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Sample records for microbial enumeration technique

  1. The influence of the microbial quality of wastewater, lettuce cultivars and enumeration technique when estimating the microbial contamination of wastewater-irrigated lettuce.

    Science.gov (United States)

    Makkaew, P; Miller, M; Cromar, N J; Fallowfield, H J

    2017-04-01

    This study investigated the volume of wastewater retained on the surface of three different varieties of lettuce, Iceberg, Cos, and Oak leaf, following submersion in wastewater of different microbial qualities (10, 10 2 , 10 3 , and 10 4 E. coli MPN/100 mL) as a surrogate method for estimation of contamination of spray-irrigated lettuce. Uniquely, Escherichia coli was enumerated, after submersion, on both the outer and inner leaves and in a composite sample of lettuce. E. coli were enumerated using two techniques. Firstly, from samples of leaves - the direct method. Secondly, using an indirect method, where the E. coli concentrations were estimated from the volume of wastewater retained by the lettuce and the E. coli concentration of the wastewater. The results showed that different varieties of lettuce retained significantly different volumes of wastewater (p 0.01) were detected between E. coli counts obtained from different parts of lettuce, nor between the direct and indirect enumeration methods. Statistically significant linear relationships were derived relating the E. coli concentration of the wastewater in which the lettuces were submerged to the subsequent E. coli count on each variety the lettuce.

  2. Enumeration of microbial populations in radioactive environments by epifluorescence microscopy

    International Nuclear Information System (INIS)

    Pansoy-Hjelvik, M.E.; Strietelmeier, B.A.; Paffett, M.T.

    1997-01-01

    Epifluorescence microscopy was utilized to enumerate halophilic bacterial populations in two studies involving inoculated, actual waste/brine mixtures and pure brine solutions. The studies include an initial set of experiments designed to elucidate potential transformations of actinide-containing wastes under salt-repository conditions, including microbially mediated changes. The first study included periodic enumeration of bacterial populations of a mixed inoculum initially added to a collection of test containers. The contents of the test containers are the different types of actual radioactive waste that could potentially be stored in nuclear waste repositories in a salt environment. The transuranic waste was generated from materials used in actinide laboratory research. The results show that cell numbers decreased with time. Sorption of the bacteria to solid surfaces in the test system is discussed as a possible mechanism for the decrease in cell numbers. The second study was designed to determine radiological and/or chemical effects of 239 Pu, 243 Am, 237 Np, 232 Th and 238 U on the growth of pure and mixed anaerobic, denitrifying bacterial cultures in brine media. Pu, Am, and Np isotopes at concentrations of ≤1x10 -6 M , ≤5x10 -6 M and ≤5x10 -4 M respectively, and Th and U isotopes ≤4x10 -3 M were tested in these media. The results indicate that high concentrations of certain actinides affected both the bacterial growth rate and morphology. However, relatively minor effects from Am were observed at all tested concentrations with the pure culture

  3. Comparison of enumeration techniques for the investigation of ...

    African Journals Online (AJOL)

    The study was aimed at assessing techniques, which would provide an accurate indication of the planktonic bacterial pollution load in the Berg River, Western Cape, South Africa. Sampling of sites started in June 2004 and continued for a period of 1 year until June 2005. The most probable number (MPN) technique was ...

  4. An interlaboratory study to find an alternative to the MPN technique for enumerating Escherichia coli in shellfish

    DEFF Research Database (Denmark)

    Ogden, I.D.; Brown, G.C.; Gallacher, S.

    1998-01-01

    Nine laboratories in eight countries tested 16 batches of common mussels (Mytilus edulis) over a 32 week period in order to find an alternative to the Most Probable Number (MPN) technique to enumerate E. coli. The alternatives investigated included the 3M Petrifilm system, the Merck Chromocult agar...

  5. Seven-hour fluorescence in situ hybridization technique for enumeration of Enterobacteriaceae in food and environmental water sample.

    Science.gov (United States)

