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Sample records for environmental molecular microbiology

  1. [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

  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.

  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. [Quality control in molecular microbiology].

    PubMed

    Orta Mira, Nieves; Guna Serrano, María Remedio; Gimeno Cardona, Concepción; Pérez, José L

    2008-07-01

    The term quality assurance (QA) refers to the quality control activities related to analytical procedures performed in the clinical microbiology laboratory. QA should include both external and internal quality assessment. Application of quality control tools in molecular microbiology assays is crucial to ensure the accuracy of results and appropriate patient management. External quality control is used for laboratory intercomparisons, detection of random and systematic errors, evaluation of the suitability of some reagents or commercial diagnostic kits, and continuing education. The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology includes quality control procedures for molecular microbiology, as well as specific programs for quantitative determination of the viral load of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV), two highly important molecular markers in clinical settings due to their prognostic value and utility as a treatment guide. Internal quality control allows random and systematic errors to be detected through the inclusion of quality control samples in the assays performed in the laboratory, equipment monitoring, and audit. Evaluation of all molecular microbiology assays before their inclusion in the daily routine work of the laboratory is of utmost importance.

  5. Establishing molecular microbiology facilities in developing countries.

    PubMed

    Ahmed, Salman S; Alp, Emine; Ulu-Kilic, Aysegul; Doganay, Mehmet

    2015-01-01

    Microbiology laboratories play an important role in epidemiology and infection control programs. Within microbiology laboratories, molecular microbiology techniques have revolutionized the identification and surveillance of infectious diseases. The combination of excellent sensitivity, specificity, low contamination levels and speed has made molecular techniques appealing methods for the diagnosis of many infectious diseases. In a well-equipped microbiology laboratory, the facility designated for molecular techniques remains indiscrete. However, in most developing countries, poor infrastructure and laboratory mismanagement have precipitated hazardous consequences. The establishment of a molecular microbiology facility within a microbiology laboratory remains fragmented. A high-quality laboratory should include both conventional microbiology methods and molecular microbiology techniques for exceptional performance. Furthermore, it should include appropriate laboratory administration, a well-designed facility, laboratory procedure standardization, a waste management system, a code of practice, equipment installation and laboratory personnel training. This manuscript lays out fundamental issues that need to be addressed when establishing a molecular microbiology facility in developing countries.

  6. 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

  7. 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,...

  8. 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...

  9. 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

  10. 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.

  11. 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

  12. Assessing the microbiological risk to stored sixteenth century parchment manuscripts: a holistic approach based on molecular and environmental studies.

    PubMed

    Troiano, Federica; Polo, Andrea; Villa, Federica; Cappitelli, Francesca

    2014-01-01

    The microbial risk for the conservation of seven sixteenth century parchment manuscripts, which showed brown discolouration putatively caused by microorganisms, was evaluated using non-invasive sampling techniques, microscopy, studies of surface-associated and airborne microflora with culture-independent molecular methods, and by measuring repository thermo-hygrometric values. Microscopic observations and ATP assays demonstrated a low level of contamination, indicating that the discolouration was not related to currently active microbial colonisation. Nevertheless, a culture-independent molecular approach was adopted to fully characterise surface-associated communities searching for biodeteriogens that could grow under appropriate thermo-hygrometric conditions. Indeed, potential biodeteriogens and microorganisms that are ecologically related to humans were found, suggesting the need to control the conservation environment and improve handling procedures. Microbial loads of air and thermo-hygrometric measurements showed that the repository was not suitable for preventing the microbial deterioration of parchment. A holistic approach to the assessment of risk of microbial deterioration of documents and heritage preservation is proposed for the first time.

  13. 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.

  14. 76 FR 63615 - Environmental Science Center Microbiology Laboratory; Notice of Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-13

    ... 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: The... at the Environmental Protection Agency's Environmental Science Center, 701 Mapes Road, Ft....

  15. 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.

  16. Application of Microbial Bioreporters in Environmental Microbiology and Bioremediation

    NASA Astrophysics Data System (ADS)

    Diplock, E. E.; Alhadrami, H. A.; Paton, G. I.

    Bioreporters have been widely acknowledged to represent new and novel approaches in applied microbiology. Despite a plethora of constructions covering a diverse range of detection devices and host organisms, genuine applications are rare. Here, their application in the areas of general environmental microbiology, analytical detection and bioremediation are summarised and critically considered. Future applications require a more integrated approach such that those constructing bioreporters are aware of the needs of the end-user. A decade ago, predictions were made of the pivotal role of bioreporters and our future reliance; this fortune telling may take another decade to reach fruition.

  17. 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.

  18. 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

  19. 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.

  20. 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)

  1. 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)

  2. 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.

  3. Molecular genetics and industrial microbiology--30 years of marriage.

    PubMed

    Demain, A L

    2001-12-01

    Thirty years ago, molecular genetics and industrial microbiology joined their hands in marriage. The event took place in Prague at the first Symposium on the Genetics of Industrial Microorganisms. My closing plenary lecture, titled "The Marriage of Genetics and Industrial Microbiology--After a long Engagement, a Bright Future," dealt with industrial uses of mutants, the lack of success with genetic recombination, control of branched and unbranched pathways and thoughts about the future, e.g., identifying the biochemical sites of beneficial mutations, exploitation of recombination and genetic means to increase production of enzymes. It is quite amazing that the Symposium was held 3 years before the advent of recombinant DNA technology. This important meeting was followed in 1976 by the first Genetics and Molecular Biology of Industrial Microorganisms (GMBIM) meeting in Orlando, all of the six subsequent GMBIM meetings being held in Bloomington, Indiana. Today, thousands of biotechnology companies are in existence making great progress in the pharmaceutical and agricultural sectors. Hundreds of new genetically engineered compounds, produced in microbial, mammalian or insect cells, are in clinical trails and many are already being marketed. The field is booming with new technologies such as transgenic animals and plants, site-directed mutagenesis, combinatorial biosynthesis, gene therapy, antisense, abzymes, high-throughput screening, monoclonal antibodies, PCR and many more. Agricultural biotechnology has made great strides but unfortunately its progress is being delayed by political controversy.

  4. Molecular microbiology: new dimensions for cutaneous biology and wound healing.

    PubMed

    Martin, Jo M; Zenilman, Jonathan M; Lazarus, Gerald S

    2010-01-01

    The role of bacteria in the pathogenesis of chronic, nonhealing wounds is unclear. All wounds are colonized with bacteria, but differentiating colonizers from invading organisms is difficult, if not impossible, at the present time. Furthermore, robust new molecular genomic techniques have shown that only 1% of bacteria can be grown in culture; anaerobes are especially difficult to identify using standard culture methods. Recent studies utilizing microbial genomic methods have demonstrated that chronic wounds are host to a wide range of microorganisms. New techniques also show that microorganisms are capable of forming highly organized biofilms within the wound that differ dramatically in gene expression and phenotype from bacteria that are typically seen in planktonic conditions. The aim of this review is to present a concise description of infectious agents as defined by new molecular techniques and to summarize what is known about the microbiology of chronic wounds in order to relate them to the pathophysiology and therapy of chronic wounds.

  5. 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.

  6. Molecular Microbiological Profile of Chronic Suppurative Otitis Media.

    PubMed

    Neeff, Michel; Biswas, Kristi; Hoggard, Michael; Taylor, Michael W; Douglas, Richard

    2016-10-01

    Chronic suppurative otitis media (CSOM) presents with purulent otorrhea (ear discharge), is characterized by chronic inflammation of the middle ear and mastoid cavity, and contributes to a significant disease burden worldwide. Current antibiotic therapy is guided by swab culture results. In the absence of detailed molecular microbiology studies of CSOM patients, our current understanding of the microbiota of CSOM (and indeed of the healthy ear) remains incomplete. In this prospective study, 24 patients with CSOM were recruited, along with 22 healthy controls. Culture-based techniques and 16S rRNA gene amplicon sequencing were used to profile the bacterial community for each patient. Comparisons between patients with and without cholesteatoma in the middle ear and mastoid cavity were also made. A major finding was that the middle ear of many healthy controls was not sterile, which is contradictory to the results of previous studies. However, sequencing data showed that Staphylococcus aureus, along with a range of other Gram-positive and Gram-negative organisms, were present in all subgroups of CSOM and healthy controls. Large interpatient variability in the microbiota was observed within each subgroup of CSOM and controls, and there was no bacterial community "signature" which was characteristic of either health or disease. Comparisons of the culture results with the molecular data show that culture-based techniques underestimate the diversity of bacteria found within the ear. This study reports the first detailed examination of bacterial profiles of the ear in healthy controls and patients with CSOM. PMID:27487953

  7. 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.''

  8. 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 ...

  9. 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

  10. 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…

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. Environmental microbiology as a mosaic of explored ecosystems and issues.

    PubMed

    Faure, Denis; Bonin, Patricia; Duran, Robert

    2015-09-01

    Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

  18. Promoting Student Involvement with Environmental Laboratory Experiments in a General Microbiology Course

    PubMed Central

    TARAS, LORETTA BRANCACCIO

    2003-01-01

    This is a descriptive study of a series of laboratory exercises on environmental microbiology carried out by students in a general microbiology course during eight of the twelve weeks of the semester. The revised laboratory component is predicated upon seawater and sediment samples collected by student pairs using marine sampling equipment on a field trip aboard a research vessel. Two longitudinal studies were performed: assay for antibiotic production from isolated actinomycetes and construction and observation of Winogradsky columns. Two additional experiments: culturing microalgae and water testing for coliforms also used the samples collected by the students. The advantages of long-term, challenging laboratory experiences actively involving the students in group process, self-direction, and scientific practices are discussed. Also considered are development of laboratory skills, scientific competencies, and students’ self-confidence in carrying out such environmental investigations. Plans for future assessment of student learning are presented. PMID:23653550

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Microbial Ecology of the Skin in the Era of Metagenomics and Molecular Microbiology

    PubMed Central

    Hannigan, Geoffrey D.; Grice, Elizabeth A.

    2013-01-01

    The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease. PMID:24296350

  5. Microbial ecology of the skin in the era of metagenomics and molecular microbiology.

    PubMed

    Hannigan, Geoffrey D; Grice, Elizabeth A

    2013-12-01

    The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

  6. 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.

  7. 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.''

  8. 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…

  9. Comparative analysis of classical and molecular microbiology methods for the detection of Escherichia coli and Enterococcus spp. in well water.

    PubMed

    Maheux, Andrée F; Huppé, Vicky; Bissonnette, Luc; Boissinot, Maurice; Rodrigue, Lynda; Bérubé, Ève; Bergeron, Michel G

    2012-11-01

    The microbiological quality of 165 1 litre well water samples collected in the Québec City region was assessed by culture-based methods (mFC agar, Chromocult coliform agar, Colilert(®), MI agar, Chromocult enterococci, Enterolert™, and mEI agar) and by a molecular microbiology strategy, dubbed CRENAME-rtPCR, developed for the detection of Escherichia coli, Enterococcus spp., Enterococcus faecalis/faecium, and Bacillus atrophaeus subsp. globigii. In these drinking water samples, approved culture-based methods detected E. coli at rates varying from 1.8 to 3.6% and Enterococcus spp. at rates varying from 3.0 to 11.5%, while the molecular microbiology approach for E. coli was found to be as efficient, detecting contamination in 3.0% of samples. In contrast, CRENAME-rtPCR detected Enterococcus spp. in 27.9% of samples while the E. faecalis/faecium molecular assay did not uncover a single contaminated sample, thereby revealing a discrepancy in the coverage of waterborne enterococcal species detected by classical and molecular microbiology methods. The validation of the CRENAME-E. coli rtPCR test as a new tool to assess the quality of drinking water will require larger scale studies elaborated to demonstrate its equivalence to approved methods.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

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

    PubMed

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

    2015-10-22

    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.

  16. 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.

  17. Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives.

    PubMed

    Jung, Jaejoon; Park, Woojun

    2015-03-01

    Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.

  18. 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

  19. 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

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

    PubMed

    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.

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

    PubMed

    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

  2. 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)

  3. 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.

  4. 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

  5. Evaluation of microbiological water quality in the Pettaquamscutt River (Rhode Island, USA) using chemical, molecular and culture-dependent methods.

    PubMed

    Atoyan, Janet A; Herron, Elizabeth M; Amador, José A

    2011-07-01

    We evaluated microbiological water quality in the Pettaquamscutt River (Rhode Island, USA), an estuarine river. Fecal coliform (FC) and enterococci (FE) bacteria, presence of Bifidobacterium adolescentis DNA (indicating human fecal contamination), and optical brightener (OB) fluorescence (associated with laundry detergents) were determined for 14 stations from May to September 2010. Six stations had high counts of FE and FC, and the presence of B. adolescentis DNA and high OB fluorescence indicated human fecal contamination - four had septic systems as likely sources of contamination; the others were in sewered areas. The ability of FC and FE to indicate human fecal contamination was assessed against a positive B. adolescentis test. FC and FE had false positive rates of 25% and 17%, respectively, and false negatives of 44% for FC and 63% for FE. Inclusion of molecular and chemical indicators should improve tracking of human fecal contamination sources in the river. PMID:21570698

  6. Molecular basis of environmentally induced birth defects.

    PubMed

    Finnell, Richard H; Waes, Janee Gelineau-van; Eudy, James D; Rosenquist, Thomas H

    2002-01-01

    Exposure of the developing conceptus to selected environmental agents can lead to deleterious and often times lethal birth defects. These malformations result in serious emotional and financial consequences to families and societies worldwide. As we continue to progress technologically, we face challenges from the introduction of new pharmacological agents and chemical compounds into the environment. This results in a concomitant need to more fully understand the relationship between in utero exposure to environmental teratogens and the risk of congenital malformations. The goal of this review is to provide a current perspective of the major concepts related to the molecular basis of environmentally induced birth defects. Starting with a discussion of commonly occurring birth defects, we consider important fundamental facets of embryonic development, teratology, and gene-environment interactions. The review then summarizes our current understanding of the molecular mechanisms involved in selected birth defects following exposure to pharmacological compounds, including thalidomide, retinoids, and valproic acid. Understanding these signaling pathways may lead to the development of safer pharmaceutical compounds and a reduction in the number of infants born with preventable birth defects.

  7. 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.

  8. 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

  9. Qualification of high-recovery, flocked swabs as compared to traditional rayon swabs for microbiological environmental monitoring of surfaces.

    PubMed

    Dalmaso, Giblerto; Bini, Manuela; Paroni, Roberto; Ferrari, Michela

    2008-01-01

    In microbiological environmental monitoring programs, swabs are widely used for hygiene monitoring of surfaces and operators. Traditional rayon swabs are generally used and considered the gold standard in swab collection. Two experimental studies were conducted to validate the performance of a new collection device for environmental monitoring of surfaces, called flocked swabs, manufactured by microRheologics (Brescia, Italy). The first experimental study consisted of comparing flocked swabs' recovery and release capacity to traditional rayon swabs from known microorganism inocula (spiked samples); the second experimental study compared the recovery capacity from samples obtained in routine environmental surfaces sampling of pharmaceutical areas, microRheologics flocked swabs compared to traditional rayon swabs showed an improvement in the percentage of recovery of contamination from surfaces from 20% up to 60%, and the findings were confirmed from a preliminary evaluation of routine environmental surface sampling of pharmaceutical areas. microRheologics flocked swabs also displayed an instant and nearly complete release of absorbed samples of more than 80%.

  10. Microbiological and molecular characterization of denitrification in biofilters treating pig manure.

    PubMed

    Gilbert, Yan; Le Bihan, Yann; Aubry, Geneviève; Veillette, Marc; Duchaine, Caroline; Lessard, Paul

    2008-07-01

    Aerated organic biofilters treating pig manure exhibit partial nitrogen removal. In order to optimize this process, a better comprehension of its colonization by denitrifiers was needed. Three pilot aerated biofilters, fed with variable Biological Oxygen Demand after five days: Total Kjeldahl Nitrogen (BOD(5):TKN) ratios, were constructed and monitored during 180 days. Nitrogen was analyzed in the gaseous and liquid flows, at different depths in the systems. Denitrifying biomass was characterized by evaluating its observed (nitrogen mass balances) and potential (adapted acetylene inhibition technique) activities and its quantity (real-time PCR on nirS), at different heights inside the biofilters. Denitrification was observed as soon as nitrate was produced by nitrifiers, after approximately 40 days of operation, but the potential to denitrify increased from the beginning of the monitoring period. Biofilter fed with the highest BOD(5):TKN ratio showed significant differences with the others, particularly after 80 days of operation, as its potential activity was lower with a higher observed nitrate removal. Data showed that denitrifiers were mainly localized near the surface of the filter and that a microbiological gradient was present from top to bottom. The potential denitrifying activities were always higher than what was being observed inside the sections studied, suggesting that the biomass could have reduced more nitrate and that conditions found inside the filter did not allow denitrification to completely occur.

  11. 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

  12. 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.

  13. 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

  14. Molecular diagnostics in infectious diseases and public health microbiology: cottage industry to postgenomics.

    PubMed

    Gilbert, Gwendolyn L

    2002-06-01

    Molecular methods have been used increasingly over the past ten years to improve the sensitivity and speed of diagnosis in infectious diseases. Although their routine use is still limited to the detection of pathogens that are difficult to culture in vitro,'real-time' methods, commercial kits, quantification and automation will increase potential applications. Molecular methods are now widely used for epidemiological fingerprinting of isolates of public health importance. Sequence-based identification and strain typing, together with the development of tools that can probe for thousands of markers, will allow detailed strain fingerprinting to assist in disease management and control.

  15. Microbiological surveillance of private water supplies in England: the impact of environmental and climate factors on water quality.

    PubMed

    Richardson, Hopi Yip; Nichols, Gordon; Lane, Chris; Lake, Iain R; Hunter, Paul R

    2009-05-01

    A passive surveillance system captured information on 34,904 microbiological samples from 11,233 private drinking water supplies within England as well as the associated constructional, climatic and environmental variables. Escherichia coli was detected in 6588 (18.87%) of samples and at least one positive sample was detected from 3638 (32.39%) of sites. However, this estimate of supplies failing to meet the European drinking water E. coli standard was probably an underestimate as the more samples taken per supply, the more likely the supply was to fail. A multivariable model of private water supplies data showed a strong seasonal impact, with samples between January and May being significantly less contaminated with E. coli than samples between June and December. Samples from springs (OR 2.5, CI 2.0-3.1) or surface waters (OR 2.4, CI 0.8-7.0) were more likely to fail than groundwater sources, as were supplies with no effective treatment (OR1.8, CI 1.5-2.3). Commercial supplies were less likely to fail than domestic supplies (OR 0.63, CI 0.48-0.83) and the probability of failure was linearly associated with the density of sheep in the area and rainfall on the previous day. A Monte Carlo modelling approach was used to estimate that, had sufficient samples been taken, 54% (95% confidence intervals 49-59%) of all private water supplies in England were likely to be unsatisfactory. These findings will be able to inform risk assessments of private water supplies prior to microbiological results being available.

  16. Prevalence of bovine tuberculosis in slaughter cattle in Kenya: a postmortem, microbiological and DNA molecular study.

    PubMed

    Gathogo, Stephen M; Kuria, Joseph K N; Ombui, Jackson N

    2012-10-01

    A study to determine the presence and prevalence of bovine tuberculosis in slaughter cattle in Kenya was carried out in two abattoirs from July to November 2009. Routine postmortem meat inspection was performed on a subpopulation of 929 cattle selected randomly from among 4,984. Carcases were inspected for gross tuberculous lesions which were then examined for acid-fast bacilli, (AFB), cultured for isolation of mycobacteria and the isolates characterised by DNA molecular analysis. Of the carcases examined, 176 (18.95 %, 95 % CI) had lesions suggestive of tuberculosis. AFB were observed in 63/176 of the lesioned cattle and mycobacteria were isolated from 64 of them. The isolates were identified as Mycobacterium bovis (19/64), Mycobacterium tuberculosis, (2/64) and mycobacteria other than tuberculosis (43/64). The prevalence of M. bovis by molecular analysis was 2.05 % (95 % CI). This study documents for the first time the presence of bovine tuberculosis among slaughter cattle in Kenya. There is therefore a need to formulate and implement control programmes in order to minimise transmission among animals and to humans. Isolation of M. tuberculosis from cattle underscores the risk tuberculous humans pose to animals.

  17. 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...

  18. 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.

  19. Evolving microbiology and molecular epidemiology of acute otitis media in the pneumococcal conjugate vaccine era.

    PubMed

    Pichichero, Michael E; Casey, Janet R

    2007-10-01

    The addition of the 7-valent pneumococcal conjugate vaccine (PCV7) to the routine immunization schedule in the United States for infants has produced a much more favorable impact on the incidence of acute otitis media (AOM) than anticipated. Because the serotypes included in PCV7 were those most frequently expressing antibiotic resistance in 2001, predictions were made that up to 98% of pneumococcal AOM episodes would be caused by penicillin susceptible strains. However, recent studies have shown that the benefits of PCV7 are becoming eroded. Replacement serotypes of pneumococci have emerged, expressing polysaccharide capsules different from those included in PCV7, with increasing frequency. These replacement strains are coming to dominate in the nasopharynx and in AOM isolates (and in invasive disease). Expansion in the isolation of serotypes 3, 7F, 15B/C/F, 19A, 22F, 33F, and 38 has been described in various surveillance systems. Pneumococcal strains expressing non-PCV7 capsular serotypes also appear to be rapidly acquiring resistance to penicillin and other antibiotics. Emergence of strains of pneumococci expressing non-PCV7 capsular serotypes is occurring by multiple mechanisms including capsular switching as suggested by molecular epidemiology studies. Expansion of the number of serotypes included in pneumococcal conjugate vaccines is needed to sustain a long-term benefit from immunization against these bacteria.

