed Central

    Welker, Martin; Erhard, Marcel; Chatellier, Sonia

    2012-01-01

    Clinical microbiology is a conservative laboratory exercise where base technologies introduced in the 19th century remained essentially unaltered. High-tech mass spectrometry (MS) has changed that. Within a few years following its adaptation to microbiological diagnostics, MS has been introduced, embraced, and broadly accepted by clinical microbiology laboratories throughout the world as an innovative tool for definitive bacterial species identification. Herein, we review the current state of the art with respect to this exciting new technology and discuss potential future applications. PMID:22357505

  14. Biomedical mass spectrometry in today's and tomorrow's clinical microbiology laboratories.

    PubMed

    van Belkum, Alex; Welker, Martin; Erhard, Marcel; Chatellier, Sonia

    2012-05-01

    Clinical microbiology is a conservative laboratory exercise where base technologies introduced in the 19th century remained essentially unaltered. High-tech mass spectrometry (MS) has changed that. Within a few years following its adaptation to microbiological diagnostics, MS has been introduced, embraced, and broadly accepted by clinical microbiology laboratories throughout the world as an innovative tool for definitive bacterial species identification. Herein, we review the current state of the art with respect to this exciting new technology and discuss potential future applications. PMID:22357505

  15. Rein and Zheng Elected to American Academy of Microbiology | Poster

    Cancer.gov

    By Nancy Parrish, Staff Writer Earlier this year, Alan Rein, Ph.D., and Zhi-Ming (Thomas) Zheng, M.D., Ph.D., were elected to fellowship in the American Academy of Microbiology, the honorific leadership group within the American Society for Microbiology (ASM). They were among 88 microbiologists who were elected to the academy “through a highly selective, peer-review process, based on their records of scientific achievement and original contributions that have advanced microbiology,” according to the society’s website.

  16. Droplet microfluidics for microbiology: techniques, applications and challenges.

    PubMed

    Kaminski, Tomasz S; Scheler, Ott; Garstecki, Piotr

    2016-06-21

    Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology. PMID:27212581

  17. A review of 'green' strategies to prevent or mitigate microbiologically influenced corrosion.

    PubMed

    Little, Brenda; Lee, Jason; Ray, Richard

    2007-01-01

    Two approaches to control microbiologically influenced corrosion (MIC) have been developed that do not require the use of biocides. These strategies include the following: i) use of biofilms to inhibit or prevent corrosion, and ii) manipulation (removal or addition) of an electron acceptor, (e.g. oxygen, sulphate or nitrate) to influence the microbial population. In both approaches the composition of the microbial community is affected by small perturbations in the environment (e.g. temperature, nutrient concentration and flow) and the response of microorganisms cannot be predicted with certainty. The following sections will review the literature on the effectiveness of these environmentally friendly, "green," strategies for controlling MIC. PMID:17453733

  18. Microbiological sampling of the forgotten components of a flexible fiberoptic laryngoscope: what lessons can we learn?

    PubMed

    Bhatt, Jay M; Peterson, Ellena M; Verma, Sunil P

    2014-02-01

    The effectiveness of a Cidex-based decontamination protocol was analyzed for its effectiveness in cleaning various components of a flexible fiberoptic laryngoscope (FFL), including the handle, eyepiece, and detachable light cable. A random microbiological sampling and aerobic bacterial culture analysis of 6 FFL eyepieces, 6 FFL driver handles, and 5 light cables prior to patient use was performed. Of 17 samples collected, 7 (41%) were contaminated with bacterial organisms. Organisms recovered represented both environmental organisms from skin and oral flora origin. This study demonstrates that potential contaminants may be present on FFL eyepieces and light cables, which are commonly overlooked in the cleaning protocols of a standard otolaryngology clinic. PMID:24334960

  19. Fundamental molecular physics and chemistry. Radiological and Environmental Research Division annual report, October 1981-December 1982. Pt. 1

    SciTech Connect

    Not Available

    1983-12-01

    This document is the twelfth Annual Report of our Fundamental Molecular Physics and Chemistry Program. Scientifically, the work of the program deals with aspects of the physics and chemistry of molecules related to their interactions with photons, electrons, and other external agents. We chose these areas of study in view of our matic goals; that is to say, we chose them so that the eventual outcome of our work meets some of the needs of the US Department of Energy (DOE) and of other government agencies that support our research. First, we endeavor to determine theoretically and experimentally cross sections for electron and photon interactions with molecules, because those cross sections are indispensable for detailed microscopic analyses of the earliest processes of radiation action on any molecular substance, including biological materials. Those analyses in turn provide a sound basis for radiology and radiation dosimetry. Second, we study the spectroscopy of certain molecules and of small clusters of molecules because this topic is fundamental to the full understanding of atmospheric-pollutant chemistry.

  20. Application of PCR-SSCP for molecular epidemiological studies on the exposure of farm children to bacteria in environmental dust.

    PubMed

    Korthals, Melanie; Ege, Markus J; Tebbe, Christoph C; von Mutius, Erika; Bauer, Johann

    2008-04-01

    The environmental exposure of farm children to microorganisms in dust has become a focus of interest, since microbial exposure on farms has been related to a reduced prevalence of asthma and atopic diseases in children. Previous studies almost exclusively focused on the determination of microbial counts using conventional culturing or the determination of microbial compounds i.e. endotoxins. In this study PCR-SSCP (single-strand conformation polymorphism) was modified for characterising bacterial communities in environmental dusts and their sensitivity and reproducibility was validated. A fivefold repeated PCR-SSCP analyses of a well homogenised mattress dust, cow-shed dust, swine-shed dust, chicken-shed dust and a horse-shed dust sample, respectively, showed similarities, based on Pearson correlations, ranging from 89.7% to 95.2%. The reproducibility of day to day variations (five days) and gel to gel variations (five gels) was also around 90%. The detection limit of Escherichia coli was 7 x 10(1) cfu g(-1) whereas Listeria monocytogenes and Bacillus licheniformis containing 30% spores showed visible bands at 7 x1 0(2) cfu g(-1). Application of this method to dust samples of 37 sheds and 63 children's mattresses showed that distinct farm environment dusts reflected different SSCP profiles. However, digital analysis of the gels showed that some bands in the profiles of shed- and mattress dusts were found at the same position in the gels. By excision, cloning, sequencing and phylogenetic analyses, these bands were identified as Corynebacterium tuberculostearicum, Corynebacterium mucifaciens, Staphylococcus epidermidis, Acinetobacter lwoffii, Brevibacterium iodinum, Brevibacterium linens and Arthrobacter spp, respectively. These results may reflect transfer of microorganisms from animal sheds to mattresses. In conclusion this study demonstrates that PCR-SSCP is a promising method with sensitive detection limits and moderate sample variances to be applied for