    Ootsubo, M; Shimizu, T; Tanaka, R; Sawabe, T; Tajima, K; Ezura, Y

    2003-01-01

    A fluorescent in situ hybridization (FISH) technique using an Enterobacteriaceae-specific probe (probe D) to target 16S rRNA was improved in order to enumerate, within a single working day, Enterobacteriaceae present in food and environmental water samples. In order to minimize the time required for the FISH procedure, each step of FISH with probe D was re-evaluated using cultured Escherichia coli. Five minutes of ethanol treatment for cell fixation and hybridization were sufficient to visualize cultured E. coli, and FISH could be performed within 1 h. Because of the difficulties in detecting low levels of bacterial cells by FISH without cultivation, a FISH technique for detecting microcolonies on membrane filters was investigated to improve the bacterial detection limit. FISH with probe D following 6 h of cultivation to grow microcolonies on a 13 mm diameter membrane filter was performed, and whole Enterobacteriaceae microcolonies on the filter were then detected and enumerated by manual epifluorescence microscopic scanning at magnification of x100 in ca 5 min. The total time for FISH with probe D following cultivation (FISHFC) was reduced to within 7 h. FISHFC can be applied to enumerate cultivable Enterobacteriaceae in food (above 100 cells g-1) and environmental water samples (above 1 cell ml-1). Cultivable Enterobacteriaceae in food and water samples were enumerated accurately within 7 h using the FISHFC method. A FISHFC method capable of evaluating Enterobacteriaceae contamination in food and environmental water within a single working day was developed.

  6. Method Verification Requirements for an Advanced Imaging System for Microbial Plate Count Enumeration.

    Science.gov (United States)

    Jones, David; Cundell, Tony

    2018-01-01

    The Growth Direct™ System that automates the incubation and reading of membrane filtration microbial counts on soybean-casein digest, Sabouraud dextrose, and R2A agar differs only from the traditional method in that micro-colonies on the membrane are counted using an advanced imaging system up to 50% earlier in the incubation. Based on the recommendations in USP Validation of New Microbiological Testing Methods , the system may be implemented in a microbiology laboratory after simple method verification and not a full method validation. LAY ABSTRACT: The Growth Direct™ System that automates the incubation and reading of microbial counts on membranes on solid agar differs only from the traditional method in that micro-colonies on the membrane are counted using an advanced imaging system up to 50% earlier in the incubation time. Based on the recommendations in USP Validation of New Microbiological Testing Methods , the system may be implemented in a microbiology laboratory after simple method verification and not a full method validation. © PDA, Inc. 2018.

  7. The use of antibiotics to improve phage detection and enumeration by the double-layer agar technique

    Directory of Open Access Journals (Sweden)

    Ferreira Eugénio C

    2009-07-01

    Full Text Available Abstract Background The Double-Layer Agar (DLA technique is extensively used in phage research to enumerate and identify phages and to isolate mutants and new phages. Many phages form large and well-defined plaques that are easily observed so that they can be enumerated when plated by the DLA technique. However, some give rise to small and turbid plaques that are very difficult to detect and count. To overcome these problems, some authors have suggested the use of dyes to improve the contrast between the plaques and the turbid host lawns. It has been reported that some antibiotics stimulate bacteria to produce phages, resulting in an increase in final titer. Thus, antibiotics might contribute to increasing plaque size in solid media. Results Antibiotics with different mechanisms of action were tested for their ability to enhance plaque morphology without suppressing phage development. Some antibiotics increased the phage plaque surface by up to 50-fold. Conclusion This work presents a modification of the DLA technique that can be used routinely in the laboratory, leading to a more accurate enumeration of phages that would be difficult or even impossible otherwise.

  8. Analysis and enumeration algorithms for biological graphs

    CERN Document Server

    Marino, Andrea

    2015-01-01

    In this work we plan to revise the main techniques for enumeration algorithms and to show four examples of enumeration algorithms that can be applied to efficiently deal with some biological problems modelled by using biological networks: enumerating central and peripheral nodes of a network, enumerating stories, enumerating paths or cycles, and enumerating bubbles. Notice that the corresponding computational problems we define are of more general interest and our results hold in the case of arbitrary graphs. Enumerating all the most and less central vertices in a network according to their eccentricity is an example of an enumeration problem whose solutions are polynomial and can be listed in polynomial time, very often in linear or almost linear time in practice. Enumerating stories, i.e. all maximal directed acyclic subgraphs of a graph G whose sources and targets belong to a predefined subset of the vertices, is on the other hand an example of an enumeration problem with an exponential number of solutions...

  9. A Comparative Study of Enumeration Techniques for Free-Roaming Dogs in Rural Baramati, District Pune, India

    Directory of Open Access Journals (Sweden)