  20. Comparison of environmental and egg microbiology associated with conventional and free-range laying hen management.

    PubMed

    Jones, D R; Anderson, K E; Musgrove, M T

    2011-09-01

    Eggs from alternative production practices are a growing niche in the market. Meeting consumer requests for greater diversity in retail egg options has resulted in some unique challenges such as understanding the food safety implications of eggs from alternative production practices. A study was conducted to determine what, if any, differences exist between nest run conventional cage-produced eggs and free range-produced eggs. A sister flock of brown egg layers was maintained in conventional cage and free-range production with egg and environmental sampling every 6 wk from 20 to 79 wk of age. Aerobic, coliform, and yeast and mold populations were monitored. Environmental microbial levels were not always indicative of egg contamination levels. When significant differences (P < 0.05 and P < 0.0001, dependent on season) were observed among treatments for coliforms, shell contamination levels of free-range nest box eggs and free-range floor eggs were always greater than those of conventional cage eggs, which remained low throughout the study (0.42-0.02 log cfu/mL). Shell yeast and mold levels were significantly greater in free-range floor eggs than in free-range nest box eggs and conventional cage eggs throughout the entire study. Egg contents contamination levels were extremely low for all monitored populations and treatments. Season of the year played a role in both environmental and egg microbial levels. Winter had the lowest levels of all populations monitored for all treatments, except for aerobic free-range floor egg shell emulsions, which were increased (3.6 log cfu/mL). Understanding the differences in microbial populations present on conventional cage-produced and free range-produced eggs can lead to the development of effective cleaning procedures, enhancing food safety. PMID:21844274

  1. Comparison of environmental and egg microbiology associated with conventional and free-range laying hen management.

    PubMed

    Jones, D R; Anderson, K E; Musgrove, M T

    2011-09-01

    Eggs from alternative production practices are a growing niche in the market. Meeting consumer requests for greater diversity in retail egg options has resulted in some unique challenges such as understanding the food safety implications of eggs from alternative production practices. A study was conducted to determine what, if any, differences exist between nest run conventional cage-produced eggs and free range-produced eggs. A sister flock of brown egg layers was maintained in conventional cage and free-range production with egg and environmental sampling every 6 wk from 20 to 79 wk of age. Aerobic, coliform, and yeast and mold populations were monitored. Environmental microbial levels were not always indicative of egg contamination levels. When significant differences (P < 0.05 and P < 0.0001, dependent on season) were observed among treatments for coliforms, shell contamination levels of free-range nest box eggs and free-range floor eggs were always greater than those of conventional cage eggs, which remained low throughout the study (0.42-0.02 log cfu/mL). Shell yeast and mold levels were significantly greater in free-range floor eggs than in free-range nest box eggs and conventional cage eggs throughout the entire study. Egg contents contamination levels were extremely low for all monitored populations and treatments. Season of the year played a role in both environmental and egg microbial levels. Winter had the lowest levels of all populations monitored for all treatments, except for aerobic free-range floor egg shell emulsions, which were increased (3.6 log cfu/mL). Understanding the differences in microbial populations present on conventional cage-produced and free range-produced eggs can lead to the development of effective cleaning procedures, enhancing food safety.

  2. 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

  3. 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…

  4. The case for biocentric microbiology

    PubMed Central

    Aziz, Ramy Karam

    2009-01-01

    Microbiology is a relatively modern scientific discipline intended to objectively study microorganisms, including pathogens and nonpathogens. However, since its birth, this science has been negatively affected by anthropocentric convictions, including rational and irrational beliefs. Among these, for example, is the artificial separation between environmental and medical microbiology that weakens both disciplines. Anthropocentric microbiology also fails to properly answer questions concerning the evolution of microbial pathogenesis. Here, I argue that an exclusively biocentric microbiology is imperative for improving our understanding not only of the microbial world, but also of our own species, our guts, and the world around us. PMID:19653908

  5. 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.

  6. 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.

  7. 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.

  8. 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)

  9. 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)

  10. 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.

  11. 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

  12. Phyllosphere microbiology.

    PubMed

    Lindow, Steven E; Leveau, Johan H J

    2002-06-01

    Aerial plant surfaces harbor large numbers of microbes, some of which are deleterious to plants whereas others are benign or beneficial. Commercial formulations of bacteria antagonistic to plant pathogenic microbes and ice nucleation active bacteria have been utilized as an environmentally safe method to manage plant disease and to prevent frost damage. Molecular genetic tools, microscopic examination and whole-cell bacterial biosensors have provided extensive information on these microbes, their complex associations and their habitat. The aerial habitat influenced by plants, termed the phyllosphere, is particularly amenable to studies of microbial ecology and the information gained should lead to more effective means of plant protection. PMID:12180099

  13. 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.

  14. 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…

  15. 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.

  16. Trends in wine microbiology.

    PubMed

    Ramón, D

    1997-12-01

    During the last few years many winemakers have started to use pure Saccharomyces cerevisiae strains, frequently isolated from their own geographical regions, to produce wines of more reproductable quality. This microbiological simplification has opened the way for the genetic modification of wine yeast strains. This review concerns the application of molecular techniques in oenology, not only from the point of view of the construction of recombinant strains but also for the study of the population dynamics of wine fermentations.

  17. 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

  18. 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.

  19. Molecular Approach to Microbiological Examination of Water Quality in the Grand Bay National Estuarine Research Reserve (NERR) in Mississippi, USA

    PubMed Central

    Kishinhi, Stephen S.; Tchounwou, Paul B.; Farah, Ibrahim O.

    2013-01-01

    Grand Bay National Estuarine Research Reserve (NERR) is an important ecosystem in the Mississippi Gulf Coast. It serves as important nursery areas for juveniles of many species of fish. The bay is also used for fishing, crabbing, oyster togging, boating as well as recreation. Like in other aquatic environments, this bay may be contaminated by microorganisms including pathogenic bacteria. The objective of this study was to evaluate the microbiological quality of water in the Grand Bay NERR and determine the levels and potential source(s) of human fecal pollution. To achieve this goal, water samples were collected aseptically every month in Bayou Heron, Bayou Cumbest, Point Aux Chenes Bay and Bangs Lake. Enterococci were concentrated from water samples by membrane filtration according to the methodology outlined in USEPA Method 1600. After incubation, DNA was extracted from bacteria colonies on the membrane filters by using QIAamp DNA extraction kit. Water samples were also tested for the presence of traditional indicator bacteria including: heterotrophic plate count, total coliforms, fecal coliforms, and Enterococcus bacteria. The marker esp gene was detected in one site of Bayou Cumbest, an area where human populations reside. Data from this study indicates higher concentrations of indicator bacteria compared to the recommended acceptable levels. Presence of esp marker and high numbers of indicator bacteria suggest a public health concern for shellfish and water contact activities. Hence, control strategies should be developed and implemented to prevent further contamination of the Grand bay NERR waters. PMID:23761974

  20. Forensic microbiology.

    PubMed

    Lehman, Donald C

    2012-01-01

    The field of forensic microbiology is fairly new and still evolving. With a threat of bioterror and biocrime, the rapid identification and subtyping of infectious agents is of upmost importance. Microbial genetic analysis is a valuable tool in this arena. The cost to sequence a microbial genome has fallen dramatically in recent years making this method more widely available. Surveillance and vigilance are important as is further research. The United States Department of Homeland Security established the Bioforensics Analysis Center to become the foremost U.S. biodefense research institution involved with bioforensics. Many countries are better prepared for biologic events than ever before, but more work is needed. Most medical laboratory scientists are not familiar with forensic principles or testifying in court. Demonstrating chain of custody and quality assurance are critical so that test results will be admissible in a court of law. The Scientific Working Group on Microbial Genetics and Forensics has published guidelines for forensic microbiology laboratories. Incorporating these guidelines help to provide test results that are useful in legal proceedings. If a laboratory scientist suspects bioterror or biocrime, or other legal case, law enforcement agents must be notified and diagnostic samples preserved. Additional sample testing might be necessary in court cases.

  1. Microbiological and molecular epidemiological analyses of community-associated methicillin-resistant Staphylococcus aureus at a tertiary care hospital in Japan.

    PubMed

    Inomata, Shinya; Yano, Hisakazu; Tokuda, Koichi; Kanamori, Hajime; Endo, Shiro; Ishizawa, Chiyuki; Ogawa, Miho; Ichimura, Sadahiro; Shimojima, Masahiro; Kakuta, Risako; Ozawa, Daiki; Aoyagi, Tetsuji; Gu, Yoshiaki; Hatta, Masumitsu; Oshima, Kengo; Nakashima, Kazutoshi; Kaku, Mitsuo

    2015-10-01

    Molecular characterization of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is generally conducted referred to staphylococcal cassette chromosome mec (SCCmec) type IV or V. CA-MRSA is now a cause of concern since such strains have been isolated not only from individuals in a community but also from patients in healthcare settings. The aim of this study was to analyze microbiological and molecular epidemiological features of CA-MRSA strains at a Japanese tertiary care hospital using PCR based-open reading frame typing (POT). This technique allows for molecular classification into CA-MRSA (POT-CA) and hospital-associated (HA-) MRSA (POT-HA) with clonal discrimination. Clinical MRSA isolates obtained from consecutive patients between October 1, 2012 and September 30, 2013 at the hospital were analyzed in combination with the clinical definition for CA-MRSA by the Centers for Disease Control and Prevention and POT. Of 219 isolates (76 clonal groups), 64 (29.3%) were clinical-HA/POT-CA isolates (22 clonal groups). Some clones of them accumulated in this hospital and might be involved in nosocomial transmission. Virulent factors of the isolates were analyzed, and only one (1.6%) Panton-Valentine leukocidin gene positive isolate but no arginine catabolic mobile element genes positive isolate were found in clinical-HA/POT-CA. Additionally, clinical-HA/POT-CA isolates showed higher antimicrobial susceptibility than clinical-HA/POT-HA, especially to minocycline, doxycycline, and amikacin. The most frequent genotype of molecular CA-MRSA was multi-locus sequence type 5-SCCmecIV, previously not detected in Japan. Although CA-MRSA at this hospital showed low virulence and higher antimicrobial susceptibility, the risk of nosocomial infection from them should be recognized, requiring stricter infection control measures.

  2. [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.

  3. [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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Molecular analysis of environmental and human isolates of Salmonella typhi.

    PubMed Central

    Thong, K L; Cordano, A M; Yassin, R M; Pang, T

    1996-01-01

    Molecular characterization of a total of 54 isolates of Salmonella typhi from Santiago, Chile, was performed by pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with three restriction endonucleases: XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3'), and SpeI (5'-ACTAGT-3'). Thirteen of the 54 isolates were obtained from environmental sources (sewage and river water), and the rest were isolates from clinical cases of typhoid fever. Considerable genetic diversity was detected among the human isolates obtained in 1994, as evidenced by the presence of 14 to 19 different PFGE patterns among 20 human isolates, with F (coefficient of similarity) values ranging from 0.69 to 1.0 (XbaI), 0.61 to 1.0 (AvrII), and 0.70 to 1.0 (SpeI). A total of eight phage types were detected among these 20 isolates, with 50% possessing the E1 or 46 phage type. There was no correlation between PFGE pattern and phage types. Similar diversity was seen among 21 isolates obtained in 1983, with 17 to 19 PFGE patterns detected and F values of 0.56 to 1.0 (XbaI), 0.55 to 1.0 (AvrII), and 0.67 to 1.0 (SpeI). Comparison of these two groups of human isolates obtained 11 years apart indicated that certain molecular types of S. typhi are shared and are able to persist for considerable periods. A similar degree of genetic diversity was also detected among the environmental isolates of S. typhi, for which 10 to 12 different PFGE patterns were detected among the 13 isolates analyzed, with F values ranging from 0.56 to 1.0 (XbaI), 0.52 to 1.0 (AvrII), and 0.69 to 1.0 (SpeI). Certain molecular types present among the environmental isolates of S. typhi were also found among the human isolates from the same time period, providing evidence for the epidemiological link between environmental reservoirs and human infection. PMID:8572705

  9. 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

  10. Look@NanoSIMS--a tool for the analysis of nanoSIMS data in environmental microbiology.

    PubMed

    Polerecky, Lubos; Adam, Birgit; Milucka, Jana; Musat, Niculina; Vagner, Tomas; Kuypers, Marcel M M

    2012-04-01

    We describe an open-source freeware programme for high throughput analysis of nanoSIMS (nanometre-scale secondary ion mass spectrometry) data. The programme implements basic data processing and analytical functions, including display and drift-corrected accumulation of scanned planes, interactive and semi-automated definition of regions of interest (ROIs), and export of the ROIs' elemental and isotopic composition in graphical and text-based formats. Additionally, the programme offers new functions that were custom-designed to address the needs of environmental microbiologists. Specifically, it allows manual and automated classification of ROIs based on the information that is derived either from the nanoSIMS dataset itself (e.g. from labelling achieved by halogen in situ hybridization) or is provided externally (e.g. as a fluorescence in situ hybridization image). Moreover, by implementing post-processing routines coupled to built-in statistical tools, the programme allows rapid synthesis and comparative analysis of results from many different datasets. After validation of the programme, we illustrate how these new processing and analytical functions increase flexibility, efficiency and depth of the nanoSIMS data analysis. Through its custom-made and open-source design, the programme provides an efficient, reliable and easily expandable tool that can help a growing community of environmental microbiologists and researchers from other disciplines process and analyse their nanoSIMS data. PMID:22221878

  11. Molecular breeding of polymerases for resistance to environmental inhibitors.

    PubMed

    Baar, Claudia; d'Abbadie, Marc; Vaisman, Alexandra; Arana, Mercedes E; Hofreiter, Michael; Woodgate, Roger; Kunkel, Thomas A; Holliger, Philipp

    2011-04-01

    Potent inhibitors limit the use of PCR assays in a wide spectrum of specimens. Here, we describe the engineering of polymerases with a broad resistance to complex environmental inhibitors using molecular breeding of eight different polymerase orthologues from the genus Thermus and directed evolution by CSR in the presence of inhibitors. Selecting for resistance to the inhibitory effects of Neomylodon bone powder, we isolated 2D9, a chimeric polymerase comprising sequence elements derived from DNA polymerases from Thermus aquaticus, Thermus oshimai, Thermus thermophilus and Thermus brockianus. 2D9 displayed a striking resistance to a broad spectrum of complex inhibitors of highly divergent composition including humic acid, bone dust, coprolite, peat extract, clay-rich soil, cave sediment and tar. The selected polymerase promises to have utility in PCR-based applications in a wide range of fields including palaeobiology, archaeology, conservation biology, forensic and historic medicine.

  12. 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.

  13. [The microbiology department].

    PubMed

    Struelens, M; Delforge, M L; Denis, O; Liesnard, C; Rodriguez-Villalobos, H

    2002-01-01

    From the outset, the Department of Microbiology of Erasme Hospital has striven to offer to clinical teams a full range of high performance tests for diagnosis and therapeutic monitoring of bacterial, viral, fungal and parasitic infections, including opportunistic infections. Furthermore, the laboratory has developed and made available cutting edge tools for the epidemiologic surveillance and outbreak investigation in support to the hospital infection control and antibiotic resistance control programmes. Research and development programmes have led to technological innovation in the fields of molecular virologic diagnosis, notably for HIV and herpes viruses, rapid bacterial identification, detection of resistance genes and epidemiological typing. Research in collaboration with clinical teams has focused on congenital infections, HIV infection, opportunistic infections and prevention of nosocomial infection. The Department acts as national reference laboratory for a number of infectious diseases and co-ordinates or actively participates to several European multicentre studies and epidemiologic surveillance networks.

  14. Prospecting Environmental Mycobacteria: Combined Molecular Approaches Reveal Unprecedented Diversity

    PubMed Central

    Pontiroli, Alessandra; Khera, Tanya T.; Oakley, Brian B.; Mason, Sam; Dowd, Scot E.; Travis, Emma R.; Erenso, Girum; Aseffa, Abraham; Courtenay, Orin; Wellington, Elizabeth M. H.

    2013-01-01

    Background Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in

  15. 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.

  16. 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

  17. 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…

  18. 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

  19. 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...

  20. 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...

  1. 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

  2. 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...

  3. 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

  4. 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...

  5. 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.

  6. 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)

  7. 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)

  8. 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

  9. 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

  10. 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...

  11. Computational Molecular Modeling for Evaluating the Toxicity of Environmental Chemicals: Prioritizing Bioassay Requirements

    EPA Science Inventory

    This commentary provides an overview of the challenges that arise from applying molecular modeling tools developed and commonly used for pharmaceutical discovery to the problem of predicting the potential toxicities of environmental chemicals.

  12. 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)

  13. 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.

  14. 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.

  15. [Bacterial identification methods in the microbiology laboratory].

    PubMed

    Bou, Germán; Fernández-Olmos, Ana; García, Celia; Sáez-Nieto, Juan Antonio; Valdezate, Sylvia

    2011-10-01

    In order to identify the agent responsible of the infectious process and understanding the pathogenic/pathological implications, clinical course, and to implement an effective antimicrobial therapy, a mainstay in the practice of clinical microbiology is the allocation of species to a microbial isolation. In daily routine practice microbiology laboratory phenotypic techniques are applied to achieve this goal. However, they have some limitations that are seen more clearly for some kinds of microorganism. Molecular methods can circumvent some of these limitations, although its implementation is not universal. This is due to higher costs and the level of expertise required for thei implementation, so molecular methods are often centralized in reference laboratories and centers. Recently, proteomics-based methods made an important breakthrough in the field of diagnostic microbiology and will undoubtedly have a major impact on the future organization of the microbiology services. This paper is a short review of the most noteworthy aspects of the three bacterial identification methods described above used in microbiology laboratories.

  16. European journals on microbiology.

    PubMed

    Ronda, C; Vázquez, M

    1997-12-01

    A survey on the scientific journals dealing with microbiology published in Europe has been carried out. Eighteen European countries publish microbiological journals with the United Kingdom. Netherlands and Germany leading in number of journals on this specialty. Most of the European journals on microbiology are published bimonthly (27%), and English is the most common language used (54%). Most of these journals (86%) are included in some database, but only 36 (25%) are indexed in the six databases studied. Out of the 146 journals registered, 71 (49%), published in 11 European countries, are included in the 1995 Journal Citation Reports (ISI, Philadelphia).

  17. 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

  18. Microbiology: a dangerous profession?

    PubMed

    Piqueras, Mercè

    2007-09-01

    The history of science contains many cases of researchers who have died because of their professional activity. In the field of microbiology, some have died or have come close to death from infection by agents that were the subject of their research (Table 1). Infections that had a lethal outcome were usually accidental. Sometimes, however, researchers inoculated themselves with the pathogen or did not take preventive measures against the potential pathogen because they wanted to prove their hypotheses--or disprove someone else's--regarding the origin of the infection. Here is an overview of several episodes in the history of microbiology since the mid nineteenth century involving researchers or workers in fields related to microbiology who have become infected. They are considered here in their historical context to provide insights into some of the pillars of modern microbiology--The giants on whose shoulders several generations of microbiologists have stood to see further.

  19. 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.

  20. 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)

  1. Prospecting Environmental Mycobacteria: combined molecular approaches reveal unprecedented diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Environmental mycobacteria (EM) include species commonly found in a variety of terrestrial and aquatic environments and encompass animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differen...

  2. The microbiological, histological, immunological and molecular determinants of Helicobacter pylori infection in guinea pigs as a convenient animal model to study pathogenicity of these bacteria and the infection dependent immune response of the host.

    PubMed

    Walencka, Maria; Gonciarz, Weronika; Mnich, Eliza; Gajewski, Adrian; Stawerski, Pawel; Knapik-Dabrowicz, Alina; Chmiela, Magdalena

    2015-01-01

    Helicobacter pylori is an etiological agent of chronic gastritis, gastric and duodenal ulcers and gastric cancers. The use of an appropriate animal model for experimental studies on the pathogenesis of H. pylori infections is necessary due to the chronic character of such infections and difficulties in identifying their early stage in humans. The aim of this study was to develop a guinea pig model of H. pylori infection and identify its microbiological, histological, serological and molecular determinants. Guinea pigs were inoculated per os with H. pylori strains: CCUG 17874 or ATCC 700312, both producing vacuolating cytotoxin A (VacA) and cytotoxin associated gene A (CagA) protein, suspended in Brucella broth with fetal calf serum (FCS) and Skirrow supplement of antibiotics. To determine H. pylori colonization, 7 and 28 days after the challenge, a panel of diagnostic methods was used. It included culturing of microorganisms from the gastric tissue, histopathological analysis of gastric sections, stained by Mayer,s haematoxylin and eosin to assess inflammatory response, by Giemsa as well as Warthin-Starry silver staining to visualise Helicobacter-like organisms (HLO) and with anti-Ki-67 antigen to assess epithelial cell proliferation. H. pylori infection was also confirmed by polymerase chain reactions (PCR) for detection in gastric tissue of ureC and cagA genes and by serological assessment of H. pylori antigens in faeces. This study showed the usefulness of microbiological, histological, immunological and molecular methods for the detection of persistent H. pylori infections in guinea pigs, which could be an appropriate model for studying H. pylori pathogenesis and the related immune response against these microbes.

  3. 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

  4. Clinical microbiology informatics.

    PubMed

    Rhoads, Daniel D; Sintchenko, Vitali; Rauch, Carol A; Pantanowitz, Liron

    2014-10-01

    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.

  5. Environmental factors and chemical and microbiological water-quality constituents related to the presence of enteric viruses in ground water from small public water supplies in southeastern Michigan

    USGS Publications Warehouse

    Francy, Donna S.; Bushon, Rebecca N.; Stopar, Julie; Luzano, Emma J.; Fout, G. Shay

    2004-01-01

    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 indicators of fecal contamination (indicators), determine whether indicators are adequate predictors of the presence of enteric viruses, and determine the factors that affect the presence of enteric viruses. Small systems are those that serve less than 3,300 people. Samples were analyzed for specific enteric viruses by reverse transcriptase-polymerase chain reaction (RT-PCR), for culturable viruses by cell culture, and for the indicators total coliforms, Escherichia coli (E. coli), enterococci, and F-specific and somatic coliphage. Ancillary environmental and water-quality data were collected or compiled. A total of 169 regular samples and 32 replicate pairs were collected from 38 wells. Replicate pairs were samples collected at the same well on the same date. One well was sampled 6 times, 30 wells were sampled five times, 6 wells were sampled twice, and 1 well was sampled once. By use of RT-PCR, enterovirus was found in four wells (10.5 percent) and hepatitis A virus (HAV) in five wells (13.2 percent). In two of these wells, investigators found both enterovirus and HAV, but on different sampling dates. Culturable viruses were found one time in two wells (5.9 percent), and neither of these wells was positive for viruses by use of RT-PCR on any sampling date. If results for all viruses are combined, 9 of the 38 small public-supply wells were positive for enteric viruses (23.7 percent) by either cell culture or RT-PCR. One or more indicators were found in 18 of 38 wells. Total coliforms, E. coli, enterococci, and F-specific and somatic coliphage were found in 34.2, 10.5, 15.8, 5.9, and 5.9 percent, respectively, of the wells tested. In only 3 out of 18 wells were samples positive for an indicator on

  6. The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata).

    PubMed

    Raftos, D A; Melwani, A R; Haynes, P A; Muralidharan, S; Birch, G F; Amaral, V; Thompson, E L; Taylor, D A

    2016-09-14

    This review describes our recent work on environmental stress in Sydney rock oysters, focusing on the identification of molecular biomarkers for ecotoxicological analysis. We begin by describing the environmental pressures facing coastal estuaries in Australia, with particular reference to Sydney Harbour. After providing that context, we summarise our transcriptional and proteomic analyses of Sydney rock oysters responding to chemical contamination and other forms of environmental stress. This work has shown that the intracellular processes of oysters are highly responsive to environmental threats. Our data agree with the broader literature, which suggests that there is a highly conserved intracellular stress response in oysters involving a limited number of biological processes. We conclude that many effective molecular markers for environmental biomonitoring are likely to lie within these biological pathways. PMID:27548823

  7. 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.

  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. 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.

  10. 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

  11. Consolidated clinical microbiology laboratories.

    PubMed

    Sautter, Robert L; Thomson, Richard B

    2015-05-01

    The manner in which medical care is reimbursed in the United States has resulted in significant consolidation in the U.S. health care system. One of the consequences of this has been the development of centralized clinical microbiology laboratories that provide services to patients receiving care in multiple off-site, often remote, locations. Microbiology specimens are unique among clinical specimens in that optimal analysis may require the maintenance of viable organisms. Centralized laboratories may be located hours from patient care settings, and transport conditions need to be such that organism viability can be maintained under a variety of transport conditions. Further, since the provision of rapid results has been shown to enhance patient care, effective and timely means for generating and then reporting the results of clinical microbiology analyses must be in place. In addition, today, increasing numbers of patients are found to have infection caused by pathogens that were either very uncommon in the past or even completely unrecognized. As a result, infectious disease specialists, in particular, are more dependent than ever on access to high-quality diagnostic information from clinical microbiology laboratories. In this point-counterpoint discussion, Robert Sautter, who directs a Charlotte, NC, clinical microbiology laboratory that provides services for a 40-hospital system spread over 3 states in the southeastern United States explains how an integrated clinical microbiology laboratory service has been established in a multihospital system. Richard (Tom) Thomson of the NorthShore University HealthSystem in Evanston, IL, discusses some of the problems and pitfalls associated with large-scale laboratory consolidation.

  12. MALDI-TOF-mass spectrometry applications in clinical microbiology.

    PubMed

    Seng, Piseth; Rolain, Jean-Marc; Fournier, Pierre Edouard; La Scola, Bernard; Drancourt, Michel; Raoult, Didier

    2010-11-01

    MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost-effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

  13. 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.

  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. 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...

  16. 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…

  17. 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…

  18. Molecular characterization of Yersinia strains isolated from human and environmental sources.

    PubMed

    Marranzano, M; Agodi, A; Gulisano, M

    1993-01-01

    Thirty-seven strains of Yersinia isolated from human and environmental sources were investigated for virulence and molecular characteristics. Clinical isolates of Y. enterocolitica serotypes 0:3 and 0:9, harbouring the 45 MDa virulence plasmid were Ca++ dependent and responded positively to the CV-binding assay. The environmental Y. kristensenii strain, although harbouring a 45 MDa plasmid proved to be negative for both assays. All the environmental strains showed pyrazinamidase activity, while isolates from human sources proved negative. Two different plasmid profiles were disclosed: one Y. enterocolitica strain (serotype 0:7, 8) showed one plasmid of 67 MDa and one plasmid of 1.5 MDa. Eleven human isolates of Y. enterocolitica and one environmental strain of Y. krinstensenii showed only one plasmid of 45 MDa. Restriction endonuclease analysis of the 45 MDa plasmids supported the hypothesis that the environmental Y. krinstensenii plasmid is unrelated to the family of homologous virulence plasmids of Y. enterocolitica.

  19. 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

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

    PubMed

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

    PubMed

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

    2015-10-23

    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.

  2. 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.

  3. 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.

  4. Circadian clocks in the cnidaria: environmental entrainment, molecular regulation, and organismal outputs.

    PubMed

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

    2013-07-01

    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.

  5. Potential for Misidentification of Environmentally Persistent Free Radicals as Molecular Pollutants in Particulate Matter

    PubMed Central

    TRUONG, HIEU; LOMNICKI, SLAWO; DELLINGER, BARRY

    2014-01-01

    Environmentally persistent free radicals (EPFRs) have been shown to form on the surfaces of various types of transition metal-containing particulate matter (PM), and it has been demonstrated they are capable of initiating adverse health impacts. Following sonification and solvent extraction for chemical analysis, they are partially converted to molecular species. Alcoholic solvents extracted the EPFRs with near 100% efficiency, while nonpolar hydrocarbon solvents exhibited <20% efficiency and dichloromethane exhibited 20–55% efficiency. The extracted radicals reacted in solution to form multiple molecular reaction products including catechol, hydroquinone, phenol, chlorinated phenols, dibenzo-p-dioxin, and dibenzofuran. This suggests that EPFRs in environmental samples are indistinguishable from molecular pollutants and are subject to misidentification as molecular adsorbates when traditional extraction and chemical analysis methods are employed. On the basis of these findings, the origin of the toxicity of particulate matter contaminated with toxic organic compounds should be considered for re-evaluation to include the possibility that EPFRs may be a significant contributor, and the impact of some molecular pollutants may have been overestimated. PMID:20155937

  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. 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

  8. 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

  9. 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.

  10. Molecular/genetic determinants of repolarization and their modification by environmental stress.

    PubMed

    Rosen, M R; Cohen, I S

    2006-01-01

    Although a variety of factors, inherited or environmental, can influence expression of ion channel proteins to impact on repolarization, that environment can affect genetic determinants of repolarization for intervals of varying duration is a concept that is not as generally appreciated as it should be. In the following pages we review the molecular/genetic determinants of cardiac repolarization and summarize how pathologic events and environmental intrusions can affect these determinants. Understanding the chains of events involved should yield insights into both the causes and potential avenues of treatment for abnormalities of repolarization.

  11. 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.

  12. 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.

  13. 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

  14. 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

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

    PubMed

    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. 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

  16. 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.

  17. 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}

  18. 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

  19. 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

  20. [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

  1. 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.

  2. 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

  3. Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans.

    PubMed

    Veldhoen, Nik; Ikonomou, Michael G; Helbing, Caren C

    2012-02-01

    Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems. PMID:22036265

  4. 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

  5. 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.

  6. The microbiological composition of airliner cabin air.

    PubMed

    Wick, R L; Irvine, L A

    1995-03-01

    Hundreds of millions of passengers travel on U.S. airliners annually. These large numbers, together with the close proximity required onboard, raise a concern about microbiologic disease transmission in cabin air. Previous air quality surveys generally concentrated on environmental tobacco smoke and particulate matter. They largely ignored the microorganisms also present. We sampled the microbiologic climate of 45 domestic and international flights. We also sampled common locations in a major southwestern city. The concentration of microorganisms in airline cabin air is much lower than in ordinary city locations. We conclude that the small number of microorganisms found in U.S. airliner cabin environments does not contribute to the risk of disease transmission among passengers.

  7. Rapid microbiology - raising awareness.

    PubMed

    Bailie, Jonathan

    2016-01-01

    A 'high-level overview' of some of the emerging rapid microbiology technologies designed to help healthcare engineering and infection control teams working in hospitals and other healthcare facilities more rapidly identify potentially hazardous levels of waterborne microorganisms in their water systems, enabling them to take prompt remedial action, and a look at the some of the 'pros and cons' of such testing techniques, was given by Nalco technical director, Howard Barnes, the vice-chair of the Legionella Control Association (LCA), at a recent LCA open day. HEJ editor, Jonathan Bailie, reports.

  8. 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.

  9. 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

  10. 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

  11. [Microbiological diagnosis of tuberculosis].

    PubMed

    Allerberger, F; Fille, M; Streif, W; Luef, G; Schmutzhard, E; Dierich, M P

    1994-01-01

    The increased incidence of tuberculosis as well as the availability of new diagnostic testing methods clearly have various implications for the routine microbiology laboratory: samples must be sent to the microbiology lab for testing immediately after being taken and microscopically investigated the same day. In other countries, difficult to treat, multi-resistant Mycobacterium tuberculosis strains have occurred. Thus decisive hygienic measures must be taken early on in cases of highly infectious patients (i.e. patients with microscopically positive sputum). Liquid media (MB Check Roche, Bactec) as well as Löwenstein Jensen media must be inoculated in the lab. Liquid media allow both faster detection of certain atypical mycobacteria and increased accuracy. Classification of culturally established agents through commercial genetic probes (AccuProbe Mycobacterien) or with high pressure liquid chromatography is possible within hours when acid-fast rods are present. Time consuming identification by determination of biochemical and culture morphological characteristics should be reserved for reference labs. Today, rapid tests like analysis of tuberculostearic acid or polymerase chain reaction are already useful for special questions like ruling out tuberculous meningitis. In most cases, however, these rapid tests cannot replace identification of microbes with culture techniques. PMID:7941601

  12. 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

  13. 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

  14. 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.

  15. [Mass spectrometry in the clinical microbiology laboratory].

    PubMed

    Jordana-Lluch, Elena; Martró Català, Elisa; Ausina Ruiz, Vicente

    2012-12-01

    Infectious diseases are still a cause of high mortality and morbidity rates. Current microbiological diagnostic methods are based on culture and phenotypic identification of isolated microorganisms, which can be obtained in about 24-48 h. Given that the microbiological identification is of major importance for patient management, new diagnostic methods are needed in order to detect and identify microorganisms in a timely and accurate manner. Over the last few years, several molecular techniques based on the amplification of microbial nucleic acids have been developed with the aim of reducing the time needed for the identification of the microorganisms involved in different infectious processes. On the other hand, mass spectrometry has emerged as a rapid and consistent alternative to conventional methods for microorganism identification. This review describes the most widely used mass spectrometry technologies -matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and electrospray ionization time-of-flight (ESI-TOF)-, both for protein and nucleic acid analysis, as well as the commercial platforms available. Related publications of most interest in clinical microbiology are also reviewed.

  16. [Laboratory unification: advantages and disadvantages for clinical microbiology].

    PubMed

    Andreu, Antonia; Matas, Lurdes

    2010-10-01

    This article aims to reflect on which areas or tasks of microbiology laboratories could be unified with those of clinical biochemistry, hematology, immunology or pathology laboratories to benefit patients and the health system, as well as the areas that should remain independent since their amalgamation would not only fail to provide a benefit but could even jeopardize the quality of microbiological diagnosis, and consequently patient care. To do this, the distinct analytic phases of diagnosis are analyzed, and the advantages and disadvantages of amalgamation are evaluated in each phase. The pros and cons of the unification of certain areas such as the computer system, occupational risk units, customer service, purchasing logistics, and materials storage, etc, are also discussed. Lastly, the effect of unification on urgent microbiology diagnosis is analyzed. Microbiological diagnosis should be unique. The microbiologist should perform an overall evaluation of the distinct techniques used for a particular patient, both those that involve direct diagnosis (staining, culture, antigen detection techniques or molecular techniques) and indirect diagnosis (antibody detection). Moreover, the microbiology laboratory should be independent, with highly trained technicians and specialists in microbiology that provide added value as experts in infection and as key figures in the process of establishing a correct etiological diagnosis.

  17. [Laboratory unification: advantages and disadvantages for clinical microbiology].

    PubMed

    Andreu, Antonia; Matas, Lurdes

    2010-10-01

    This article aims to reflect on which areas or tasks of microbiology laboratories could be unified with those of clinical biochemistry, hematology, immunology or pathology laboratories to benefit patients and the health system, as well as the areas that should remain independent since their amalgamation would not only fail to provide a benefit but could even jeopardize the quality of microbiological diagnosis, and consequently patient care. To do this, the distinct analytic phases of diagnosis are analyzed, and the advantages and disadvantages of amalgamation are evaluated in each phase. The pros and cons of the unification of certain areas such as the computer system, occupational risk units, customer service, purchasing logistics, and materials storage, etc, are also discussed. Lastly, the effect of unification on urgent microbiology diagnosis is analyzed. Microbiological diagnosis should be unique. The microbiologist should perform an overall evaluation of the distinct techniques used for a particular patient, both those that involve direct diagnosis (staining, culture, antigen detection techniques or molecular techniques) and indirect diagnosis (antibody detection). Moreover, the microbiology laboratory should be independent, with highly trained technicians and specialists in microbiology that provide added value as experts in infection and as key figures in the process of establishing a correct etiological diagnosis. PMID:21129589

  18. 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.

  19. 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

  20. The microbiology of metalworking fluids.

    PubMed

    Saha, Ratul; Donofrio, Robert S

    2012-06-01

    Metalworking fluids (MWFs) are complex mixtures of chemicals and are indispensable materials in industry. They are used as cooling and lubricating agents in different machining process such as grinding, milling, and cutting. The quality of MWFs is affected by physical, chemical, and microbial contaminates. In particular, MWFs are highly vulnerable to microbial contamination, which may act both as potential pathogens and deteriorgens. Microbial contamination is of major concern due to potential health hazards such as skin dermatitis and hypersensitivity pneumonitis. The contaminated MWFs can exhibit high degrees of microbial loading, ranging from 10(4) to 10(10) colony-forming units (CFU)/ml. Wide varieties of microorganisms are reported to colonize MWFs. Traditional culturing techniques are not only laborious and time consuming but also underestimate the actual distribution of the microorganisms present in the contaminated MWFs. Therefore, rapid molecular methods such as real-time PCR and fluorescent in situ hybridization are implemented to monitor the microbial load. In industry, biocides are presently used to control microbial contamination. However, it has its own disadvantages and therefore, in recent years, alternative methods such as UV irradiation were evaluated to reduce microbial contamination in MWFs. Microbes inhabiting the MWF are also capable of forming biofilm which is detrimental to the MWF system. Biofilm is resistant to common disinfectant methods, and thus further research and development is required to effectively control its formation within MWF systems. This review is intended to discuss the overall microbiological aspects of MWF. PMID:22543351

  1. 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.

  2. Oxidative metabolism of chemical pollutants in marine organisms: molecular and biochemical biomarkers in environmental toxicology.

    PubMed

    Benedetti, Maura; Giuliani, Maria Elisa; Regoli, Francesco

    2015-03-01

    Oxidative stress biomarkers are widely used in marine ecotoxicology. Environmental pollutants enhance intracellular formation of oxyradicals through several mechanisms, but complex oxidative interactions occur in response to chemical mixtures. Metabolism of individual classes of pollutants can be influenced by a sophisticated network of prooxidant relationships, reciprocal and cascade effects, changes of redox-sensitive signaling proteins, and transcription factors. Chemically mediated pathways can affect antioxidant responses at different levels, including pretranscriptional, transcriptional, protein, and catalytic functions; such mechanisms remain largely unexplored in marine organisms. Molecular responses of antioxidants are frequently not paralleled by expected biochemical changes or cellular effects, and caution is needed when interpreting the effects of environmental pollutants. Results on antioxidant variations can be influenced by mRNA stability and protein turnover, different timing for transcriptional and translational mechanisms, metabolic capability of tissues, posttranscriptional modifications of proteins, biphasic responses of antioxidant enzymes, and adaptation mechanisms to chronic pollution. PMID:25712694

  3. 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

  4. 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

  5. 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

  6. 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

  7. Microbiological safety of water.

    PubMed

    Dawson, D J; Sartory, D P

    2000-01-01

    Significant advances in water treatment over the last century have resulted in massive improvements in the microbiological safety of public drinking water supplies in the UK and the developed countries. Incidences of illness due to poor treatment or post-treatment contamination are rare, but when they occur tend to attract considerable media attention. A well managed water treatment works and supply system can provide high quality drinking water wherever in the world it is located. As a rule, throughout the world, private supplies tend to be of a poorer quality than public supplies, but poorly managed public supplies have the potential to make a large number of people ill and continued effort is needed to maintain and improve drinking water quality world-wide.

  8. New microbiological features.

    PubMed

    Lee, A

    1995-04-01

    Recent developments in the microbiology of Helicobacter pylori have aimed to improve our understanding of the organism in order to define better methods of diagnosis and cure, and to explore possible methods of prevention. Investigations of the basic biochemistry of the bacterium have revealed many interesting physiological anomalies including characteristics of a eukaryotic parasite rather than a bacterium. The latest in a growing list of adhesins to be identified shows specificity for the Lewis b antigen, possibly providing an explanation for the postulated link between blood group and peptic ulceration. However, there are many contradictory features in the H. pylori adhesin story in urgent need of resolution. The search for the ulcerogenic strain has revealed only one possible candidate to date, the cagA phenotype, which appears to be inflammatory. Recently, the cloning frenzy has resulted in the sequencing of a multitude of putative virulence factors, the challenge now is to prove their importance in relevant animal models. PMID:7600134

  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. [Rapid antibiotic susceptibility test in Clinical Microbiology].

    PubMed

    March Rosselló, Gabriel Alberto; Bratos Pérez, Miguel Ángel

    2016-01-01

    The most widely used antibiotic susceptibility testing methods in Clinical Microbiology are based on the phenotypic detection of antibiotic resistance by measuring bacterial growth in the presence of the antibiotic being tested. These conventional methods take typically 24hours to obtain results. A review is presented here of recently developed techniques for the rapid determination of antibiotic susceptibility. Data obtained with different methods such as molecular techniques, flow cytometry, chemiluminescence, mass spectrometry, commercial methods used in routine work, colorimetric methods, nephelometry, microarrays, microfluids, and methods based on cell disruption and sequencing, are analyzed and discussed in detail.

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

    DOE PAGES

    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

  12. 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.

  13. 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.

  14. Application of combined morphological-molecular approaches to the identification of planktonic protists from environmental samples.

    PubMed

    Duff, Robert Joel; Ball, Hope; Lavrentyev, Peter J

    2008-01-01

    The value of molecular databases for unicellular eukaryotic identification and phylogenetic reconstruction is predicated on the availability of sequences and accuracy of taxonomic identifications that accompany those sequences. Biased representation of sequences is due in part to the differing ability to isolate and culture various groups of protists. Techniques that allow for parallel single-cell morphological and molecular identifications have been reported for a few groups of unicellular protists. We have sought to explore how those techniques can be adapted to work across a greater phylogenetic diversity of taxa. Twelve morphologically diverse and abundant members of limnetic microplankton, including ciliates, dinoflagellates, cryptophytes, stramenopiles, and synurophytes, were targeted for analysis. These cells were captured directly from environmental samples, identified, and prepared for sequence analyses using variations of single-cell extraction techniques depending on their size, mobility, and the absence or presence of the cell wall. The application of these techniques yielded a strong congruence between the morphological and molecular identifications of the targeted taxa. Challenges to the single-cell approach in some groups are discussed. The general ability to obtain DNA sequences and morphological descriptions from individual cells should open new avenues to studying either rare or difficult to culture taxa, even directly at the point of collection (e.g. remote locations or shipboard).