    Harish Kumar Tiwari

    2018-05-01

    Full Text Available The presence of unvaccinated free-roaming dogs (FRD amidst human settlements is a major contributor to the high incidence of rabies in countries such as India, where the disease is endemic. Estimating FRD population size is crucial to the planning and evaluation of interventions, such as mass immunisation against rabies. Enumeration techniques for FRD are resource intensive and can vary from simple direct counts to statistically complex capture-recapture techniques primarily developed for ecological studies. In this study we compared eight capture-recapture enumeration methods (Lincoln–Petersen’s index, Chapman’s correction estimate, Beck’s method, Schumacher-Eschmeyer method, Regression method, Mark-resight logit normal method, Huggin’s closed capture models and Application SuperDuplicates on-line tool using direct count data collected from Shirsuphal village of Baramati town in Western India, to recommend a method which yields a reasonably accurate count to use for effective vaccination coverage against rabies with minimal resource inputs. A total of 263 unique dogs were sighted at least once over 6 observation occasions with no new dogs sighted on the 7th occasion. Besides this direct count, the methods that do not account for individual heterogeneity yielded population estimates in the range of 248–270, which likely underestimate the real FRD population size. Higher estimates were obtained using the Huggin’s Mh-Jackknife (437 ± 33, Huggin’s Mth-Chao (391 ± 26, Huggin’s Mh-Chao (385 ± 30, models and Application “SuperDuplicates” tool (392 ± 20 and were considered more robust. When the sampling effort was reduced to only two surveys, the Application SuperDuplicates online tool gave the closest estimate of 349 ± 36, which is 74% of the estimated highest population of free-roaming dogs in Shirsuphal village. This method may thus be considered the most reliable method for estimating the FRD population with

  10. Comparison of Enzymatic Assay and Multiple Tube Fermentation Technique in the Assessment of Microbial Quality of the Karoon River

    Directory of Open Access Journals (Sweden)

    Mahnaz Nikaeen

    2010-09-01

    Full Text Available Microbiological monitoring of surface waters designated for use as drinking water is essential by water utilities for the design and operation of drinking water treatment plants. Enzymatic assays have been applied as a rapid alternative approach to assess the microbiological quality of freshwater. In this study, the LMX broth (LMX as an enzymatic assay was compared with the standard method of multiple tube fermentation technique (MTF for the microbial monitoring of the Karoon River. Enumeration of total coliforms and E. coli averaged 9928 and 6684 MPN/ 100 ml by the LMX and 7564 and 6546 MPN/ 100 ml for the MTF, respectively. This difference was statistically significant for TC but the overall analysis revealed no difference between E. coli recoveries on LMX and MTF. In conclusion, LMX can be used for the enumeration of coliforms and E. coli in surface waters as it is less lobar-intensive, yields faster result, and simultaneously detects both total coliforms and E. coli.

  11. Molecular Technique to Understand Deep Microbial Diversity

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2012-01-01

    Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

  12. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

    Directory of Open Access Journals (Sweden)

    Gemma Henderson

    Full Text Available Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However

  13. Enumeration of phenanthrene-degrading bacteria by an overlayer technique and its use in evaluation of petroleum-contaminated sites

    International Nuclear Information System (INIS)

    Bogardt, A.H.; Hemmingsen, B.B.

    1992-01-01

    Bacteria that are capable of degrading polycyclic aromatic hydrocarbons were enumerated by incorporating soil and water dilutions together with fine particles of phenanthrene, a polycyclic aromatic hydrocarbon, into an agarose overlayer and pouring the mixture over a mineral salts underlayer. The phenanthrene-degrading bacteria embedded in the overlayer were recognized by a halo of clearing in the opaque phenanthrene layer. Diesel fuel- or creosote-contaminated soil and water that were undergoing bioremediation contained 6 x 10 6 to 100 x 10 6 phenanthrene-degrading bacteria per g and ca. 5 x 10 5 phenanthrene-degrading bacteria per ml, respectively, whereas samples from untreated polluted sites contained substantially lower numbers. Unpolluted soil and water contained no detectable phenanthrene degraders or only very modest numbers of these organisms

  14. Influence of composting techniques on microbial succession ...

    African Journals Online (AJOL)

    pH also stabilized as the composting process progressed in the pit. Good quality compost was obtained in 5 weeks when PACT was used. Conventional pit method lasted over several weeks. Key Words: Municipal wastes; passive aeration; pit composting; temperature; microbial succession. African Journal of Biotechnology ...

  15. Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Fliermans, C.B.; Dougherty, J.M.; Franck, M.M.; McKinzey, P.C.; Hazen, T.C.

    1992-01-01

    Effective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site's microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog [reg sign] evaluation of enzyme activity in collected water samples. Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog[reg sign] activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.

  16. Immunological techniques as tools to characterize the subsurface microbial community at a trichloroethylene contaminated site

    Energy Technology Data Exchange (ETDEWEB)

    Fliermans, C.B.; Dougherty, J.M.; Franck, M.M.; McKinzey, P.C.; Hazen, T.C.