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. Molecular characterisation of clinical and environmental isolates of Mycobacterium kansasii isolates from South African gold mines.

    PubMed

    Kwenda, Geoffrey; Churchyard, Gavin J; Thorrold, Catherine; Heron, Ian; Stevenson, Karen; Duse, Adriano G; Marais, Elsé

    2015-03-01

    Mycobacterium kansasii (M. kansasii) is a major cause of non-tuberculous mycobacterial pulmonary disease in the South African gold-mining workforce, but the source of infection and molecular epidemiology are unknown. This study investigated the presence of M. kansasii in gold and coal mine and associated hostel water supplies and compared the genetic diversity of clinical and environmental isolates of M. kansasii. Five M. kansasii and ten other potentially pathogenic mycobacteria were cultured mainly from showerhead biofilms. Polymerase chain reaction-restriction analysis of the hsp65 gene on 196 clinical and environmental M. kansasii isolates revealed 160 subtype I, eight subtype II and six subtype IV strains. Twenty-two isolates did not show the typical M. kansasii restriction patterns, suggesting that these isolates may represent new subtypes of M. kansasii. In contrast to the clonal population structure found amongst the subtype I isolates from studies in other countries, DNA fingerprinting of 114 clinical and three environmental subtype I isolates demonstrated genetic diversity amongst the isolates. This study demonstrated that showerheads are possible sources of M. kansasii and other pathogenic non-tuberculous mycobacterial infection in a gold-mining region, that subtype I is the major clinical isolate of M. kansasii strain and that this subtype exhibits genetic diversity. PMID:25719478

  20. [Microbiological diagnosis of HIV infection].

    PubMed

    López-Bernaldo de Quirós, Juan Carlos; Delgado, Rafael; García, Federico; Eiros, José M; Ortiz de Lejarazu, Raúl

    2007-12-01

    Currently, there are around 150,000 HIV-infected patients in Spain. This number, together with the fact that this disease is now a chronic condition since the introduction of antiretroviral therapy, has generated an increasing demand on the clinical microbiology laboratories in our hospitals. This increase has occurred not only in the diagnosis and treatment of opportunistic diseases, but also in tests related to the diagnosis and therapeutic management of HIV infection. To meet this demand, the Sociedad de Enfermedades Infecciosas y Microbiología Clinica (Spanish Society of Infectious Diseases and Clinical Microbiology) has updated its standard Procedure for the microbiological diagnosis of HIV infection. The main advances related to serological diagnosis, plasma viral load, and detection of resistance to antiretroviral drugs are reviewed in this version of the Procedure.

  1. 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.

  2. 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.

  3. 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.

  4. 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...

  5. 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.

  6. Spectrometric microbiological analyzer

    NASA Astrophysics Data System (ADS)

    Schlager, Kenneth J.; Meissner, Ken E.

    1996-04-01

    Currently, there are four general approaches to microbiological analysis, i.e., the detection, identification and quantification of micro-organisms: (1) Traditional culturing and staining procedures, metabolic fermentations and visual morphological characteristics; (2) Immunological approaches employing microbe-specific antibodies; (3) Biotechnical techniques employing DNA probes and related genetic engineering methods; and (4) Physical measurement techniques based on the biophysical properties of micro-organisms. This paper describes an instrumentation development in the fourth of the above categories, physical measurement, that uses a combination of fluorometric and light scatter spectra to detect and identify micro-organisms at the species level. A major advantage of this approach is the rapid turnaround possible in medical diagnostic or water testing applications. Fluorometric spectra serve to define the biochemical characteristics of the microbe, and light scatter spectra the size and shape morphology. Together, the two spectra define a 'fingerprint' for each species of microbe for detection, identification and quantification purposes. A prototype instrument has been developed and tested under NASA sponsorship based on fluorometric spectra alone. This instrument demonstrated identification and quantification capabilities at the species level. The paper reports on test results using this instrument, and the benefits of employing a combination of fluorometric and light scatter spectra.

  7. 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.

  8. [Current panorama of the teaching of microbiology and parasitology in Spain].

    PubMed

    Cantón, Rafael; Sánchez-Romero, María Isabel; Gómez-Mampaso, Enrique

    2010-10-01

    The training program of residents in microbiology and parasitology in Spain includes clinical skills, ranging from the diagnostic approach to the patient and adequate sample collection for diagnosis of infectious diseases to antimicrobial therapy and infection control measures. Training also includes new challenges in clinical microbiology that ensure residents' participation in infection control programs of health-care associated infections, training in the resolution of public health problems, and application of new molecular microbiology methods. Specialization in clinical microbiology may be undertaken by graduates in Medicine, Biology, Biochemistry and Chemistry. The training is performed in accredited microbiology laboratories at different hospitals (n = 61) across the country through 4-year residency programs. In the last few years, there has been a major imbalance between the number of intended residents (0.17 per 100,000 inhabitants) and those graduating as specialists in clinical microbiology (0.13 per 100,000 inhabitants), with wide variations across the country. The current tendency in Europe is to strengthen the role of clinical microbiologists as key figures in the diagnosis of infectious diseases and in public health microbiology. Training programs have been hampered by the practice of sending samples for microbiological tests to external, centralized multipurpose laboratories with few clinical microbiologists and without a core curriculum. Essential elements in the training of specialists in clinical microbiology are a close relationship between the laboratory and the clinical center and collaboration with other specialists.

  9. 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

  10. Disentangling the molecular mechanisms of action of endogenous and environmental estrogens.

    PubMed

    Nadal, Angel; Alonso-Magdalena, Paloma; Ripoll, Cristina; Fuentes, Esther

    2005-01-01

    The gonadal hormone 17beta-estradiol is involved in numerous cellular processes. In many cases, 17beta-estradiol actions are imitated by synthetic and natural chemicals in the environment. Their actions differ depending on the target tissue, the receptors involved and the molecular pathways activated. The plethora of estrogenic actions is triggered by different receptors and other specific structures that activate different signalling pathways. This amount of information may lead to a maze of effects triggered by endogenous and environmental estrogens that we intend to clarify in this review. Understanding the variety of estrogen receptors, their different locations and the signalling pathways activated by estrogenic ligands is fundamental for understanding the diversity of actions that estrogens have in different tissues and cells.

  11. 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

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

    PubMed Central

    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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Cellular and molecular etiology of hepatocyte injury in a murine model of environmentally induced liver abnormality

    PubMed Central

    Al-Griw, M.A.; Alghazeer, R.O.; Al-Azreg, S.A.; Bennour, E.M.

    2016-01-01

    Exposures to a wide variety of environmental substances are negatively associated with many biological cell systems both in humans and rodents. Trichloroethane (TCE), a ubiquitous environmental toxicant, is used in large quantities as a dissolvent, metal degreaser, chemical intermediate, and component of consumer products. This increases the likelihood of human exposure to these compounds through dermal, inhalation and oral routes. The present in vivo study was aimed to investigate the possible cellular and molecular etiology of liver abnormality induced by early exposure to TCE using a murine model. The results showed a significant increase in liver weight. Histopathological examination revealed a TCE-induced hepatotoxicity which appeared as heavily congested central vein and blood sinusoids as well as leukocytic infiltration. Mitotic figures and apoptotic changes such as chromatin condensation and nuclear fragments were also identified. Cell death analysis demonstrates hepatocellular apoptosis was evident in the treated mice compared to control. TCE was also found to induce oxidative stress as indicated by an increase in the levels of lipid peroxidation, an oxidative stress marker. There was also a significant decrease in the DNA content of the hepatocytes of the treated groups compared to control. Agarose gel electrophoresis also provided further biochemical evidence of apoptosis by showing internucleosomal DNA fragmentation in the liver cells, indicating oxidative stress as the cause of DNA damage. These results suggest the need for a complete risk assessment of any new chemical prior to its arrival into the consumer market. PMID:27800299

  1. Testicular connexin 43, a precocious molecular target for the effect of environmental toxicants on male fertility

    PubMed Central

    Gilleron, Jérôme; Carette, Diane; Segretain, Dominique

    2011-01-01

    Many recent epidemiological, clinical and experimental findings support the hypothesis that environmental toxicants are responsible for the increasing male reproductive disorders (congenital malformations, declining sperm counts and testicular cancer) over the past 20 years. It has also been reported that exposure to these toxicants, during critical periods of development (fetal and neonatal), represents a more considerable risk for animals and humans than exposure during adulthood. However, the molecular targets for these chemicals have not been clearly identified. Recent studies showed that a family of transmembranous proteins, named connexins, regulates numerous physiological processes involved in testicular development and function, such as Sertoli and germ cell proliferation, differentiation, germ cell migration and apoptosis. In the testis, knockout strategy revealed that connexin 43, the predominant connexin in this organ, is essential for spermatogenesis. In addition, there is evidence that many environmental toxicants could alter testicular connexin 43 by dysregulation of numerous mechanisms controlling its function. In the present work, we propose first to give an overview of connexin expression and intercellular gap junction coupling in the developing fetal and neonatal testes. Second, we underline the impact of maternally chemical exposure on connexin 43 expression in the perinatal developing testis. Lastly, we attempt to link this precocious effect to male offspring fertility. PMID:22332114

  2. Molecular modeling for screening environmental chemicals for estrogenicity: use of the toxicant-target approach.

    PubMed

    Rabinowitz, James R; Little, Stephen B; Laws, Susan C; Goldsmith, Michael-Rock

    2009-09-01

    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 preliminary evaluation of risk and the establishment of priorities for obtaining missing data for environmental chemicals. The differential step in many mechanisms of toxicity may be generalized as the interaction between a small molecule (a potential toxicant) and one or more macromolecular targets. An approach based on computation of the interaction between a potential molecular toxicant and a library of macromolecular targets of toxicity has been proposed for preliminary chemical screening. In the current study, the interaction between a series of environmentally relevant chemicals and models of the rat estrogen receptors (ER) was computed and the results compared to an experimental data set of their relative binding affinities. The experimental data set consists of 281 chemicals, selected from the U.S. EPA's Toxic Substances Control Act (TSCA) inventory, that were initially screened using the rat uterine cytosolic ER-competitive binding assay. Secondary analysis, using Lineweaver-Burk plots and slope replots, was applied to confirm that only 15 of these test chemicals were true competitive inhibitors of ER binding with experimental inhibition constants (K(i)) less than 100 microM. Two different rapid computational docking methods have been applied. Each provides a score that is a surrogate for the strength of the interaction between each ligand-receptor pair. Using the score that indicates the strongest interaction for each pair, without consideration of the geometry of binding between the toxicant and the target, all of the active molecules were discovered in the first 16% of the chemicals. When a filter is applied on the basis of the geometry of a simplified pharmacophore for binding to

  3. Molecular modeling for screening environmental chemicals for estrogenicity: use of the toxicant-target approach.

    PubMed

    Rabinowitz, James R; Little, Stephen B; Laws, Susan C; Goldsmith, Michael-Rock

    2009-09-01

    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 preliminary evaluation of risk and the establishment of priorities for obtaining missing data for environmental chemicals. The differential step in many mechanisms of toxicity may be generalized as the interaction between a small molecule (a potential toxicant) and one or more macromolecular targets. An approach based on computation of the interaction between a potential molecular toxicant and a library of macromolecular targets of toxicity has been proposed for preliminary chemical screening. In the current study, the interaction between a series of environmentally relevant chemicals and models of the rat estrogen receptors (ER) was computed and the results compared to an experimental data set of their relative binding affinities. The experimental data set consists of 281 chemicals, selected from the U.S. EPA's Toxic Substances Control Act (TSCA) inventory, that were initially screened using the rat uterine cytosolic ER-competitive binding assay. Secondary analysis, using Lineweaver-Burk plots and slope replots, was applied to confirm that only 15 of these test chemicals were true competitive inhibitors of ER binding with experimental inhibition constants (K(i)) less than 100 microM. Two different rapid computational docking methods have been applied. Each provides a score that is a surrogate for the strength of the interaction between each ligand-receptor pair. Using the score that indicates the strongest interaction for each pair, without consideration of the geometry of binding between the toxicant and the target, all of the active molecules were discovered in the first 16% of the chemicals. When a filter is applied on the basis of the geometry of a simplified pharmacophore for binding to

  4. [The modern microbiology in the clinical managing].

    PubMed

    Casal Román, Manuel

    2012-01-01

    The tuberculosis is one of the most important and mortal diseases of the world. The microbiological confirmatory diagnosis and the microbiological therapeutic orientation are fundamental nowadays in the tuberculosis in AIDS and in the Resistant tuberculosis. They are described throughout the time by the classic Microbiology: From 1882 to final 20th century (130 years). With the modern current Microbiology: In the beginning of the 21st century (20-30 years). And as will be done with the future Microbiology: From the years 2020-30. The important advances are outlined in the modern and future clinical microbiology, for the control of the Tuberculosis.

  5. 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.

  6. Microbiological studies on hamburgers

    PubMed Central

    Tamminga, S. K.; Beumer, R. R.; Kampelmacher, E. H.

    1982-01-01

    One hundred and eighty-two raw, 112 pre-cooked and 750 cooked hamburgers composed mainly of beef or beef and pork were subjected to microbiological examination. Raw hamburgers gave total bacterial counts from 106 to 108 per g, counts of Enterobacteriaceae from 104 to 106 per g, of Escherichia coli from 103 to 105, of group D streptococci from 102 to 104, of Staphylococcus aureus from 3 to 102 and of Clostridium perfringens less than 10 bacteria per g. Of the samples, 32% contained salmonellas; the highest most probable number was 102 per g but most estimates were below 1 per g. Corresponding figures for the pre-cooked samples were 2-3 log cycles lower, and only one sample contained salmonella. Yersinia enterocolitica was not isolated from any raw or pre-cooked sample. Three hundred and ninety-five of the cooked hamburgers were prepared by grilling raw hamburgers for between 2 and 5·5 min. These gave total bacterial counts from 105 to 107 per g, and counts of Enterobacteriaceae from 102 to 105 per g. Of the samples, 9·4% contained salmonellas, always in numbers below 1 per g. The remaining 355 cooked hamburgers were prepared from samples pre-cooked for 10 min at 80 °C. Some were grilled and some fat fried. The total bacterial counts were from 103 to 105 per g, and counts of Enterobacteriaceae below 102 per g. Salmonellae, again in small numbers only, were recovered from 3·5% of samples. When hamburgers were artificially contaminated with Salmonella typhimurium it took 5·5 min on a commercial grill, 2·25 min frying in a frying pan and 1·75 min on a household grill to reliably reduce the salmonella count one hundredfold. This means that at many vending places hamburgers are often cooked for too short a time. D-values were determined for S. typhimurium in hamburger meat at 50, 55, 60, 65 and 70 °C, these values were 7·1, 5·1, 1·2, 0·9 and 0·6 min respectively. It can be concluded that the heating action in the centre of the hamburgers will take place more

  7. Imaging mass spectrometry in microbiology

    PubMed Central

    Watrous, Jeramie D.; Dorrestein, Pieter C.

    2013-01-01

    Mass spectrometry tools which allow for the 2-D visualization of the distribution of trace metals, metabolites, surface lipids, peptides and proteins directly from biological samples without the need for chemical tagging or antibodies are becoming increasingly useful for microbiology applications. These tools, comprised of different imaging mass spectrometry techniques, are ushering in an exciting new era of discovery by allowing for the generation of chemical hypotheses based on of the spatial mapping of atoms and molecules that can correlate to or transcend observed phenotypes. In this review, we explore the wide range of imaging mass spectrometry techniques available to microbiologists and describe their unique applications to microbiology with respect to the types of microbiology samples to be investigated. PMID:21822293

  8. 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.

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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

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

    PubMed

    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.

  6. 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%.

  7. [Future applications of mass spectrometry in microbiology].

    PubMed

    Vila, Jordi; Zboromyrska, Yuliya; Burillo, Almudena; Bouza, Emilio

    2016-06-01

    MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) mass spectrometry (MS) has been vigorously introduced in many clinical microbiology laboratories for the rapid and accurate identification of bacteria and fungi. In fact, the implementation of this methodology can be considered a revolution in these laboratories. In addition to microbial identification, MALDI-TOF MS is being used for the detection of some mechanisms of antibiotic resistance and for the molecular typing of bacteria. A number of current and future applications that increase the versatility of this methodology may also be mentioned. Among these are its direct application on clinical samples, the detection of toxins or specific microbial antigens, and its application in the fields of virology and parasitology.

  8. 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...

  9. 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...

  10. Definition of a near real-time microbiological monitor for application in space vehicles

    NASA Technical Reports Server (NTRS)

    Kilgore, Melvin V., Jr.; Zahorchak, Robert J.; Arendale, William F.; Woodward, Samuel S.; Pierson, Duane L.

    1989-01-01

    The concepts and methodologies for microbiological monitoring in space are examined, focusing on the determination of the requirements of a near real-time microbiological monitor. Results are presented from the technical evaluation of five microbiological monitor concepts, including cultural methods, single cell detection, biomolecular detection, specific product detection, and general molecular composition. Within these concepts, twenty-eight specific methodolgies were assessed and the five candidate methodologies with the highest engineering and feasibility scores were selected for further evaluations. The candidate methodologies are laser light scattering, primary fluorescence, secondary fluorescence, volatile product detection, and electronic particle detection. The advantages and disadvantages of these five candidate methodologies are discussed.

  11. 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

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

    PubMed

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

    2016-01-01

    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.

  13. 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

  14. [Application of predictive microbiology in fungi growth and mycotoxin production].

    PubMed

    Wang, Wei; Yu, Hongxia; Li, Fengqin

    2009-11-01

    Food spoilage and food poisoning caused by fungi is an important issue in the field of food safety. The linear regression equations and predictive models are developed through the study on the effect of environmental factors on fungi growth and mycotoxin production. This is easier to understand fungi activities. Predictive microbiology plays an important role in evaluation of food spoilage and food poisoning. The application of predictive modelling in fungi growth and mycotoxin production are reviewed.

  15. Integration of molecular functions at the ecosystemic level: breakthroughs and future goals of environmental genomics and post-genomics

    PubMed Central

    Vandenkoornhuyse, Philippe; Dufresne, Alexis; Quaiser, Achim; Gouesbet, Gwenola; Binet, Françoise; Francez, André-Jean; Mahé, Stéphane; Bormans, Myriam; Lagadeuc, Yvan; Couée, Ivan

    2010-01-01

    Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism–environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored. PMID:20426792

  16. 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.

  17. Microbiology and Human Spaceflight Applications

    NASA Technical Reports Server (NTRS)

    Ott, C. Mark

    2016-01-01

    As humans continue to travel further into space, microorganisms will accompany them. Thus, understanding how microorganisms can impact the crew, the spacecraft, and spacecraft systems is critical to enable future spaceflight exploration. To mitigate microbial risks during spaceflight, NASA relies heavily on preventative measures, including appropriate vehicle design, crew quarantine prior to flight, and extensive microbial monitoring. While these precautions minimize the proliferation of infectious agents, their presence cannot be completely eliminated. Microbiological contamination of vehicle systems can also be a key issue for long duration missions, as system deterioration and fouling have been previously observed in spacecraft. Current studies of the microbiomes of the crew and the International Space Station environment are providing a wealth of information and hold the potential to help refine microbiological requirements for NASA mission beyond low Earth orbit, as spaceflight environments and mission architectures rapidly evolve.

  18. 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.

  19. Microbiological Testing of Skylab Foods

    PubMed Central

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

    1973-01-01

    The Skylab manned space flight program presented unique food microbiology problems. This challenge was successfully met by careful evaluation of the total Skylab food system by considering the nature of Skylab foods, their processing and handling, and Skylab food safety requirements. Some of the unique problems encountered with the Skylab foods involved: extended storage times, variations in storage temperatures, no opportunity to resupply or charge 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 the food as an accurately controlled segment of sophisticated life science experiments. Consideration of all of these situations generated the need for definitive microbiological tests and test limits. These tests are described in this paper along with the rationale for their selection. Test results are reported which show successful compliance with the test limits. Images PMID:4346978

  20. 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

  1. 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.

  2. Microbiological quality of natural waters.

    PubMed

    Borrego, J J; Figueras, M J

    1997-12-01

    Several aspects of the microbiological quality of natural waters, especially recreational waters, have been reviewed. The importance of the water as a vehicle and/or a reservoir of human pathogenic microorganisms is also discussed. In addition, the concepts, types and techniques of microbial indicator and index microorganisms are established. The most important differences between faecal streptococci and enterococci have been discussed, defining the concept and species included. In addition, we have revised the main alternative indicators used to measure the water quality.

  3. [Modified lateral condensation (microbiological analysis)].

    PubMed

    Jácome Musule, J L; Vázquez del Mercado, M A; Hernández, J L; Granillo, N E

    1989-05-01

    In order to ascertain the presence of endodontobacterial flora, an in vivo microbiological study on fifty human teeth with necrotic pulp and periapical bone destruction, is submitted. The study verifies elimination of bacteria through a technique for the preparation of root canals. Results of this research ratify the presence of aerobic and anaerobic microorganisms, as well as the means to inhibit them. That will allow performing obturation under optimal conditions, thus increasing assurance of success in the endodontic therapy.