    1992-12-31

    Effective in situ bioremediation strategies require an understanding of the effects pollutants and remediation techniques have on subsurface microbial communities. Therefore, detailed characterization of a site`s microbial communities is important. Subsurface sediment borings and water samples were collected from a trichloroethylene (TCE) contaminated site, before and after horizontal well in situ air stripping and bioventing, as well as during methane injection for stimulation of methane-utilizing microorganisms. Subsamples were processed for heterotrophic plate counts, acridine orange direct counts (AODC), community diversity, direct fluorescent antibodies (DFA) enumeration for several nitrogen-transforming bacteria, and Biolog {reg_sign} evaluation of enzyme activity in collected water samples. Plate counts were higher in near-surface depths than in the vadose zone sediment samples. During the in situ air stripping and bioventing, counts increased at or near the saturated zone, remained elevated throughout the aquifer, but did not change significantly after the air stripping. Sporadic increases in plate counts at different depths as well as increased diversity appeared to be linked to differing lithologies. AODCs were orders of magnitude higher than plate counts and remained relatively constant with depth except for slight increases near the surface depths and the capillary fringe. Nitrogen-transforming bacteria, as measured by serospecific DFA, were greatly affected both by the in situ air stripping and the methane injection. Biolog{reg_sign} activity appeared to increase with subsurface stimulation both by air and methane. The complexity of subsurface systems makes the use of selective monitoring tools imperative.

  17. Analysis of the structural diversity of the microbial community in a ...

    African Journals Online (AJOL)

    drinie

    2002-10-04

    Oct 4, 2002 ... Microbial populations in paper-mill water systems are usually enumerated using microbiological techniques such as plate counts and the most probable number technique. These conventional methods can only quantify a limited percentage of the microbial populations and the microbial numbers are, ...

  18. Monitoring Techniques for Microbially Influenced Corrosion of Carbon Steel

    DEFF Research Database (Denmark)

    Hilbert, Lisbeth Rischel

    2000-01-01

    corrosion rates, when biofilm and corrosion products cover the steel surface. However, EIS might be used for detection of MIC. EN is a suitable technique to characterise the type of corrosion attack, but is unsuitable for corrosion rate estimation. The concentric electrodes galvanic probe arrangement......Abstract Monitoring Techniques for Microbially Influenced Corrosion of Carbon Steel Microbially influenced corrosion (MIC) of carbon steel may occur in media with microbiological activity of especially sulphate-reducing bacteria, e.g. on pipelines buried in soil and on marine structures. MIC...... of carbon steel must be monitored on-line in order to provide an efficient protection and control the corrosion. A number of monitoring techniques is industrially used today, and the applicability and reliability of these for monitoring MIC is evaluated. Coupons and ER are recommended as necessary basic...

  19. Application of multivariate statistical techniques in microbial ecology.

    Science.gov (United States)

    Paliy, O; Shankar, V

    2016-03-01

    Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure. © 2016 John Wiley & Sons Ltd.

  20. Enumerating submultisets of multisets

    NARCIS (Netherlands)

    Hage, J.

    2001-01-01

    In this paper we consider the problem of enumerating the submultisets of a multiset, in which each element has equal multiplicity. The crucial property is that consecutive submultisets in this listing differ one in the cardinality of only one of the elements. This is a generalization to k-ary

  1. Trends in microbial control techniques for poultry products.

    Science.gov (United States)

    Silva, Filomena; Domingues, Fernanda C; Nerín, Cristina

    2018-03-04

    Fresh poultry meat and poultry products are highly perishable foods and high potential sources of human infection due to the presence of several foodborne pathogens. Focusing on the microbial control of poultry products, the food industry generally implements numerous preventive measures based on the Hazard Analysis and Critical Control Points (HACCP) food safety management system certification together with technological steps, such as refrigeration coupled to modified atmosphere packaging that are able to control identified potential microbial hazards during food processing. However, in recent years, to meet the demand of consumers for minimally processed, high-quality, and additive-free foods, technologies are emerging associated with nonthermal microbial inactivation, such as high hydrostatic pressure, irradiation, and natural alternatives, such as biopreservation or the incorporation of natural preservatives in packaging materials. These technologies are discussed throughout this article, emphasizing their pros and cons regarding the control of poultry microbiota and their effects on poultry sensory properties. The discussion for each of the preservation techniques mentioned will be provided with as much detail as the data and studies provided in the literature for poultry meat and products allow. These new approaches, on their own, have proved to be effective against a wide range of microorganisms in poultry meat. However, since some of these emergent technologies still do not have full consumer's acceptability and, taking into consideration the hurdle technology concept for poultry processing, it is suggested that they will be used as combined treatments or, more frequently, in combination with modified atmosphere packaging.