  4. 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.

  5. Molecular simulations for energy, environmental and pharmaceutical applications of nanoporous materials: from zeolites, metal-organic frameworks to protein crystals.

    PubMed

    Jiang, Jianwen; Babarao, Ravichandar; Hu, Zhongqiao

    2011-07-01

    Nanoporous materials have widespread applications in chemical industry, but the pathway from laboratory synthesis and testing to practical utilization of nanoporous materials is substantially challenging and requires fundamental understanding from the bottom up. With ever-growing computational resources, molecular simulations have become an indispensable tool for material characterization, screening and design. This tutorial review summarizes the recent simulation studies in zeolites, metal-organic frameworks and protein crystals, and provides a molecular overview for energy, environmental and pharmaceutical applications of nanoporous materials with increasing degree of complexity in building blocks. It is demonstrated that molecular-level studies can bridge the gap between physical and engineering sciences, unravel microscopic insights that are otherwise experimentally inaccessible, and assist in the rational design of new materials. The review is concluded with major challenges in future simulation exploration of novel nanoporous materials for emerging applications.

  6. 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

  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.

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

    PubMed

    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

    2011-10-01

    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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 7 CFR 58.528 - Microbiological requirements.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage Cheese Bearing Usda Official Identification § 58.528 Microbiological requirements. Compliance shall...

  15. [Microbiology of ground water and drinking water].

    PubMed

    Dott, W; Frank, C; Kämpfer, P; Tuschewitzki, G J; Wernicke, F

    1986-10-01

    Groundwater has been considered a safe source for drinking water protected against surface contamination. However, a number of reports about chemical and microbiological contamination have disproved this assumption. Besides hygienical monitoring, little is known about the microbiology of ground- and drinking water. The purpose of this paper is to give a review about the main fields of investigation concerning microbial activity in ground- and drinking-water-action. The hygienical relevant topics are: survival and transport of microorganisms, microbiological degradation of organic pollutants, turn-over of nitrogen compounds, oxidation and reduction of iron and manganese and development of methods for microbiological water examination.

  16. Interpretation of Blood Microbiology Results - Function of the Clinical Microbiologist.

    PubMed

    Kristóf, Katalin; Pongrácz, Júlia

    2016-04-01

    The proper use and interpretation of blood microbiology results may be one of the most challenging and one of the most important functions of clinical microbiology laboratories. Effective implementation of this function requires careful consideration of specimen collection and processing, pathogen detection techniques, and prompt and precise reporting of identification and susceptibility results. The responsibility of the treating physician is proper formulation of the analytical request and to provide the laboratory with complete and precise patient information, which are inevitable prerequisites of a proper testing and interpretation. The clinical microbiologist can offer advice concerning the differential diagnosis, sampling techniques and detection methods to facilitate diagnosis. Rapid detection methods are essential, since the sooner a pathogen is detected, the better chance the patient has of getting cured. Besides the gold-standard blood culture technique, microbiologic methods that decrease the time in obtaining a relevant result are more and more utilized today. In the case of certain pathogens, the pathogen can be identified directly from the blood culture bottle after propagation with serological or automated/semi-automated systems or molecular methods or with MALDI-TOF MS (matrix-assisted laser desorption-ionization time of flight mass spectrometry). Molecular biology methods are also suitable for the rapid detection and identification of pathogens from aseptically collected blood samples. Another important duty of the microbiology laboratory is to notify the treating physician immediately about all relevant information if a positive sample is detected. The clinical microbiologist may provide important guidance regarding the clinical significance of blood isolates, since one-third to one-half of blood culture isolates are contaminants or isolates of unknown clinical significance. To fully exploit the benefits of blood culture and other (non- culture

  17. Interpretation of Blood Microbiology Results - Function of the Clinical Microbiologist.

    PubMed

    Kristóf, Katalin; Pongrácz, Júlia

    2016-04-01

    The proper use and interpretation of blood microbiology results may be one of the most challenging and one of the most important functions of clinical microbiology laboratories. Effective implementation of this function requires careful consideration of specimen collection and processing, pathogen detection techniques, and prompt and precise reporting of identification and susceptibility results. The responsibility of the treating physician is proper formulation of the analytical request and to provide the laboratory with complete and precise patient information, which are inevitable prerequisites of a proper testing and interpretation. The clinical microbiologist can offer advice concerning the differential diagnosis, sampling techniques and detection methods to facilitate diagnosis. Rapid detection methods are essential, since the sooner a pathogen is detected, the better chance the patient has of getting cured. Besides the gold-standard blood culture technique, microbiologic methods that decrease the time in obtaining a relevant result are more and more utilized today. In the case of certain pathogens, the pathogen can be identified directly from the blood culture bottle after propagation with serological or automated/semi-automated systems or molecular methods or with MALDI-TOF MS (matrix-assisted laser desorption-ionization time of flight mass spectrometry). Molecular biology methods are also suitable for the rapid detection and identification of pathogens from aseptically collected blood samples. Another important duty of the microbiology laboratory is to notify the treating physician immediately about all relevant information if a positive sample is detected. The clinical microbiologist may provide important guidance regarding the clinical significance of blood isolates, since one-third to one-half of blood culture isolates are contaminants or isolates of unknown clinical significance. To fully exploit the benefits of blood culture and other (non- culture

  18. 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

  19. 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.

  20. MICROBIOLOGICAL QUALITY OF FOOD SUPPLEMENTS.

    PubMed

    Ratajczak, Magdalena; Kubicka, Marcelina M; Kamińska, Dorota; Długaszewska, Jolanta

    2015-01-01

    Many specialists note that the food offered today - as a result of very complex technological processing - is devoid of many components that are important for the organism and the shortages have to be supplemented. The simplest for it is to consume diet supplements that provide the missing element in a concentrated form. In accordance with the applicable law, medicinal products include all substances or mixtures of substances that are attributed with properties of preventing or treating diseases with humans or animals. Permits to admit supplements to the market are issued by the Chief Sanitary Inspector and the related authorities; permits for medicines are issued by the Chief Pharmaceutical Inspector and the Office for Registration of Medicinal Products, Medical Devices and Biocidal Products. Therefore, admittance of a supplement to the market is less costly and time consuming_than admittance of a medicine. Supplements and medicines may contain the same component but medicines will have a larger concentration than supplements. Sale of supplements at drug stores and in the form of tablets, capsules, liquids or powders makes consumer often confusing supplements with medicines. Now there are no normative documents specifying limits of microbiological impurities in diet supplements. In Polish legislation, diet supplements are subject to legal acts concerning food. Medicines have to comply with microbiological purity requirements specified in the Polish Pharmacopeia. As evidenced with the completed tests, the proportion of diet supplement samples with microbiological impurities is 6.5%. Sales of diet supplements have been growing each year, they are consumed by healthy people but also people with immunology deficiencies and by children and therefore consumers must be certain that they buy safe products. PMID:26642690

  1. 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)

  2. 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

  3. 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.

  4. Microbiology Learning and Education Online

    PubMed Central

    Niño, Silvia M.

    2016-01-01

    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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Molecular mechanisms of environmental enrichment: impairments in Akt/GSK3β, neurotrophin-3 and CREB signaling.

    PubMed

    Hu, Yuan-Shih; Long, Nancy; Pigino, Gustavo; Brady, Scott T; Lazarov, Orly

    2013-01-01

    Experience of mice in a complex environment enhances neurogenesis and synaptic plasticity in the hippocampus of wild type and transgenic mice harboring familial Alzheimer's disease (FAD)-linked APPswe/PS1ΔE9. In FAD mice, this experience also reduces levels of tau hyperphosphorylation and oligomeric β-amyloid. Although environmental enrichment has significant effects on brain plasticity and neuropathology, the molecular mechanisms underlying these effects are unknown. Here we show that environmental enrichment upregulates the Akt pathway, leading to the downregulation of glycogen synthase kinase 3β (GSK3β), in wild type but not FAD mice. Several neurotrophic signaling pathways are activated in the hippocampus of both wild type and FAD mice, including brain derived neurotrophic factor (BDNF) and nerve growth factor (NGF), and this increase is accompanied by the upregulation of the BDNF receptor, tyrosine kinase B (TrkB). Interestingly, neurotrophin-3 (NT-3) is upregulated in the brains of wild type mice but not FAD mice, while insulin growth factor-1 (IGF-1) is upregulated exclusively in the brains of FAD mice. Upregulation of neurotrophins is accompanied by the increase of N-Methyl-D-aspartic acid (NMDA) receptors in the hippocampus following environmental enrichment. Most importantly, we observed a significant increase in levels of cAMP response element- binding (CREB) transcripts in the hippocampus of wild type and FAD mice following environmental enrichment. However, CREB phosphorylation, a critical step for the initiation of learning and memory-required gene transcription, takes place in the hippocampus of wild type but not of FAD mice. These results suggest that experience of wild type mice in a complex environmental upregulates critical signaling that play a major role in learning and memory in the hippocampus. However, in FAD mice, some of these pathways are impaired and cannot be rescued by environmental enrichment.

  12. Molecular Mechanisms of Environmental Enrichment: Impairments in Akt/GSK3β, Neurotrophin-3 and CREB Signaling

    PubMed Central

    Hu, Yuan-Shih; Long, Nancy; Pigino, Gustavo; Brady, Scott T.; Lazarov, Orly

    2013-01-01

    Experience of mice in a complex environment enhances neurogenesis and synaptic plasticity in the hippocampus of wild type and transgenic mice harboring familial Alzheimer's disease (FAD)-linked APPswe/PS1ΔE9. In FAD mice, this experience also reduces levels of tau hyperphosphorylation and oligomeric β-amyloid. Although environmental enrichment has significant effects on brain plasticity and neuropathology, the molecular mechanisms underlying these effects are unknown. Here we show that environmental enrichment upregulates the Akt pathway, leading to the downregulation of glycogen synthase kinase 3β (GSK3β), in wild type but not FAD mice. Several neurotrophic signaling pathways are activated in the hippocampus of both wild type and FAD mice, including brain derived neurotrophic factor (BDNF) and nerve growth factor (NGF), and this increase is accompanied by the upregulation of the BDNF receptor, tyrosine kinase B (TrkB). Interestingly, neurotrophin-3 (NT-3) is upregulated in the brains of wild type mice but not FAD mice, while insulin growth factor-1 (IGF-1) is upregulated exclusively in the brains of FAD mice. Upregulation of neurotrophins is accompanied by the increase of N-Methyl-D-aspartic acid (NMDA) receptors in the hippocampus following environmental enrichment. Most importantly, we observed a significant increase in levels of cAMP response element- binding (CREB) transcripts in the hippocampus of wild type and FAD mice following environmental enrichment. However, CREB phosphorylation, a critical step for the initiation of learning and memory-required gene transcription, takes place in the hippocampus of wild type but not of FAD mice. These results suggest that experience of wild type mice in a complex environmental upregulates critical signaling that play a major role in learning and memory in the hippocampus. However, in FAD mice, some of these pathways are impaired and cannot be rescued by environmental enrichment. PMID:23700479

  13. Humic substances biological activity at the plant-soil interface: from environmental aspects to molecular factors.

    PubMed

    Trevisan, Sara; Francioso, Ornella; Quaggiotti, Silvia; Nardi, Serenella

    2010-06-01

    Humic substances (HS) represent the organic material mainly widespread in nature. HS have positive effects on plant physiology by improving soil structure and fertility and by influencing nutrient uptake and root architecture. The biochemical and molecular mechanisms underlying these events are only partially known. HS have been shown to contain auxin and an "auxin-like" activity of humic substances has been proposed, but support to this hypothesis is fragmentary. In this review article, we are giving an overview of available data concerning molecular structures and biological activities of humic substances, with special emphasis on their hormone-like activities. PMID:20495384

  14. 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.

  15. Microbiological Food Safety Surveillance in China.

    PubMed

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

    2015-09-01

    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.

  16. 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

  17. The Automated Clinical Microbiology Laboratory: Fact or Fantasy?

    PubMed Central

    2014-01-01

    Automated chemistry laboratories dependent on robotic processes are the standard in both academic and large community hospital settings. Diagnostic microbiology manufacturers are betting that robotics will be used for specimen processing, plate reading, and organism identification in the near future. These systems are highly complex and have large footprints and hefty price tags. However, they are touted as being more efficient, rapid, and accurate than standard processes. Certain features, such as image collection, are highly innovative. Hospital administrators may be swayed to institute these new systems because of the promise of the need for fewer skilled workers, higher throughput, and greater efficiency. They also may be swayed by the fact that workers with the requisite clinical microbiology skills are becoming more difficult to find, and this technology should allow fewer skilled workers to handle larger numbers of cultures. In this Point-Counterpoint, Nate Ledeboer, Medical Director, Clinical Microbiology and Molecular Diagnostics, Dynacare Laboratories, and Froedtert Hospital, Milwaukee, WI, will explain why he believes that this approach will become widespread, while Steve Dallas of the University of Texas Health Science Center San Antonio explains why he thinks that this automation may not become widely used. PMID:24648549

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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...

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. [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

  13. 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

  14. 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.

  15. 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

  16. 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

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

    PubMed

    Jiang, Xingfu; Luo, Lizhi; Zhang, Lei; Sappington, Thomas W; Hu, Yi

    2011-06-01

    Each year the Mythimna separate (Walker), undertakes a seasonal, long-distance, multigeneration roundtrip migration between southern and northern China. Despite its regularity, the decision to migrate is facultative, and is controlled by environmental, physiological, hormonal, genetic, and molecular factors. Migrants take off on days 1 or 2 after eclosion, although the preoviposition period lasts ≈7 d. The trade-offs among the competing physiological demands of migration and reproduction are coordinated in M. separata by the "oogenesis-flight syndrome." Larvae that experience temperatures above or below certain thresholds accompanied by appropriate humidity, short photoperiod, poor nutrition, and moderate density tend to develop into migrants. However, there is a short window of sensitivity within 24 h after adult eclosion when migrants can be induced to switch to reproductive residents if they encounter extreme environmental factors including starvation, low temperature and long photoperiod. Juvenile hormone (JH) titer is low before migration but high titers are associated with termination of migratory behavior and the switch to reproduction. Early release of JH by the corpora allata in environmentally stressed 1-d old adults, otherwise destined by larval conditions to be migrants, switches them to residents. Offspring inherit parental additive genetic effects governing migratory behavior. However, they also retain flexibility in expression of both flight and reproductive life history traits. The insect neuropeptide, allatotropin, which activates corpora allata to synthesize JH, controls adult flight and reproduction. Future research directions to better understand regulation of migration in this species are discussed.

  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. 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

  1. 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

  2. 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.

  3. 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.

  4. Isolation and molecular characterization of Salmonella enterica serovar Javiana from food, environmental and clinical samples.

    PubMed

    Mezal, Ezat H; Stefanova, Rossina; Khan, Ashraf A

    2013-06-01

    A total of 50 Salmonella enterica serovar Javiana isolates, isolated from food, environmental and clinical samples, were analyzed for antibiotic resistance, presence of virulence genes, plasmids and plasmid replicon types. To assess the genetic diversity, pulsed-field gel electrophoresis (PFGE) fingerprinting and plasmid profiles were performed. All of the isolates were sensitive to chloramphenicol, nalidixic acid, and sulfisoxazole, and four isolates showed intermediate resistance to gentamicin or kanamycin. Eleven isolates, including representatives from each of the source types, were resistant to ampicillin. Four isolates from either clinical or environmental sources were resistant to tetracycline, while an additional 20 isolates showed intermediate resistance to this drug. Fourteen isolates, primarily from food sources, showed intermediate resistance to streptomycin. The S. Javiana isolates were screened by PCR for 17 virulence genes (spvB, spiA, pagC, msgA, invA, sipB, prgH, spaN, orgA, tolC, iroN, sitC, IpfC, sifA, sopB, cdtB, and pefA). All isolates were positive for nine to fourteen of these genes, but none were positive for pefA, spvB and lpfC, which are typically present on the Salmonella virulence plasmid. Seven of the virulence genes including cdtB were found in all 50 isolates, suggesting that S. Javiana from food and environmental sources had virulence similar to clinical isolates. Four clinical isolates and two food isolates carried one or more plasmids of approximately 30, 38, and 58 kb, with the 58 kb plasmids belonging to incompatibility group IncFIIA. Two clinical isolates carried IncI1 type mega plasmid (80 kb), and one clinical isolate carried plasmids of 4.5 and 7 kb. The PFGE profiles resulted 34 patterns in five clusters at a 90% similarity threshold. Our results indicate that S. Javiana isolates have a diverse clonal population among the clinical, food and environmental samples and this serotype possesses several virulent genes and plasmids

  5. Clinical microbiology: Should microbiology be a clinical or a laboratory speciality?

    PubMed

    Bhattacharya, Sanjay

    2010-01-01

    Clinical microbiology is a specific combination of knowledge, attitude and practice aimed at direct clinical involvement in infectious disease management using the core principles of medical microbiology and clinical medicine. In this article certain areas in microbiology, where a more proactive approach could make a significant difference in clinical outcome has been delineated. The article reiterates the role of a medical microbiologist in a hospital setting. The practices described are the norm in well-organized hospitals. These areas include management of positive blood cultures, management of patients in intensive care units (ICUs), hospital infection control and public health microbiology, development of hospital and community anti-infective policy, organization of clinical-microbiological meetings and provision of emergency out-of-hours service. The implementation of this clinical approach and increased engagement with direct patient care would require changes in existing training structure and working patterns of medical and technical staffs in microbiology.

  6. 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.

  7. 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

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

    PubMed

    Skinner, Michael K

    2015-04-26

    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.

  9. Molecular screening of 246 Portuguese Aspergillus isolates among different clinical and environmental sources.

    PubMed

    Sabino, Raquel; Veríssimo, Cristina; Parada, Helena; Brandão, João; Viegas, Carla; Carolino, Elisabete; Clemons, Karl V; Stevens, David A

    2014-07-01

    Clinical and environmental samples from Portugal were screened for the presence of Aspergillus and the distributions of the species complexes were determined in order to understand how their distributions differ based on their source. Fifty-seven Aspergillus isolates from clinical samples were collected from 10 health institutions. Six species complexes were detected by internal transcribed spacer sequencing; Fumigati, Flavi, and Nigri were found most frequently (50.9%, 21.0%, and 15.8%, respectively). β-tubulin and calmodulin sequencing resulted in seven cryptic species (A. awamorii, A. brasiliensis, A. fructus, A. lentulus, A. sydowii, A. tubingensis, Emericella echinulata) being identified among the 57 isolates. Thirty-nine isolates of Aspergillus were recovered from beach sand and poultry farms, 31 from swine farms, and 80 from hospital environments, for a total 189 isolates. Eleven species complexes were found in these 189 isolates, and those belonging to the Versicolores species complex were found most frequently (23.8%). There was a significant association between the different environmental sources and distribution of the species complexes; the hospital environment had greater variability of species complexes than other environmental locations. A high prevalence of cryptic species within the Circumdati complex was detected in several environments; from the isolates analyzed, at least four cryptic species were identified, most of them growing at 37ºC. Because Aspergillus species complexes have different susceptibilities to antifungals, knowing the species-complex epidemiology for each setting, as well as the identification of cryptic species among the collected clinical isolates, is important. This may allow preventive and corrective measures to be taken, which may result in decreased exposure to those organisms and a better prognosis.

  10. Environmental Risk Factors for Multiple Sclerosis: A Review with a Focus on Molecular Mechanisms

    PubMed Central

    O’Gorman, Cullen; Lucas, Robyn; Taylor, Bruce

    2012-01-01

    Multiple sclerosis (MS) is a chronic disabling disease of the central nervous system commonly affecting young adults. Pathologically, there are patches of inflammation (plaques) with demyelination of axons and oligodendrocyte loss. There is a global latitude gradient in MS prevalence, and incidence of MS is increasing (particularly in females). These changes suggest a major role for environmental factors in causation of disease. We have reviewed the evidence and potential mechanisms of action for three exposures: vitamin D, Epstein Barr virus and cigarette smoking. Recent advances supporting gene-environment interactions are reviewed. Further research is needed to establish mechanisms of causality in humans and to explore preventative strategies. PMID:23109880

  11. 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

  12. 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.

  13. Even therapeutic antimicrobial use in animal husbandry may generate environmental hazards to human health.

    PubMed

    Cabello, Felipe C; Godfrey, Henry P

    2016-02-01

    The potential negative impact for human health of veterinary use of antimicrobials in prophylaxis, metaphylaxis and growth promotion in animal husbandry was first established in the 1960s and 1970s. Determination of the molecular structure of antimicrobial resistance plasmids at that time explained the ability of antimicrobial resistance genes to disseminate among bacterial populations and elucidated the reasons for the negative effects of antimicrobials used in food animals for human health. In this issue of Environmental Microbiology, Liu et al. (2016) show that even therapeutic use of antimicrobials in dairy calves has an appreciable environmental microbiological footprint. We discuss the negative implications of this footprint for human health and the possibility they may lead to calls for increased regulation of veterinary antimicrobial use in terrestrial and aquatic environments.

  14. Even therapeutic antimicrobial use in animal husbandry may generate environmental hazards to human health.

    PubMed

    Cabello, Felipe C; Godfrey, Henry P

    2016-02-01

    The potential negative impact for human health of veterinary use of antimicrobials in prophylaxis, metaphylaxis and growth promotion in animal husbandry was first established in the 1960s and 1970s. Determination of the molecular structure of antimicrobial resistance plasmids at that time explained the ability of antimicrobial resistance genes to disseminate among bacterial populations and elucidated the reasons for the negative effects of antimicrobials used in food animals for human health. In this issue of Environmental Microbiology, Liu et al. (2016) show that even therapeutic use of antimicrobials in dairy calves has an appreciable environmental microbiological footprint. We discuss the negative implications of this footprint for human health and the possibility they may lead to calls for increased regulation of veterinary antimicrobial use in terrestrial and aquatic environments. PMID:26913818

  15. 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

  16. 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)

  17. 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)

  18. 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

  19. 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 ...

  20. 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... Goals and Maximum Residual Disinfectant Level Goals § 141.52 Maximum contaminant level goals...

  1. 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... Goals and Maximum Residual Disinfectant Level Goals § 141.52 Maximum contaminant level goals...

  2. 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... Goals and Maximum Residual Disinfectant Level Goals § 141.52 Maximum contaminant level goals...

  3. 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... Goals and Maximum Residual Disinfectant Level Goals § 141.52 Maximum contaminant level goals...

  4. 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... Goals and Maximum Residual Disinfectant Level Goals § 141.52 Maximum contaminant level goals...

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Molecular subtyping of Vibrio cholerae O1 strains recently isolated from patient, food and environmental samples in Spain.

    PubMed

    Usera, M A; Echeita, A; Olsvik, O; Evins, G M; Cameron, D N; Popovic, T

    1994-04-01

    Nineteen Vibrio cholerae O1 strains isolated in Spain from patient, food and environmental samples in the period 1990-1992 were characterized by detection of cholera toxin by enzyme immunoassay, detection of cholera toxin gene by polymerase chain reaction, and by biotyping, ribotyping and pulsed-field gel electrophoresis. Ten isolates were toxigenic and were further characterized by multilocus enzyme electrophoresis. Molecular subtyping methods allowed precise differentiation between isolates, indicating their geographic origin. Isolates associated with the ongoing seventh pandemic were distinguishable from those associated with the present Latin American epidemic. All isolates from the environment and seafood were nontoxigenic, and were genetically different and more diverse than toxigenic isolates. The data suggest that a focus of endemic cholera does not exist in Spain, and that the analyzed nontoxigenic Vibrio cholerae O1 isolates from imported seafood were not a threat to public health.

  10. 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.

  11. Dissecting microbiological systems using materials science.

    PubMed

    Muralimohan, Abishek; Eun, Ye-Jin; Bhattacharyya, Basudeb; Weibel, Douglas B

    2009-03-01

    Materials science offers microbiologists a wide variety of organic and inorganic materials with chemical and physical properties that can be precisely controlled. These materials present new capabilities for isolating, manipulating and studying bacteria and other microorganisms and are poised to transform microbiology. This review summarizes three classes of materials that span a range of length scales (nano, micro and meso) and describes a variety of fundamental questions in microbiology that can be studied by leveraging their properties.

  12. 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.

  13. 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).

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. Environmentally induced epigenetic transgenerational inheritance of altered Sertoli cell transcriptome and epigenome: molecular etiology of male infertility.

    PubMed

    Guerrero-Bosagna, Carlos; Savenkova, Marina; Haque, Md Muksitul; Nilsson, Eric; Skinner, Michael K

    2013-01-01

    Environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of adult onset disease, including testis disease and male infertility. The current study was designed to determine the impact of an altered sperm epigenome on the subsequent development of an adult somatic cell (Sertoli cell) that influences the onset of a specific disease (male infertility). A gestating female rat (F0 generation) was exposed to the agriculture fungicide vinclozolin during gonadal sex determination and then the subsequent F3 generation progeny used for the isolation of Sertoli cells and assessment of testis disease. As previously observed, enhanced spermatogenic cell apoptosis was observed. The Sertoli cells provide the physical and nutritional support for the spermatogenic cells. Over 400 genes were differentially expressed in the F3 generation control versus vinclozolin lineage Sertoli cells. A number of specific cellular pathways were identified to be transgenerationally altered. One of the key metabolic processes affected was pyruvate/lactate production that is directly linked to spermatogenic cell viability. The Sertoli cell epigenome was also altered with over 100 promoter differential DNA methylation regions (DMR) modified. The genomic features and overlap with the sperm DMR were investigated. Observations demonstrate that the transgenerational sperm epigenetic alterations subsequently alters the development of a specific somatic cell (Sertoli cell) epigenome and transcriptome that correlates with adult onset disease (male infertility). The environmentally induced epigenetic transgenerational inheritance of testis disease appears to be a component of the molecular etiology of male infertility.

  2. 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.

  3. Environmental effects on molecular and phenotypic variation in populations of Eruca sativa across a steep climatic gradient

    PubMed Central

    Westberg, Erik; Ohali, Shachar; Shevelevich, Anatoly; Fine, Pinchas; Barazani, Oz

    2013-01-01

    steep climatic gradient. In addition to molecular marker data, we made use of phenotypic evaluation from common garden experiments, and a broad GIS based environmental data with edaphic information gathered in the field. This study, among others, lead to the identification of an outlier locus with an association to trichome formation and herbivore defense, and its ecological adaptive value is discussed. PMID:24567822

  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. 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.

  6. Mineral-organic-microbe interactions: Environmental impacts from molecular to macroscopic scales

    NASA Astrophysics Data System (ADS)

    Vaughan, David J.; Lloyd, Jonathan R.

    2011-02-01

    The role of microbes in geological processes is discussed with particular reference to the geochemical cycle involving iron. Microbial oxidation of Fe(II) minerals can occur via at least three mechanisms, the most important involving acidophilic prokaryotes which promote oxidation of iron sulphides. Accelerated breakdown of arsenopyrite is a good example, where multi-step electrochemical reactions are facilitated by the presence of organisms such as Leptospirillum ferrooxidans. Other organisms actively promote the reduction of Fe(III) to more soluble Fe(II). Reduction rates are highly variable, depending on mineral substrate, with oxyhydroxides being most reactive. Proper understanding of such redox processes requires knowledge of interactions at the molecular scale. Advances are being made through genetic studies of relevant organisms, and of mineral surfaces as exemplified by our experimental and computational studies of iron oxides such as magnetite, the reaction of which with simple organic molecules shows diverse behaviour. Mineral-organic interactions precede formation of bacterial biofilms, which can create local geochemical environments causing mineral precipitation. Biofilms and precipitate phases can have a major influence on fluid flow through fractures or porous media as we demonstrate using experiments from micro- to macro-scales.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. Influence of density and environmental factors on decomposition kinetics of amorphous polylactide - Reactive molecular dynamics studies.

    PubMed

    Mlyniec, A; Ekiert, M; Morawska-Chochol, A; Uhl, T

    2016-06-01

    In this work, we investigate the influence of the surrounding environment and the initial density on the decomposition kinetics of polylactide (PLA). The decomposition of the amorphous PLA was investigated by means of reactive molecular dynamics simulations. A computational model simulates the decomposition of PLA polymer inside the bulk, due to the assumed lack of removal of reaction products from the polymer matrix. We tracked the temperature dependency of the water and carbon monoxide production to extract the activation energy of thermal decomposition of PLA. We found that an increased density results in decreased activation energy of decomposition by about 50%. Moreover, initiation of decomposition of the amorphous PLA is followed by a rapid decline in activation energy caused by reaction products which accelerates the hydrolysis of esters. The addition of water molecules decreases initial energy of activation as well as accelerates the decomposition process. Additionally, we have investigated the dependency of density on external loading. Comparison of pressures needed to obtain assumed densities shows that this relationship is bilinear and the slope changes around a density equal to 1.3g/cm(3). The conducted analyses provide an insight into the thermal decomposition process of the amorphous phase of PLA, which is particularly susceptible to decomposition in amorphous and semi-crystalline PLA polymers.

  12. 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

  13. Development of an effective method for recovery of viral genomic RNA from environmental silty sediments for quantitative molecular detection.

    PubMed

    Miura, Takayuki; Masago, Yoshifumi; Sano, Daisuke; Omura, Tatsuo

    2011-06-01

    Nine approaches to recover viral RNA from environmental silty sediments were newly developed and compared to quantify RNA viruses in sediments using molecular methods. Four of the nine approaches employed direct procedures for extracting RNA from sediments (direct methods), and the remaining five approaches used indirect methods wherein viral particles were recovered before RNA extraction. A direct method using an SDS buffer with EDTA to lyse viral capsids in sediments, phenol-chloroform-isoamyl alcohol to extract RNA, isopropanol to concentrate RNA, and magnetic beads to purify RNA resulted in the highest rate of recovery (geometric mean of 11%, with a geometric standard deviation of 0.02; n = 7) of poliovirus 1 (PV1) inoculated in an environmental sediment sample. The direct method exhibiting the highest rate of PV1 recovery was applied to environmental sediment samples. One hundred eight sediment samples were collected from the Takagi River, Miyagi, Japan, and its estuary from November 2007 to April 2009, and the genomic RNAs of enterovirus and human norovirus in these samples were quantified by reverse transcription (RT)-quantitative PCR (qPCR). The human norovirus genome was detected in one sample collected at the bay, although its concentration was below the quantification limit. Meanwhile, the enterovirus genome was detected in two samples at the river mouth and river at concentrations of 8.6 × 10(2) and 2.4 × 10(2) copies/g (wet weight), respectively. This is the first report to obtain quantitative data for a human pathogenic virus in a river and in estuarine sediments using RT-qPCR.

  14. 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.

  15. Molecular Control of TiO2-NPs Toxicity Formation at Predicted Environmental Relevant Concentrations by Mn-SODs Proteins

    PubMed Central

    Wu, Qiuli; Li, Yiping; Tang, Meng; Ye, Boping; Wang, Dayong

    2012-01-01

    With growing concerns of the safety of nanotechnology, the in vivo toxicity of nanoparticles (NPs) at environmental relevant concentrations has drawn increasing attentions. We investigated the possible molecular mechanisms of titanium nanoparticles (Ti-NPs) in the induction of toxicity at predicted environmental relevant concentrations. In nematodes, small sizes (4 nm and 10 nm) of TiO2-NPs induced more severe toxicities than large sizes (60 nm and 90 nm) of TiO2-NPs on animals using lethality, growth, reproduction, locomotion behavior, intestinal autofluorescence, and reactive oxygen species (ROS) production as endpoints. Locomotion behaviors could be significantly decreased by exposure to 4-nm and 10-nm TiO2-NPs at concentration of 1 ng/L in nematodes. Among genes required for the control of oxidative stress, only the expression patterns of sod-2 and sod-3 genes encoding Mn-SODs in animals exposed to small sizes of TiO2-NPs were significantly different from those in animals exposed to large sizes of TiO2-NPs. sod-2 and sod-3 gene expressions were closely correlated with lethality, growth, reproduction, locomotion behavior, intestinal autofluorescence, and ROS production in TiO2-NPs-exposed animals. Ectopically expression of human and nematode Mn-SODs genes effectively prevented the induction of ROS production and the development of toxicity of TiO2-NPs. Therefore, the altered expression patterns of Mn-SODs may explain the toxicity formation for different sizes of TiO2-NPs at predicted environmental relevant concentrations. In addition, we demonstrated here a strategy to investigate the toxicological effects of exposure to NPs upon humans by generating transgenic strains in nematodes for specific human genes. PMID:22973466

  16. 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.

  17. Environmental impacts of steel slag reused in road construction: a crystallographic and molecular (XANES) approach.

    PubMed

    Chaurand, Perrine; Rose, Jerome; Briois, Valérie; Olivi, Luca; Hazemann, Jean-Louis; Proux, Olivier; Domas, Jérémie; Bottero, Jean-Yves

    2007-01-31

    Basic oxygen furnace (BOF) steel slag is a residue from the basic oxygen converter in steel-making operations, and is partially reused as an aggregate for road constructions. Although BOF slag is an attractive building material, its long-term behaviour and the associated environmental impacts must be taken into account. Indeed BOF slag is mainly composed of calcium, silicon and iron but also contains trace amounts of potential toxic elements, specifically chromium and vanadium, which can be released. The present research focuses (i) on the release of Cr and V during leaching and (ii) on their speciation within the bearing phase. Indeed the mobility and toxicity of heavy metals strongly depend on their speciation. Leaching tests show that only low amounts of Cr, present at relatively high concentration in steel slag, are released while the release of V is significantly high. X-ray absorption near-edge structure (XANES) spectroscopy indicates that Cr is present in the less mobile and less toxic trivalent form and that its speciation does not evolve during leaching. On the contrary, V which is predominantly present in the 4+ oxidation state seems to become oxidized to the pentavalent form (the most toxic form) during leaching.

  18. Molecular and physiological effects of environmental UV radiation on fungal conidia.

    PubMed

    Braga, Gilberto U L; Rangel, Drauzio E N; Fernandes, Éverton K K; Flint, Stephan D; Roberts, Donald W

    2015-08-01

    Conidia are specialized structures produced at the end of the asexual life cycle of most filamentous fungi. They are responsible for fungal dispersal and environmental persistence. In pathogenic species, they are also involved in host recognition and infection. Conidial production, survival, dispersal, germination, pathogenicity and virulence can be strongly influenced by exposure to solar radiation, although its effects are diverse and often species dependent. UV radiation is the most harmful and mutagenic waveband of the solar spectrum. Direct exposure to solar radiation for a few hours can kill conidia of most fungal species. Conidia are killed both by solar UV-A and UV-B radiation. In addition to killing conidia, which limits the size of the fungal population and its dispersion, exposures to sublethal doses of UV radiation can reduce conidial germination speed and virulence. The focus of this review is to provide an overview of the effects of solar radiation on conidia and on the major systems involved in protection from and repair of damage induced by solar UV radiation. The efforts that have been made to obtain strains of fungi of interest such as entomopathogens more tolerant to solar radiation will also be reviewed.

  19. Molecular characterization of a potato MAP kinase transcriptionally regulated by multiple environmental stresses.

    PubMed

    Blanco, Flavio Antonio; Zanetti, María Eugenia; Casalongué, Claudia Anahí; Daleo, Gustavo Raúl

    2006-01-01

    The MAPK cascade is an evolutionary conserved signaling pathway that links external stimuli with cellular responses. Using polymerase chain reaction (PCR), a DNA fragment corresponding to a Solanum tuberosum MAPK, StMPK1, was isolated. StMPK1 amino acid sequence displayed over 90% identity with tomato MPK1 (LeMPK1) and tobacco SIPK. Southern blot analysis indicated that the gene encoding StMPK1 is present in a single copy in the potato genome. StMPK1 mRNA levels differentially accumulated in potato tuber in response to wounding and to wounding plus Fusarium solani f. sp. eumartii. Transcript accumulation after infection was transient and started earlier than what was observed in wounded tubers. StMPK1 mRNA levels also increased in potato tuber after 24 h of treatment with jasmonic acid (JA) and abscicic acid (ABA), but not in response to ethylene or salicylic acid. In addition, StMPK1 transcript levels increased after a heat-shock treatment at 42 degrees C. The results suggest that StMPK1 may participate in the cellular responses against multiple environmental stimuli in potato tubers.

  20. N2 fixation in marine heterotrophic bacteria: dynamics of environmental and molecular regulation.

    PubMed Central

    Coyer, J A; Cabello-Pasini, A; Swift, H; Alberte, R S

    1996-01-01

    Molecular and immunological techniques were used to examine N2 fixation in a ubiquitous heterotrophic marine bacterium, the facultative anaerobic Vibrio natriegens. When batch cultures were shifted from aerobic N-replete to anaerobic N-deplete conditions, transcriptional and post-translational regulation of N2 fixation was observed. Levels of nifHDK mRNA encoding the nitrogenase enzyme were highest at 140 min postshift and undetectable between 6 and 9 h later. Immunologically determined levels of nitrogenase enzyme (Fe protein) were highest between 6 and 15 h postshift, and nitrogenase activity peaked between 6 and 9 h postshift, declining by a factor of 2 after 12-15 h. Unlike their regulation in cyanobacteria, Fe protein and nitrogenase activity were present when nifHDK mRNA was absent in V. natriegens, indicating that nitrogenase is stored and stable under anaerobic conditions. Both nifHDK mRNA and Fe protein disappeared within 40 min after cultures were shifted from N2-fixing conditions (anaerobic, N-deplete) to non- N2-fixing conditions (aerobic, N-enriched) but reappeared when shifted to conditions favoring N2 fixation. Thus, unlike other N2-fixing heterotrophic bacteria, nitrogenase must be resynthesized after aerobic exposure in V. natriegens. Immunological detection based on immunoblot (Western) analysis and immunogold labeling correlated positively with nitrogenase activity; no localization of nitrogenase was observed. Because V. natriegens continues to fix N2 for many hours after anaerobic induction, this species may play an important role in providing "new" nitrogen in marine ecosystems. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:11607653

  1. Virulence, serotype, and molecular characteristics of environmental strains of Cryptococcus neoformans var. gattii.

    PubMed Central

    Kwon-Chung, K J; Wickes, B L; Stockman, L; Roberts, G D; Ellis, D; Howard, D H

    1992-01-01

    Four strains of Cryptococcus neoformans var. gattii originating from Eucalyptus camaldulensis, three from Australia and one from San Francisco, were tested for their serotype, virulence for mice, and a number of genetic and molecular characteristics. All were found to be serotype B and showed significantly higher virulence for mice than did the type strains of C. neoformans var. gattii and Filobasidiella neoformans var. bacillispora, which were obtained from human cryptococcosis cases. Electrophoretic karyotypes of the strains from Australia were identical, although they were collected from sites at least 15 to 500 km apart. The electrophoretic karyotype of the strain from San Francisco was the same as that of the Australian isolates except for the mobility of one chromosome. On the contrary, no two isolates of serotype B (of a total of 11) from clinical sources were the same, regardless of their geographic origin. Furthermore, none of the clinical isolates showed a chromosomal banding pattern identical to that of Eucalyptus-originated strains. The Eucalyptus-originated strains failed to form dikaryons when crossed with the tester strains of the two varieties of F. neoformans. Hybridization analysis with a nucleic acid probe (AccuProbe C. neoformans Culture Confirmation Test; Gen-Probe Inc., San Diego, Calif.), however, showed signals of equal intensity for clinical strains and the Eucalyptus-originated strains. Various fungi phylogenetically related to C. neoformans, including a phenol oxidase-positive strain of Cryptococcus laurentii obtained from E. camaldulensis, were negative in the nucleic acid hybridization test. These observations confirm that, in spite of karyotypic differences and the lack of dikaryon formation with the tester strains of F. neoformans, Eucalyptus-originated C. neoformans var. gattii is the same organism as those isolated from cases of human infection. Furthermore, the C. neoformans culture confirmation test using a commercial nucleic acid

  2. 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.

  3. 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

  4. A molecular dosimetry approach to assess human exposure to environmental tobacco smoke in pubs.

    PubMed

    Besaratinia, A; Maas, L M; Brouwer, E M C; Moonen, E J C; De Kok, T M C M; Wesseling, G J; Loft, S; Kleinjans, J C S; Van Schooten, F J

    2002-07-01

    Although the involvement of environmental tobacco smoke (ETS) in human lung cancer is no longer a matter of dispute, the magnitude of its impact still is. This is mainly due to the inefficiency of methodology to assess exposure to ETS especially in public places. Setting a real life exposure condition (3 h stay in local pubs) and using a matched-control study design, we quantified smoke-related DNA adducts in induced sputum and peripheral blood lymphocytes (PBL) of healthy non-smokers (n = 15) before and after a single pub visit by means of the (32)P-post-labeling assay. For verification, we also measured a spectrum of polycyclic aromatic hydrocarbons (PAH) in the ambient air of the pubs by personal air monitors, and determined the plasma concentrations of nicotine and cotinine by gas chromatography/mass spectrometry. The ambient air concentrations of all PAH were several orders of magnitude higher than those already reported for other indoor environments. The plasma concentrations of both nicotine and cotinine increased significantly after the pub visit (P = 0.001 and P = 0.0007, respectively). Accordingly, the overall DNA adduct profile in induced sputum, but not in PBL, changed quantitatively and qualitatively after the pub visit. Of most significance was the formation of a distinct DNA adduct in induced sputum of three individuals consequent to ETS exposure. This adduct co-migrated with the standard (+/-)-anti-benzo[a]pyrene diol epoxide-DNA adduct, which is known to form at lung cancer mutational hotspots. We conclude that real life exposure to ETS can give rise to pro-mutagenic lesions in the lower airway, and this can be best investigated in a relevant surrogate matrix such as induced sputum. PMID:12117775

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. IPMP 2013--a comprehensive data analysis tool for predictive microbiology.