  2. Characterisation of Microbial Cellulose Modified by Graft Copolymerization Technique

    International Nuclear Information System (INIS)

    Tita Puspitasari; Cynthia Linaya Radiman

    2008-01-01

    Chemical and phisycal modifications of polymer can be carried out by radiation induced graft copolymerization. This research was carried out to study the morphology and crystallinity of microbial cellulose copolymer grafted by acrylic acid (MC-g-AAC). The SEM microstructural analysis proved that the acrylic acid could diffuse into the microbial celullose and resulted a dense structure. Crystallinity measurement showded that the crystalinity of microbial cellulose increase from 50 % to 53 % after modification. (author)

  3. Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

    International Nuclear Information System (INIS)

    Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz

    2002-01-01

    Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. 32 P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

  4. Rumen microbial growth estimation using in vitro radiophosphorous incorporation technique

    Energy Technology Data Exchange (ETDEWEB)

    Bueno, Ives Claudio da Silva; Machado, Mariana de Carvalho; Cabral Filho, Sergio Lucio Salomon; Gobbo, Sarita Priscila; Vitti, Dorinha Miriam Silber Schmidt; Abdalla, Adibe Luiz [Centro de Energia Nuclear na Agricultura (CENA), Piracicaba, SP (Brazil)

    2002-07-01

    Rumen microorganisms are able to transform low biological value nitrogen of feed stuff into high quality protein. To determine how much microbial protein that process forms, radiomarkers can be used. Radiophosphorous has been used to mark microbial protein, as element P is present in all rumen microorganisms (as phospholipids) and the P:N ratio of rumen biomass is quite constant. The aim of this work was to estimate microbial synthesis from feedstuff commonly used in ruminant nutrition in Brazil. Tested feeds were fresh alfalfa, raw sugarcane bagasse, rice hulls, rice meal, soybean meal, wheat meal, Tifton hay, leucaena, dehydrated citrus pulp, wet brewers' grains and cottonseed meal. {sup 32} P-labelled phosphate solution was used as marker for microbial protein. Results showed the diversity of feeds by distinct quantities of nitrogen incorporated into microbial mass. Low nutrient availability feeds (sugarcane bagasse and rice hulls) promoted the lowest values of incorporated nitrogen. Nitrogen incorporation showed positive relationship (r=0.56; P=0.06) with the rate of degradation and negative relationship (r=-0.59; P<0.05) with fiber content of feeds. The results highlight that easier fermentable feeds (higher rates of degradation) and/or with lower fiber contents promote a more efficient microbial growth and better performance for the host animal. (author)

  5. Enumeration of petroleum hydrocarbon utilizing bacteria

    International Nuclear Information System (INIS)

    Mukherjee, S.; Barot, M.; Levine, A.D.

    1996-01-01

    In-situ biological treatment is one among a number of emerging technologies that may be applied to the remediation of contaminated soils and groundwater. In 1985, a surface spill of 1,500 gallons of dielectric transformer oil at the Sandia National Laboratories (HERMES II facility) resulted in contamination of soil up to depths of 160 feet. The extent of contamination and site characteristics favored the application of in-situ bioremediation as a potential remedial technology. The purpose of this research was to enumerate indigenous microbial populations capable of degrading petroleum hydrocarbons. Microbial enumeration and characterization methods suitably adapted for hydrocarbon utilizing bacteria were used as an indicator of the presence of viable microbial consortia in excavated oil samples with hydrocarbon (TPH) concentrations ranging from 300 to 26,850 ppm. Microbial activity was quantified by direct and streak plating soil samples on silica gel media. Effects of toxicity and temperature were studied using batch cultures of hydrocarbon utilizing bacteria (selectively isolated in an enrichment medium), at temperatures of 20 and 35 C. It was concluded from this study that it is possible to isolate native microorganisms from contaminated soils from depths of 60 to 160 feet, and with oil concentration ranging from 300 to 26,850 ppm. About 62% of the microorganisms isolated form the contaminated soil were capable of using contaminant oil as a substrate for growth and metabolism under aerobic conditions. Growth rates were observed to be 50% higher for the highest contaminant concentration at 20 C. Resistance to toxicity to contaminant oil was also observed to be greater at 20 C than at 35 C

  6. Recent advances in molecular techniques to study microbial communities in food-associated matrices and processes

    NARCIS (Netherlands)

    Justé, A.; Thomma, B.P.H.J.; Lievens, B.

    2008-01-01

    In the last two decades major changes have occurred in how microbial ecologists study microbial communities. Limitations associated with traditional culture-based methods have pushed for the development of culture-independent techniques, which are primarily based on the analysis of nucleic acids.

  7. Enumeration of fungi in barley

    CSIR Research Space (South Africa)

    Rabie, CJ

    1997-04-01

    Full Text Available Estimation of fungal contamination of barley grain is important as certain fungi can proliferate during the malting process. The following factors which may affect the enumeration of fungi were evaluated: dilution versus direct plating, pre...