    PubMed

    Huang, Lihan

    2014-02-01

    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 exposed to complex environmental changes during processing, transportation, distribution, and storage. It finds applications in shelf-life prediction and risk assessments of foods. The objective of this research was to describe the performance of a new user-friendly comprehensive data analysis tool, the Integrated Pathogen Modeling Model (IPMP 2013), recently developed by the USDA Agricultural Research Service. This tool allows users, without detailed programming knowledge, to analyze experimental kinetic data and fit the data to known mathematical models commonly used in predictive microbiology. Data curves previously published in literature were used to test the models in IPMP 2013. The accuracies of the data analysis and models derived from IPMP 2013 were compared in parallel to commercial or open-source statistical packages, such as SAS® or R. Several models were analyzed and compared, including a three-parameter logistic model for growth curves without lag phases, reduced Huang and Baranyi models for growth curves without stationary phases, growth models for complete growth curves (Huang, Baranyi, and re-parameterized Gompertz models), survival models (linear, re-parameterized Gompertz, and Weibull models), and secondary models (Ratkowsky square-root, Huang square-root, Cardinal, and Arrhenius-type models). The comparative analysis suggests that the results from IPMP 2013 were equivalent to those obtained from SAS® or R. This work suggested that the IPMP 2013 could be used as a free alternative to SAS®, R, or other more sophisticated statistical packages for model development in predictive microbiology.

  14. [Quality assurance in food microbiology laboratories].

    PubMed

    Cwiek-Ludwicka, K; Windyga, B; Karłowski, K

    1996-01-01

    In the paper the quality assurance system in food microbiology laboratories to ensure the reliability of the analytical data are discussed. To introduce quality assurance system in the laboratory all activities such as sampling, method selection, laboratory environment, equipment, reagents and media, staff, reference materials, internal quality control and external quality control (proficiency testing) that effect on the results must be documented and controlled. The kind of food sample, condition and time of storage before analysis and proper selection of methodology have significant influence on the result of the microbiological analysis. Equipment used to carry out the test must work properly. Implementation of of the internal and external quality control to the routine work of the food microbiology laboratory means that the production of the results is under control and that the data are reliable. If the quality assurance system is properly implemented and well documented it makes the base for the laboratory to get the accreditation.

  15. Transforming clinical microbiology with bacterial genome sequencing

    PubMed Central

    2016-01-01

    Whole genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here we review the current status of clinical microbiology and how it has already begun to be transformed by the use of next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. The application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow. PMID:22868263

  16. Transforming clinical microbiology with bacterial genome sequencing.

    PubMed

    Didelot, Xavier; Bowden, Rory; Wilson, Daniel J; Peto, Tim E A; Crook, Derrick W

    2012-09-01

    Whole-genome sequencing of bacteria has recently emerged as a cost-effective and convenient approach for addressing many microbiological questions. Here, we review the current status of clinical microbiology and how it has already begun to be transformed by using next-generation sequencing. We focus on three essential tasks: identifying the species of an isolate, testing its properties, such as resistance to antibiotics and virulence, and monitoring the emergence and spread of bacterial pathogens. We predict that the application of next-generation sequencing will soon be sufficiently fast, accurate and cheap to be used in routine clinical microbiology practice, where it could replace many complex current techniques with a single, more efficient workflow.

  17. 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.

  18. 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.

  19. [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

  20. 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

  1. Molecular cloning and expression analysis of Pleurodeles waltl complement component C3 under normal physiological conditions and environmental stresses.

    PubMed

    Guéguinou, Nathan; Huin-Schohn, Cécile; Ouzren-Zarhloul, Nassima; Ghislin, Stéphanie; Frippiat, Jean-Pol

    2014-10-01

    C3 is a component of the complement system that plays a central role in immunity, development and tissue regeneration. In this study, we isolated the C3 cDNA of the Iberian ribbed newt Pleurodeles waltl. This cDNA encodes a 1637 amino acid protein with an estimated molecular mass of 212.5 kDa. The deduced amino acid sequence showed that P. waltl C3 contains all the conserved domains known to be critical for C3 function. Quantitative real-time PCR (qRT-PCR) demonstrated that under normal physiological conditions, P. waltl C3 mRNA is expressed early during development because it is likely required for neurulation. Then, its expression increased as the immune system developed. In adults, the liver is the richest source of C3, though other tissues can also contribute. Further analysis of C3 expression demonstrated that C3 transcription increased when P. waltl larvae were exposed to pH or temperature stress, suggesting that environmental modifications might affect this animal's defenses against pathogens.

  2. 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

  3. Models and microbiology: Pasteur and the body.

    PubMed

    Hanley, James G

    2003-01-01

    Louis Pasteur developed a model of the body as a culture vessel in the late 1870s as an explanation of both natural and acquired immunity, and other investigators quickly applied the model in the explanation of other microbiological phenomena, principally the tissue tropism seen in the normal and the pathological flora. This paper will argue that although Pasteur quickly abandoned the model, it persisted as an explanation of tissue tropism for nearly 70 years, structuring the interpretation of data by and guiding the research of a diverse group of microbiological researchers.

  4. [The opportunities, challenges and trends in the rejuvenation of microbiology].

    PubMed

    Shen, Ping; Chen, Xiangdong

    2010-01-01

    In history, the development of microbiology had undergone two golden ages and some depression time as well. In the last two decades, the application of many physiochemical technologies including genomics, structural biology, bioinformatics, PCR, and high-resolution microscopy has led to a series of breakthroughs in microbiology. Microbiology has now awakened and entered its third golden age for development. This review discusses our view of the opportunities, challenges, and trends in the current advancement of microbiology. The topics include: (1) The two golden ages for microbiology in history. (2) The opportunities and challenges in the rejuvenation of microbiology. (3) The characteristics and trends of the current development of microbiology. (4) Integral microbiology--the hallmark of the third golden age.

  5. 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)

  6. Microbiological Diagnosis of Severe Diarrhea in Kidney Transplant Recipients by Use of Multiplex PCR Assays

    PubMed Central

    Coste, Jean-François; Vuiblet, Vincent; Moustapha, Betoul; Bouin, Alexis; Lavaud, Sylvie; Toupance, Olivier; de Rougemont, Alexis; Benejat, Lucie; Megraud, Francis; Wolak-Thierry, Aurore; Villena, Isabelle; Chemla, Cathy; Le Magrex, Elisabeth; de Champs, Christophe; Andreoletti, Laurent; Rieu, Philippe

    2013-01-01

    Diarrhea is a frequent complication after kidney transplantation, ascribed to adverse effects of the immunosuppressive therapy in case of negative microbiological examination of the stools. The aim of this study was to improve the microbiological diagnosis by implementing molecular tests. Fifty-four severe diarrhea events that occurred in 49 adult kidney transplant recipients from September 2010 to November 2011 were investigated. One or several enteric pathogens were detected in 13 (23%) stool samples using classical microbiological methods versus 39 (72%) for the seven commercially available multiplex PCR assays used retrospectively (P = 0.006). Interestingly, molecular diagnosis identified 15 multiple infections compared to none using classical techniques. The primary pathogens detected were enteropathogenic Escherichia coli (EPEC) (n = 15; 38%), Campylobacter spp. (n = 15; 38%), and Norovirus (n = 14; 36%). Specificities for Campylobacter and Norovirus infection diagnosis were 75 and 100%, respectively, by comparison to reference methods. Based on molecular findings, a cyclosporine-mycophenolate mofetil combination was identified as a risk factor for developing Norovirus-induced diarrhea. Norovirus infections were also responsible for higher weight loss than all the other causes of diarrhea. In samples from asymptomatic immunocompromised and immunocompetent patients, EPEC but not Norovirus and Campylobacter infections were detected at a frequency similar to that observed in symptomatic kidney transplant recipients. In conclusion, molecular tools significantly improved the detection of single and multiple enteric infections by comparison to classical techniques and could quickly become the key element in the management of severe acute diarrhea in transplant recipients. PMID:23554205

  7. 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.

  8. Microbiological quality of saffron from the main producer countries.

    PubMed

    Cosano, Inmaculada; Pintado, Concepción; Acevedo, Olga; Novella, José Luis; Alonso, Gonzalo Luis; Carmona, Manuel; de la Rosa, Carmen; Rotger, Rafael

    2009-10-01

    A microbiological study of saffron spice was undertaken in the context of a European research project (Methodologies for Implementing International Standards for Saffron Purity and Quality, the acronym for which is SAFFIC), analyzing 79 samples obtained from the main producer countries, namely Greece, Iran, Italy, Morocco, and Spain. Current microbiological quality criteria are the same as for other spices, but saffron is added in minute quantities during the cooking process, so the health risk associated with microbial contamination might be lower. We did not detect Salmonella either by culture or by PCR methods in any sample, and Escherichia coli was only found in five samples. Enterobacteriaceae were frequently found (70.9% of the samples), but most of them belonged to species of probable environmental origin. Aerobic sporulated bacteria were also common, but only three samples contained Bacillus cereus at low levels (<200 CFU g(-1)). Clostridium perfringens counts were also very low, with only one sample reaching >100 CFU g(-1), an acceptable value. Overall, microbial contamination in saffron was markedly lower than it was in other spices.

  9. Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations.

    PubMed

    Sengupta, Aditi; Wang, Yadi; Meira Neto, Antonio A; Matos, Katarena A; Dontsova, Katerina; Root, Rob; Neilson, Julie W; Maier, Raina M; Chorover, Jon; Troch, Peter A

    2016-01-01

    Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative in improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. We present an experimental method, designed to capture sub-surface heterogeneity of an initially homogeneous soil system. This method is based on destructive sampling of a soil lysimeter designed to simulate a small-scale hillslope. A weighing lysimeter of one cubic meter capacity was divided into sections (voxels) and was excavated layer-by-layer, with sub samples being collected from each voxel. The excavation procedure was aimed at detecting the incipient heterogeneity of the system by focusing on the spatial assessment of hydrological, geochemical, and microbiological properties of the soil. Representative results of a few physicochemical variables tested show the development of heterogeneity. Additional work to test interactions between hydrological, geochemical, and microbiological signatures is planned to interpret the observed patterns. Our study also demonstrates the possibility of carrying out similar excavations in order to observe and quantify different aspects of soil-development under varying environmental conditions and scale. PMID:27684738

  10. Microbiological quality and safety assessment of lettuce production in Brazil.

    PubMed

    Ceuppens, Siele; Hessel, Claudia Titze; de Quadros Rodrigues, Rochele; Bartz, Sabrina; Tondo, Eduardo César; Uyttendaele, Mieke

    2014-07-01

    The microbiological quality and safety of lettuce during primary production in Brazil were determined by enumeration of hygiene indicators Escherichia coli, coliforms and enterococci and detection of enteric pathogens Salmonella and E. coli O157:H7 in organic fertilizers, soil, irrigation water, lettuce crops, harvest boxes and worker's hands taken from six different lettuce farms throughout the crop growth cycle. Generic E. coli was a suitable indicator for the presence of Salmonella and E. coli O157:H7, while coliforms and enterococci were not. Few pathogens were detected: 5 salmonellae and 2 E. coli O157:H7 from 260 samples, of which only one was lettuce and the others were manure, soil and water. Most (5/7) pathogens were isolated from the same farm and all were from organic production. Statistical analysis revealed the following environmental and agro-technical risk factors for increased microbial load and pathogen prevalence in lettuce production: high temperature, flooding of lettuce fields, application of contaminated organic fertilizer, irrigation with water of inferior quality and large distances between the field and toilets. Control of the composting process of organic fertilizers and the irrigation water quality appear most crucial to improve and/or maintain the microbiological quality and safety during the primary production of lettuce.

  11. Practical microbiology in schools: a survey of UK teachers.

    PubMed

    Redfern, James; Burdass, Dariel; Verran, Joanna

    2013-11-01

    A survey of secondary school teachers investigated practical microbiology in the classroom. The results were heartening (practical microbiology was common), but concerns were expressed regarding equipment, time, cost, and expertise. Microbiologists should engage more with school education to support teachers and maintain the health of microbiology for future generations.

  12. 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... Microbiological assay culture medium. (a) Identification. A microbiological assay culture medium is a device that... organism in the innoculated medium. Test results aid in the diagnosis of disease resulting from...

  13. 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... Microbiological assay culture medium. (a) Identification. A microbiological assay culture medium is a device that... organism in the innoculated medium. Test results aid in the diagnosis of disease resulting from...

  14. 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... Microbiological assay culture medium. (a) Identification. A microbiological assay culture medium is a device that... organism in the innoculated medium. Test results aid in the diagnosis of disease resulting from...

  15. 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... Microbiological assay culture medium. (a) Identification. A microbiological assay culture medium is a device that... organism in the innoculated medium. Test results aid in the diagnosis of disease resulting from...

  16. 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... Microbiological assay culture medium. (a) Identification. A microbiological assay culture medium is a device that... organism in the innoculated medium. Test results aid in the diagnosis of disease resulting from...

  17. Undergraduate Laboratory Exercises Specific to Food Spoilage Microbiology

    ERIC Educational Resources Information Center

    Snyder, Abigail B.; Worobo, Randy W.; Orta-Ramirez, Alicia

    2016-01-01

    Food spoilage has an enormous economic impact, and microbial food spoilage plays a significant role in food waste and loss; subsequently, an equally significant portion of undergraduate food microbiology instruction should be dedicated to spoilage microbiology. Here, we describe a set of undergraduate microbiology laboratory exercises that focus…

  18. [Applications of MALDI-TOF-MS in clinical microbiology laboratory].

    PubMed

    Carbonnelle, Etienne; Nassif, Xavier

    2011-10-01

    For twenty years, mass spectrometry (MS) has emerged as a particularly powerful tool for analysis and characterization of proteins in research. It is only recently that this technology, especially MALDI-TOF-MS (Matrix Assisted Laser Desorption Ionization Time-Of-Flight) has entered the field of routine microbiology. This method has proven to be reliable and safe for the identification of bacteria, yeasts, filamentous fungi and dermatophytes. MALDI-TOF-MS is a rapid, precise and cost-effective method for identification, compared to conventional phenotypic techniques or molecular biology. Its ability to analyse whole microorganisms with few sample preparation has greatly reduced the time to identification (1-2 min). Furthermore, this technology can be used to identify bacteria directly from clinical samples as blood culture bottles or urines. Future applications will be developed in order to provide direct information concerning virulence or resistance protein markers.

  19. Microbiological quality of pediatric oral liquid formulations.

    PubMed

    Cabañas Poy, Maria Josep; Cañete Ramírez, Carme; González di Lauro, Sabina X; Rodríguez Garrido, Virginia; Roig Carbajosa, Gloria; Fernández-Polo, Aurora; Clemente Bautista, Susana

    2016-09-01

    The oral administration of drugs to the pediatric population involves the extemporaneous preparation of liquid formulations. These formulations have studies on their physicochemical stability, but they often lack microbiological studies. The objective of this study is to check the microbiological quality of five oral liquid formulations prepared with different excipients, which represent five major combinations, in two conditions: kept unopened until the day of the test, and in a multi-dose vial opened daily. The formulations were prepared according to standard operating procedures. Half of each batch was packaged in vials that remained closed until the day of testing, and the other half in a single container which was opened daily. Both the vials and the containers had been previously sterilized. Microbiological tests were performed weekly during the first month of the study, and then every two weeks, until the expiration date. The microbiological quality of oral liquid formulations is determined by the Royal Spanish Pharmacopoeia. The conclusion was that none of the formulations prepared that were packaged in sterilized containers became contaminated, either in unopened vials or in multi-dose containers when they were opened daily.

  20. Reasons for Suboptimal Learning in Medical Microbiology

    ERIC Educational Resources Information Center

    Struwig, Magdalena C.; Beylefeld, Adriana A.; Joubert, Georgina

    2016-01-01

    Medical microbiology presents a challenge to undergraduate students, mostly due to its extensive content and complexity of unfamiliar terminology. In addition to a narrative review of the literature, we report findings on students' motivation for and approach to learning in the Infections module of an undergraduate medical curriculum, and their…

  1. 7 CFR 58.528 - Microbiological requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., GENERAL SPECIFICATIONS FOR APPROVED PLANTS AND STANDARDS FOR GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection and Grading Service 1 Requirements for Cottage Cheese Bearing Usda Official Identification § 58.528 Microbiological requirements. Compliance shall...

  2. 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…

  3. 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...

  4. Developing virtual patients for medical microbiology education.

    PubMed

    McCarthy, David; O'Gorman, Ciaran; Gormley, Gerry J

    2013-12-01

    The landscape of medical education is changing as students embrace the accessibility and interactivity of e-learning. Virtual patients are e-learning resources that may be used to advance microbiology education. Although the development of virtual patients has been widely considered, here we aim to provide a coherent approach for clinical educators.

  5. Microbiologically influenced corrosion in wastewater treatment plants

    SciTech Connect

    Soebbing, J.B.; Yolo, R.A.

    1996-09-01

    Microbiologically influenced corrosion (MIC) activity in wastewater treatment plans is discussed. Three case histories are presented showing throughwall pitting from MIC in recycle activated sludge process piping systems. Field and laboratory investigation activities are reported. Alternatives are reviewed for corrosion prevention and mitigation.

  6. 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...

  7. 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...

  8. [Analysis of the results of the 2010 External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology].

    PubMed

    Ruiz de Gopegui Bordes, Enrique; Serrano, M del Remedio Guna; Orta Mira, Nieves; Ovies, María Rosario; Poveda, Marta; Cardona, Concepción Gimeno

    2011-12-01

    The External Quality Control Program of the Spanish Society of Infectious Diseases and Clinical Microbiology includes controls for bacteriology, serology, mycology, parasitology, mycobacteria, virology and molecular microbiology. This article presents the most important conclusions and lessons of the 2010 controls. As a whole, the results obtained in 2010 confirm the excellent skill and good technical standards found in previous years. However, erroneous results can be obtained in any laboratory and in clinically relevant determinations. The results of this program highlight the need to implement both internal and external controls to ensure maximal quality of microbiological tests(1).

  9. 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

  10. [The microbiology laboratory's contribution to the surveillance and control of outbreaks caused by nonfermentative Gram-negative bacilli].

    PubMed

    Fernández-Cuenca, Felipe; López-Cortés, Luis E; Rodríguez-Baño, Jesús

    2011-03-01

    Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia are, among others, the most important nonfermentative Gram-negative bacilli within hospitals. These organisms are able to cause different types of nosocomial infections in predisposed patients, and P. aeruginosa and A. baumannii in particular may cause extensive clonal outbreaks and complex situations in which sporadic isolates may coexist with some epidemic strains. Some common features are their intrinsic resistance to many antimicrobials, their capacity to further develop antimicrobial resistance, and the possibility of environmental reservoirs as sources of these microorganisms in healthcare centers. The microbiology laboratory plays a key role in the detection of potential outbreaks, in the identification of new resistance mechanisms and in the characterization of local epidemiology, by detecting colonized patients and/or environmental reservoirs if needed, appropriately identifying the isolates, phenotypically or genotypically characterizing their mechanisms of resistance, if appropriate, and finally by using different molecular techniques for clonal typing, which are reviewed in this article. Such activities must be performed in the context of the surveillance and control programs of specific institutions and as part of the daily work of multidisciplinary infection control teams.

  11. Isolation and molecular characterization of multidrug-resistant Enterobacteriaceae strains from pork and environmental samples in Xiamen, China.

    PubMed

    Liu, Zongbao; Zhang, Zhigang; Yan, He; Li, Jianrong; Shi, Lei

    2015-01-01

    This study was conducted to investigate the prevalence and molecular characterization of multidrug-resistant (MDR) Enterobacteriaceae isolated from swine meat and the breeding environment. A total of 102 MDR Enterobacteriaceae strains belonging to five genera were obtained from 210 samples collected from a large-scale swine farm from March 2012 to June 2013 in Xiamen, People's Republic of China. Among these MDR isolates, Escherichia coli strains were found most frequently in both meat and environmental samples, followed by Citrobacter spp., Klebsiella spp., and Shigella spp. The neighbor-joining phylogenetic tree indicated that 70.3 % of Escherichia and 50 % of Citrobacter isolates from meat samples shared 100 % homology with relevant isolates from environmental samples. Resistance was most frequently observed to sulfonamide, trimethoprim, aminoglycoside, chloramphenicol, β-lactam, and tetracycline. Close correlation was noted between antibiotic resistance phenotype and the genes responsible for resistance to sulfonamide (sulI), trimethoprim (dhfrI), aminoglycoside (aadA, aac(3)-I, aphA-1, and aac(3)-IV), chloramphenicol (catI and cmlA), β-lactam (blaSHV, blaOXA, and blaTEM), florfenicol (floR), and tetracycline (tet(A) and tet(B)), which were widely distributed with prevalences of 72.5, 6.9, 62.7, 14.7, 78.4, 11.8, 25.5, 42.2, 12.7, 14.7, 39.2, 87.2, 68.6, and 34.3 % , respectively. Class 1 integrons carrying aadA22, dfrA17-aadA5, or dfrA12-aadA2 cassette arrays were commonly found in isolates from all samples. The gene cassette aac(6')-Ib-cr-arr-3-dfrA27-aadA16 was first found in an Enterobacter amnigenus isolate. Conjugation experiments revealed the plasmid-mediated transfer of class 1 integrons. Our results indicate that swine meat and the farming environment can be sources of antibiotic-resistant bacteria, which could be potentially transmitted to humans via the meat products industry chain.

  12. Isolation and molecular characterization of multidrug-resistant Enterobacteriaceae strains from pork and environmental samples in Xiamen, China.