  8. Top-k Based Adaptive Enumeration in Constraint Programming

    Directory of Open Access Journals (Sweden)

    Ricardo Soto

    2015-01-01

    order for variables and values is employed along the search. In this paper, we present a new and more lightweight approach for performing adaptive enumeration. We incorporate a powerful classification technique named Top-k in order to adaptively select strategies along the resolution. We report results on a set of well-known benchmarks where the proposed approach noticeably competes with classical and modern adaptive enumeration methods for constraint satisfaction.

  9. Emerging mass spectrometry techniques for the direct analysis of microbial colonies

    OpenAIRE

    Fang, Jinshu; Dorrestein, Pieter C.

    2014-01-01

    One of the emerging areas in microbiology is detecting specialized metabolites produced by microbial colonies and communities with mass spectrometry. In this review/perspective, we illustrate the emerging mass spectrometry methodologies that enable the interrogation of specialized metabolites directly from microbial colonies. Mass spectrometry techniques such as imaging mass spectrometry and real-time mass spectrometry allow two and three dimensional visualization of the distri...

  10. Almost computably enumerable families of sets

    International Nuclear Information System (INIS)

    Kalimullin, I Sh

    2008-01-01

    An almost computably enumerable family that is not Φ'-computably enumerable is constructed. Moreover, it is established that for any computably enumerable (c.e.) set A there exists a family that is X-c.e. if and only if the set X is not A-computable. Bibliography: 5 titles.

  11. Further validation of the HPCD-technique for the evaluation of PAH microbial availability in soil

    International Nuclear Information System (INIS)

    Doick, Kieron J.; Clasper, Paula J.; Urmann, Karina; Semple, Kirk T.

    2006-01-01

    There is currently considerable scientific interest in finding a chemical technique capable of predicting bioavailability; non-exhaustive extraction techniques (NEETs) offer such potential. Hydroxypropyl-beta-cyclodextrin (HPCD), a NEET, is further validated through the investigation of concentration ranges, differing soil types, and the presence of co-contaminants. This is the first study to demonstrate the utility of the HPCD-extraction technique to predict the microbial availability to phenanthrene across a wide concentration range and independent of soil-contaminant contact time (123 d). The efficacy of the HPCD-extraction technique for the estimation of PAH microbial availability in soil is demonstrated in the presence of co-contaminants that have been aged for the duration of the experiment together in the soil. Desorption dynamics are compared in co-contaminant and single-PAH contaminated spiked soils to demonstrate the occurrence of competitive displacement. Overall, a single HPCD-extraction technique proved accurate and reproducible for the estimation of PAH bioavailability from soil. - HPCD extractions can determine the microbial availability of PAHs in mixtures and over a range of concentrations

  12. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.

    Science.gov (United States)

    Ishii, Satoshi; Sadowsky, Michael J

    2009-04-01

    A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

  13. Aboriginal fractions: enumerating identity in Taiwan.

    Science.gov (United States)

    Liu, Jennifer A

    2012-01-01

    Notions of identity in Taiwan are configured in relation to numbers. I examine the polyvalent capacities of enumerative technologies in both the production of ethnic identities and claims to political representation and justice. By critically historicizing the manner in which Aborigines in Taiwan have been, and continue to be, constructed as objects and subjects of scientific knowledge production through technologies of measuring, I examine the genetic claim made by some Taiwanese to be "fractionally" Aboriginal. Numbers and techniques of measuring are used ostensibly to know the Aborigines, but they are also used to construct a genetically unique Taiwanese identity and to incorporate the Aborigines within projects of democratic governance. Technologies of enumeration thus serve within multiple, and sometimes contradictory, projects of representation and knowledge production.

  14. Application of hyperplane arrangements to weight enumeration

    NARCIS (Netherlands)

    Jurrius, R.P.M.J.; Pellikaan, G.R.

    2014-01-01

    Many research in coding theory is focussed on linear error-correcting codes. Since these codes are subspaces, linear algebra plays a prominent role in studying them. An important polynomial invariant of linear error-correcting codes is the (extended) weight enumerator. The weight enumerator gives

  15. Soil solution extraction techniques for microbial ecotoxicity testing: a comparative evaluation.

    Science.gov (United States)

    Tiensing, T; Preston, S; Strachan, N; Paton, G I

    2001-02-01

    The suitability of two different techniques (centrifugation and Rhizon sampler) for obtaining the interstitial pore water of soil (soil solution), integral to the ecotoxicity assessment of metal contaminated soil, were investigated by combining chemical analyses and a luminescence-based microbial biosensor. Two different techniques, centrifugation and Rhizon sampler, were used to extract the soil solution from Insch (a loamy sand) and Boyndie (a sandy loam) soils, which had been amended with different concentrations of Zn and Cd. The concentrations of dissolved organic carbon (DOC), major anions (F- , CI-, NO3, SO4(2-)) and major cations (K+, Mg2+, Ca2+) in the soil solutions varied depending on the extraction technique used. Overall, the concentrations of Zn and Cd were significantly higher in the soil solution extracted using the centrifugation technique compared with that extracted using the Rhizon sampler technique. Furthermore, the differences observed between the two extraction techniques depended on the type of soil from which the solution was being extracted. The luminescence-based biosensor Escherichia coli HB101 pUCD607 was shown to respond to the free metal concentrations in the soil solutions and showed that different toxicities were associated with each soil, depending on the technique used to extract the soil solution. This study highlights the need to characterise the type of extraction technique used to obtain the soil solution for ecotoxicity testing in order that a representative ecotoxicity assessment can be carried out.