    PubMed

    Liu, Zongbao; Zhang, Zhigang; Yan, He; Li, Jianrong; Shi, Lei

    2015-01-01

    This study was conducted to investigate the prevalence and molecular characterization of multidrug-resistant (MDR) Enterobacteriaceae isolated from swine meat and the breeding environment. A total of 102 MDR Enterobacteriaceae strains belonging to five genera were obtained from 210 samples collected from a large-scale swine farm from March 2012 to June 2013 in Xiamen, People's Republic of China. Among these MDR isolates, Escherichia coli strains were found most frequently in both meat and environmental samples, followed by Citrobacter spp., Klebsiella spp., and Shigella spp. The neighbor-joining phylogenetic tree indicated that 70.3 % of Escherichia and 50 % of Citrobacter isolates from meat samples shared 100 % homology with relevant isolates from environmental samples. Resistance was most frequently observed to sulfonamide, trimethoprim, aminoglycoside, chloramphenicol, β-lactam, and tetracycline. Close correlation was noted between antibiotic resistance phenotype and the genes responsible for resistance to sulfonamide (sulI), trimethoprim (dhfrI), aminoglycoside (aadA, aac(3)-I, aphA-1, and aac(3)-IV), chloramphenicol (catI and cmlA), β-lactam (blaSHV, blaOXA, and blaTEM), florfenicol (floR), and tetracycline (tet(A) and tet(B)), which were widely distributed with prevalences of 72.5, 6.9, 62.7, 14.7, 78.4, 11.8, 25.5, 42.2, 12.7, 14.7, 39.2, 87.2, 68.6, and 34.3 % , respectively. Class 1 integrons carrying aadA22, dfrA17-aadA5, or dfrA12-aadA2 cassette arrays were commonly found in isolates from all samples. The gene cassette aac(6')-Ib-cr-arr-3-dfrA27-aadA16 was first found in an Enterobacter amnigenus isolate. Conjugation experiments revealed the plasmid-mediated transfer of class 1 integrons. Our results indicate that swine meat and the farming environment can be sources of antibiotic-resistant bacteria, which could be potentially transmitted to humans via the meat products industry chain. PMID:25581181

  13. [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.

  14. [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

  15. Cellular microbiology and molecular ecology of Legionella-amoeba interaction.

    PubMed

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

    2013-05-15

    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.

  16. 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…

  17. Cellular microbiology and molecular ecology of Legionella-amoeba interaction.

    PubMed

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

    2013-05-15

    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

  18. MOLECULAR APPROACHES TO MICROBIOLOGICAL MONITORING: FECAL SOURCE DETECTION. (R827639)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  19. Microbiological and Molecular Characterization of Staphylococcus hominis Isolates from Blood

    PubMed Central

    Mendoza-Olazarán, Soraya; Morfin-Otero, Rayo; Rodríguez-Noriega, Eduardo; Llaca-Díaz, Jorge; Flores-Treviño, Samantha; González-González, Gloria Ma; Villarreal-Treviño, Licet; Garza-González, Elvira

    2013-01-01

    Background Among Coagulase-Negative Staphylococci (CoNS), Staphylococcus hominis represents the third most common organism recoverable from the blood of immunocompromised patients. The aim of this study was to characterize biofilm formation, antibiotic resistance, define the SCCmec (Staphylococcal Chromosomal Cassette mec) type, and genetic relatedness of clinical S. hominis isolates. Methodology S. hominis blood isolates (n = 21) were screened for biofilm formation using crystal violet staining. Methicillin resistance was evaluated using the cefoxitin disk test and the mecA gene was detected by PCR. Antibiotic resistance was determined by the broth microdilution method. Genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE) and SCCmec typed by multiplex PCR using two different methodologies described for Staphylococcus aureus. Results Of the S. hominis isolates screened, 47.6% (10/21) were categorized as strong biofilm producers and 23.8% (5/21) as weak producers. Furthermore, 81% (17/21) of the isolates were methicillin resistant and mecA gene carriers. Resistance to ampicillin, erythromycin, and trimethoprim was observed in >70% of isolates screened. Each isolate showed a different PFGE macrorestriction pattern with similarity ranging between 0–95%. Among mecA-positive isolates, 14 (82%) harbored a non-typeable SCCmec type: eight isolates were not positive for any ccr complex; four contained the mec complex A ccrAB1 and ccrC, one isolate contained mec complex A, ccrAB4 and ccrC, and one isolate contained the mec complex A, ccrAB1, ccrAB4, and ccrC. Two isolates harbored the association: mec complex A and ccrAB1. Only one strain was typeable as SCCmec III. Conclusions The S. hominis isolates analyzed were variable biofilm producers had a high prevalence of methicillin resistance and resistance to other antibiotics, and high genetic diversity. The results of this study strongly suggested that S. hominis isolates harbor new SCCmec structural elements and might be reservoirs of ccrC1 in addition to ccrAB1 and mec complex A. PMID:23585877

  20. High susceptibility of neonatal mice to molecular, biochemical and cytogenetic alterations induced by environmental cigarette smoke and light.

    PubMed

    De Flora, Silvio; D'Agostini, Francesco; Balansky, Roumen; Camoirano, Anna; Cartiglia, Cristina; Longobardi, Mariagrazia; Travaini, Giorgia; Steele, Vernon E; Pesce, Carlo; Izzotti, Alberto

    2008-01-01

    Our recent studies have shown that both cigarette smoke and UV-containing light, which are the most widespread and ubiquitous mutagens and carcinogens in the world, cause systemic genotoxic damage in hairless mice. Further studies were designed with the aim of evaluating the induction of genotoxic and carcinogenic effects in Swiss albino mice exposed to smoke and/or light since birth. We observed that a 4-month whole-body exposure of mice to mainstream cigarette smoke, starting at birth, caused an early and potent carcinogenic response in the lung and other organs. Our further experiments showed that exposure of mice to environmental cigarette smoke, during the first 5 weeks of life, resulted in a variety of significant alterations of intermediate biomarkers, including cytogenetic damage in bone marrow and peripheral blood, formation of lipid peroxidation products, increase of bulky DNA adduct levels, induction of oxidative DNA damage, and overexpression of OGG1 gene in lung, stimulation of apoptosis, hyperproliferation and loss of Fhit protein in pulmonary alveolar macrophages and/or bronchial epithelial cells, and early histopathological alterations in the respiratory tract. Moreover, exposure of mice to UV-containing light, mimicking solar irradiation, significantly enhanced oxidative DNA damage and bulky DNA adduct levels in lung, and synergized with smoke in inducing molecular alterations in the respiratory tract. The baseline OGG1 expression in lung was particularly high at birth and decreased in post-weanling mice. Oxidative DNA damage and other investigated end-points exhibited differential patterns in post-weanling mice and adult mice. The findings of these studies provide a mechanistic clue to the general concept that the neonatal period and early stages of life are critical in affecting susceptibility to carcinogens.

  1. 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

  2. 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.

  3. Microbiological quality of retail spices in Tehran, Iran.

    PubMed

    Koohy-Kamaly-Dehkordy, Paliz; Nikoopour, Houshang; Siavoshi, Farideh; Koushki, Mohammadreza; Abadi, Alireza

    2013-05-01

    The microbiological quality of 351 samples of nine types of spices including black pepper, caraway, cinnamon, cow parsnip, curry powder, garlic powder, red pepper, sumac, and turmeric, collected from retail shops in Tehran during 2007, was determined. The numbers of aerobic mesophilic bacteria, Escherichia coli, and molds exceeded Iran's National Standard limits, at 63.2% (>5 × 10(5) CFU/g), 23.4% (>0.3 MPN/g), and 21.9% (>5 × 10(3) CFU/g) of the studied samples, respectively. Coliform contamination was more than 10(3) MPN/g in 24.8% of samples. High contamination of retail spices is considered an indication of environmental or fecal contamination due to unhygienic practices in their production. Use of spices with high microbial content could increase the chance of food spoilage and transmission of foodborne pathogens. Accordingly, application of food safety measurements to reduce microbial counts in spices is strongly recommended.

  4. 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

  5. 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…

  6. 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.

  7. 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

  8. 72 hours standby time of wet-primed cardiopulmonary bypass circuits: a microbiological quality assurance study.

    PubMed

    Schulz-Stübner, Sebastian; Schorer, Cornelia; Ennker, Jürgen; Bauer, Stefan; Schaumann, Reiner

    2014-10-01

    In a microbiological sample study of 15 wet-primed cardiopulmonary bypass circuits in standby mode for 72 hours under regular clinical conditions, no contamination of the priming fluid or the connectors could be detected. Hand contact surfaces of the machines demonstrated environmental microorganisms. These findings indicate the safe use of primed cardiopulmonary bypass circuits in standby mode for 72 hours. A surface disinfection of hand contact surfaces immediately before use is recommended. PMID:24788708

  9. An experimental test of the role of environmental temperature variability on ectotherm molecular, physiological and life-history traits: implications for global warming.

    PubMed

    Folguera, Guillermo; Bastías, Daniel A; Caers, Jelle; Rojas, José M; Piulachs, Maria-Dolors; Bellés, Xavier; Bozinovic, Francisco

    2011-07-01

    Global climate change is one of the greatest threats to biodiversity; one of the most important effects is the increase in the mean earth surface temperature. However, another but poorly studied main characteristic of global change appears to be an increase in temperature variability. Most of the current analyses of global change have focused on mean values, paying less attention to the role of the fluctuations of environmental variables. We experimentally tested the effects of environmental temperature variability on characteristics associated to the fitness (body mass balance, growth rate, and survival), metabolic rate (VCO(2)) and molecular traits (heat shock protein expression, Hsp70), in an ectotherm, the terrestrial woodlouse Porcellio laevis. Our general hypotheses are that higher values of thermal amplitude may directly affect life-history traits, increasing metabolic cost and stress responses. At first, results supported our hypotheses showing a diversity of responses among characters to the experimental thermal treatments. We emphasize that knowledge about the cellular and physiological mechanisms by which animals cope with environmental changes is essential to understand the impact of mean climatic change and variability. Also, we consider that the studies that only incorporate only mean temperatures to predict the life-history, ecological and evolutionary impact of global temperature changes present important problems to predict the diversity of responses of the organism. This is because the analysis ignores the complexity and details of the molecular and physiological processes by which animals cope with environmental variability, as well as the life-history and demographic consequences of such variability.

  10. 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

  11. 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.

  12. 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

  13. Recent applications of hyperspectral imaging in microbiology.

    PubMed

    Gowen, Aoife A; Feng, Yaoze; Gaston, Edurne; Valdramidis, Vasilis

    2015-05-01

    Hyperspectral chemical imaging (HSI) is a broad term encompassing spatially resolved spectral data obtained through a variety of modalities (e.g. Raman scattering, Fourier transform infrared microscopy, fluorescence and near-infrared chemical imaging). It goes beyond the capabilities of conventional imaging and spectroscopy by obtaining spatially resolved spectra from objects at spatial resolutions varying from the level of single cells up to macroscopic objects (e.g. foods). In tandem with recent developments in instrumentation and sampling protocols, applications of HSI in microbiology have increased rapidly. This article gives a brief overview of the fundamentals of HSI and a comprehensive review of applications of HSI in microbiology over the past 10 years. Technical challenges and future perspectives for these techniques are also discussed.

  14. 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.

  15. Genomics and metagenomics in medical microbiology.

    PubMed

    Padmanabhan, Roshan; Mishra, Ajay Kumar; Raoult, Didier; Fournier, Pierre-Edouard

    2013-12-01

    Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.

  16. 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.

  17. Anaerobic microbiology in the NASA space program.

    PubMed

    Brewer, J H

    1980-01-01

    After briefly reviewing the earlier methods used to monitor the microbial load of returned lunar material, the author reports the more accurate research on the ability of terrestrial organisms to grow under simulated Martian environments. The possible importance of anaerobic microbiology can readily be seen because of the low level of O2 found on Mars. The question of whether any of the experiments on board the Viking landers show any indication of life on Mars is discussed in detail.

  18. Microbiologically influenced corrosion in wastewater treatment plants

    SciTech Connect

    Soebbing, J.B.; Yolo, R.A.

    1995-12-01

    Microbiologically influenced corrosion (MIC) activity in wastewater treatment plants is discussed. Three case histories are presented showing through-wall pitting from MIC in return activated sludge (RAS) process piping systems. Field and laboratory investigation activities are reported. Alternatives are reviewed for initial corrosion prevention and mitigation following identification. A brief discussion of wastewater treatment and specifically, the activated sludge process is also provided. The applicability of common MIC prevention and mitigation practices to wastewater treatment facilities or processes is also reviewed.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. Rapid diagnostic testing for community-acquired pneumonia: can innovative technology for clinical microbiology be exploited?

    PubMed

    Yu, Victor L; Stout, Janet E

    2009-12-01

    Two nonsynchronous events have affected the management of community-acquired pneumonia (CAP): spiraling empiricism for CAP and the "golden era" of clinical microbiology. The development of broad-spectrum antibiotics has led to widespread empiric use without ascertaining the etiology of the infecting microbe. Unfortunately, this approach clashes with the second event, which is the advent of molecular-based microbiology that can identify the causative pathogen rapidly at the point of care. The urinary antigen is a most effective rapid test that has allowed targeted therapy for Legionnaire disease at the point of care. The high specificity (> 90%) allows the clinician to administer appropriate anti-Legionella therapy based on a single rapid test; however, its low sensitivity (76%) means that a notable number of cases of Legionnaire disease will go undiagnosed if other tests, especially culture, are not performed. Further, culture for Legionella is not readily available. If a culture is not performed, epidemiologic identification of the source of the bacterium cannot be ascertained by molecular fingerprinting of the patient and the putative source strain. We recommend resurrection of the basic principles of infectious disease, which are to identify the microbial etiology of the infection and to use narrow, targeted antimicrobial therapy. To reduce antimicrobial overuse with subsequent antimicrobial resistance, these basic principles must be applied in concert with traditional and newer tests in the clinical microbiology laboratory.

  5. Risk factors contributing to microbiological contamination of shallow groundwater in Kampala, Uganda.

    PubMed

    Howard, Guy; Pedley, Stephen; Barrett, Mike; Nalubega, Mai; Johal, Kali

    2003-08-01

    A study of water quality variation in shallow protected springs in Kampala was undertaken over a 12-month period to assess the causes of microbiological contamination. The microbiological quality of water was assessed using thermotolerant coliforms and faecal streptococci. Sanitary inspections and hazard assessments were undertaken to identify faecal sources (hazards), contaminant pathways and contributory factors. Data were collected on rainfall and population as additional factors potentially exerting an influence on microbiological quality. Initial analysis of the data showed a significant relationship between median level of contamination and rainfall, in particular to short-term rainfall events. Total sanitary risk score showed a significant relationship with median level of contamination, but population density may be a confounding factor. The raw microbiological data were transformed into five water quality targets: <1 and < or =10 cfu 100ml(-1) for faecal streptococci; and <1, < or =10 and < or=50 cfu 100 ml(-1) for thermotolerant coliforms. The presence of individual risk factors as well as variables for rainfall and population density were analysed with respect to failure to meet these water quality targets using contingency tables. Logistic regression models were developed for each of the five water quality targets. The analysis strongly suggested that there is rapid recharge of the springs after rainfall and this leads to microbiological contamination. On-site sanitation was less important than other sources of faecal matter, which was consistent with a low sanitation coverage in the study area. The study suggested that improving sanitary completion and local environmental hygiene was more important than controlling on-site sanitation in improving the quality of these springs.

  6. [Quality assessment program of the Spanish Society of Infectious Diseases and Clinical Microbiology. Analysis of results. 2005].

    PubMed

    Orta Mira, Nieves; Guna Serrano, M del Remedio; Pérez, José L; Gimeno Cardona, Concepción

    2006-10-01

    Quality assurance of the analytical processes performed at the clinical microbiology laboratory is mandatory and should be carried out by using external and internal quality control activities. External quality assessment programs allow intercomparison within laboratories, detection of errors, and evaluation of the suitability of some reagents or diagnostic kits for the purpose for which they were designed; these activities are also useful for continuous education. The program launched 15 years ago by the Spanish Society of Infectious Diseases and Clinical Microbiology is based on sending typified materials along with a clinical and microbiological case related to these control materials. The spectrum of the samples is broad, including bacteriology (monthly and three-monthly), serology, mycology, parasitology, mycobacteria, virology, and molecular microbiology. After receiving the results from the participants, the program organization delivers an individual certificate comparing the results with those of a reference laboratory. Additionally, a report is generated by analyzing all the results sent by the participants; laboratories are also sent review articles on the subject of each assessment as a tool for continuous education in clinical microbiology. In this article, the most relevant conclusions and lessons from the 2005 assessments are presented.

  7. [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

  8. 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.

  9. 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

  10. [Special aspects of microbiological monitoring of drinking water quality].

    PubMed

    Feuerpfeil, I; Hummel, A; Renner, P

    2007-03-01

    The new drinking water ordinance (TrinkwV 2001) entered into force in 2003. In this paper we report about experiences with monitoring microbiological quality of drinking water. Special problems, for instance requirements concerning the quality of raw water, new and "old" microbiological parameters, microbiological methods, assessment of parametric values, especially in the case of values higher than the imperative value, are also described. Possible developments in this field are discussed. The paper should support microbiological laboratories, public health officers and other public authorities in monitoring and assessment of drinking water quality.

  11. Interpretation of Blood Microbiology Results – Function of the Clinical Microbiologist

    PubMed Central

    Pongrácz, Júlia

    2016-01-01

    The proper use and interpretation of blood microbiology results may be one of the most challenging and one of the most important functions of clinical microbiology laboratories. Effective implementation of this function requires careful consideration of specimen collection and processing, pathogen detection techniques, and prompt and precise reporting of identification and susceptibility results. The responsibility of the treating physician is proper formulation of the analytical request and to provide the laboratory with complete and precise patient information, which are inevitable prerequisites of a proper testing and interpretation. The clinical microbiologist can offer advice concerning the differential diagnosis, sampling techniques and detection methods to facilitate diagnosis. Rapid detection methods are essential, since the sooner a pathogen is detected, the better chance the patient has of getting cured. Besides the gold-standard blood culture technique, microbiologic methods that decrease the time in obtaining a relevant result are more and more utilized today. In the case of certain pathogens, the pathogen can be identified directly from the blood culture bottle after propagation with serological or automated/semi-automated systems or molecular methods or with MALDI-TOF MS (matrix-assisted laser desorption-ionization time of flight mass spectrometry). Molecular biology methods are also suitable for the rapid detection and identification of pathogens from aseptically collected blood samples. Another important duty of the microbiology laboratory is to notify the treating physician immediately about all relevant information if a positive sample is detected. The clinical microbiologist may provide important guidance regarding the clinical significance of blood isolates, since one-third to one-half of blood culture isolates are contaminants or isolates of unknown clinical significance. To fully exploit the benefits of blood culture and other (non- culture

  12. Interpretation of Blood Microbiology Results – Function of the Clinical Microbiologist

    PubMed Central

    Pongrácz, Júlia

    2016-01-01

    The proper use and interpretation of blood microbiology results may be one of the most challenging and one of the most important functions of clinical microbiology laboratories. Effective implementation of this function requires careful consideration of specimen collection and processing, pathogen detection techniques, and prompt and precise reporting of identification and susceptibility results. The responsibility of the treating physician is proper formulation of the analytical request and to provide the laboratory with complete and precise patient information, which are inevitable prerequisites of a proper testing and interpretation. The clinical microbiologist can offer advice concerning the differential diagnosis, sampling techniques and detection methods to facilitate diagnosis. Rapid detection methods are essential, since the sooner a pathogen is detected, the better chance the patient has of getting cured. Besides the gold-standard blood culture technique, microbiologic methods that decrease the time in obtaining a relevant result are more and more utilized today. In the case of certain pathogens, the pathogen can be identified directly from the blood culture bottle after propagation with serological or automated/semi-automated systems or molecular methods or with MALDI-TOF MS (matrix-assisted laser desorption-ionization time of flight mass spectrometry). Molecular biology methods are also suitable for the rapid detection and identification of pathogens from aseptically collected blood samples. Another important duty of the microbiology laboratory is to notify the treating physician immediately about all relevant information if a positive sample is detected. The clinical microbiologist may provide important guidance regarding the clinical significance of blood isolates, since one-third to one-half of blood culture isolates are contaminants or isolates of unknown clinical significance. To fully exploit the benefits of blood culture and other (non- culture

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  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. Combined immunomagnetic separation-molecular beacon-reverse transcription-PCR assay for detection of hepatitis A virus from environmental samples.

    PubMed

    Abd El Galil, Khaled H; El Sokkary, M A; Kheira, S M; Salazar, Andre M; Yates, Marylynn V; Chen, Wilfred; Mulchandani, Ashok

    2004-07-01

    In this study, a molecular-beacon-based real-time reverse transcription (RT)-PCR assay was developed to detect the presence of hepatitis A virus (HAV) in environmental samples. A 125-bp, highly conserved 5' noncoding region of HAV was targeted. The sensitivity of the real-time RT-PCR assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, and only HAV was positively identified. When combined with immunomagnetic separation, the real-time RT-PCR assay successfully detected as few as 20 PFU in seeded groundwater samples. Because of its simplicity and specificity, this assay has broad applications for the rapid detection of HAV in contaminated foods or water.

  20. 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