  16. The Effect of Therapeutic Clowning on Handwashing Technique and Microbial Colonization in Preschool Children.

    Science.gov (United States)

    Arıkan, Duygu; Gürarslan Baş, Nazan; Kurudirek, Fatma; Baştopcu, Ayşe; Uslu, Hakan

    2018-05-15

    This study aimed to determine the effect of therapeutic clowning on handwashing technique and microbial colonization in preschool children. This randomized controlled trial was conducted using pre-test and post-test experimental and control groups. The study was conducted between March and June 2016 in two kindergartens in eastern Turkey. The study was completed with a total of 195 students, including 90 students in the experimental group and 105 students in the control group. A questionnaire was used for data collection. This questionnaire included sections about the subjects' descriptive characteristics and the results of the bacterial cultures of their hand swabs. For the collection of these swabs, the subjects were informed in advance, and samples were collected at predetermined times. The swabs were analyzed to determine the bacterial colonization of the subjects' hands. Clowns and video activities were used as intervention tools in the study. In the post-test, the microbial growth was ≤10 3 in 68.9% and >10 3 in 31.1% of the subjects in the experimental group. In contrast, the growth was ≤10 3 in 34.3% and >10 3 in 65.7% of the control group subjects. The difference in the post-test microbial growths of the two groups was statistically significant (p < .000). The hygienic handwashing technique taught in the therapeutic clowning and videos reduced the bacterial colonization on the preschool children's hands by 50%. Moreover, this method was effective in reducing the growth rate of coliform bacteria that indicate undesirable, poor hygiene of the hands. Considering these results, we recommend that pediatric healthcare professionals use entertaining methods such as those involving clowns to teach and guide children regarding hygienic handwashing techniques. © 2018 Sigma Theta Tau International.

  17. Rapid detection, characterization, and enumeration of foodborne pathogens.

    Science.gov (United States)

    Hoorfar, J

    2011-11-01

    enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount. © 2011 The Author. APMIS © 2011 APMIS.

  18. Detection of microbial concentration in ice-cream using the impedance technique.

    Science.gov (United States)

    Grossi, M; Lanzoni, M; Pompei, A; Lazzarini, R; Matteuzzi, D; Riccò, B

    2008-06-15

    The detection of microbial concentration, essential for safe and high quality food products, is traditionally made with the plate count technique, that is reliable, but also slow and not easily realized in the automatic form, as required for direct use in industrial machines. To this purpose, the method based on impedance measurements represents an attractive alternative since it can produce results in about 10h, instead of the 24-48h needed by standard plate counts and can be easily realized in automatic form. In this paper such a method has been experimentally studied in the case of ice-cream products. In particular, all main ice-cream compositions of real interest have been considered and no nutrient media has been used to dilute the samples. A measurement set-up has been realized using benchtop instruments for impedance measurements on samples whose bacteria concentration was independently measured by means of standard plate counts. The obtained results clearly indicate that impedance measurement represents a feasible and reliable technique to detect total microbial concentration in ice-cream, suitable to be implemented as an embedded system for industrial machines.

  19. Microbial composition of the Korean traditional food "kochujang" analyzed by a massive sequencing technique.

    Science.gov (United States)

    Nam, Young-Do; Park, So-lim; Lim, Seong-Il

    2012-04-01

    Kochujang is a traditional Korean fermented food that is made with red pepper, glutinous rice, salt, and soybean. Kochujang is fermented by naturally occurring microorganisms through which it obtains various health-promoting properties. In this study, the bacterial diversities of 9 local and 2 commercial brands of kochujang were analyzed with a barcoded pyrosequencing technique targeting the hyper-variable regions V1/V2 of the 16S rRNA gene. Through the analysis of 13524 bacterial pyrosequences, 223 bacterial species were identified, most of which converged on the phylum Firmicutes (average 93.1%). All of the kochujang samples were largely populated (>90.9% of abundance) by 12 bacterial families, and Bacillaceae showed the highest abundance in all but one sample. Bacillus subtilis and B. licheniformis were the most dominant bacterial species and were broadly distributed among the kochujang samples. Each sample contained a high abundance of region-specific bacterial species, such as B. sonorensis, B. pumilus, Weissella salipiscis, and diverse unidentified Bacillus species. Phylotype- and phylogeny-based community comparison analysis showed that the microbial communities of the two commercial brands were different from those of the local brands. Moreover, each local brand kochujang sample had region-specific microbial community reflecting the manufacturing environment. © 2012 Institute of Food Technologists®

  20. Essential Data and Techniques for Conducting Microbial Fuel Cell and other Types of Bioelectrochemical System Experiments

    KAUST Repository

    Logan, Bruce E.

    2012-01-01

    Microbial fuel cells (MFCs) and other bioelectrochemical systems are new technologies that require expertise in a variety of technical areas, ranging from electrochemistry to biological wastewater treatment. There are certain data and critical information that should be included in every MFC study, such as specific surface area of the electrodes, solution conductivity, and power densities normalized to electrode surface area and volumes. Electrochemical techniques such as linear sweep voltammetry can be used to understand the performance of the MFC, but extremely slow scans are required for these biological systems compared to more traditional fuel cells. In this Minireview, the critical information needed for MFC studies is provided with examples of how results can be better conveyed through a full description of materials, the use of proper controls, and inclusion of a more complete electrochemical analysis. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Irradiation of dates: insect disinfestation, microbial and chemical assessments, and use of thermoluminescence technique

    Energy Technology Data Exchange (ETDEWEB)

    Al-Kahtani, Hassan A.; Abu-Tarboush, Hamza M.; Ahmed, Mohamed A.; Bajaber, Adnan S. [Food Science and Nutrition Department, College of Agriculture, King Saud University, Riyadh (Saudi Arabia); Al-Dryhim, Yousif N.; Adam, El-Shami E. [Plant Protection Department, College of Agriculture, King Saud University, Riyadh (Saudi Arabia); El-Mojaddidi, Mohamed A. [King Faisal Specialist Hospital and Research Center, Riyadh (Saudi Arabia)

    1998-08-01

    Irradiation of dates (Khalas variety) at 0.9 kGy was sufficient to eliminate single insect infestation (Oryzaephilus surinamensis) and mixed infestation (O. surinamensis and Tribolium castaneum), whereas 0.3 kGy was effective only in controlling single infestation. Sensory properties were not affected but irradiation contributed to some reduction in microbial counts immediately after irradiation and counts remained low till the end of 6 months storage period. All sugars were significantly reduced immediately after irradiation but they increased gradually with increasing storage time. Thermoluminescence (TL) technique was useful in discriminating between irradiated and unirradiated dates during the entire storage period but was less sensitive as far as the dose estimation is concerned.

  2. Irradiation of dates: insect disinfestation, microbial and chemical assessments, and use of thermoluminescence technique

    International Nuclear Information System (INIS)

    Al-Kahtani, Hassan A.; Abu-Tarboush, Hamza M.; Ahmed, Mohamed A.; Bajaber, Adnan S.; Al-Dryhim, Yousif N.; Adam, El-Shami E.; El-Mojaddidi, Mohamed A.

    1998-01-01

    Irradiation of dates (Khalas variety) at 0.9 kGy was sufficient to eliminate single insect infestation (Oryzaephilus surinamensis) and mixed infestation (O. surinamensis and Tribolium castaneum), whereas 0.3 kGy was effective only in controlling single infestation. Sensory properties were not affected but irradiation contributed to some reduction in microbial counts immediately after irradiation and counts remained low till the end of 6 months storage period. All sugars were significantly reduced immediately after irradiation but they increased gradually with increasing storage time. Thermoluminescence (TL) technique was useful in discriminating between irradiated and unirradiated dates during the entire storage period but was less sensitive as far as the dose estimation is concerned

  3. Essential Data and Techniques for Conducting Microbial Fuel Cell and other Types of Bioelectrochemical System Experiments

    KAUST Repository

    Logan, Bruce E.

    2012-04-19

    Microbial fuel cells (MFCs) and other bioelectrochemical systems are new technologies that require expertise in a variety of technical areas, ranging from electrochemistry to biological wastewater treatment. There are certain data and critical information that should be included in every MFC study, such as specific surface area of the electrodes, solution conductivity, and power densities normalized to electrode surface area and volumes. Electrochemical techniques such as linear sweep voltammetry can be used to understand the performance of the MFC, but extremely slow scans are required for these biological systems compared to more traditional fuel cells. In this Minireview, the critical information needed for MFC studies is provided with examples of how results can be better conveyed through a full description of materials, the use of proper controls, and inclusion of a more complete electrochemical analysis. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Ensemble Weight Enumerators for Protograph LDPC Codes

    Science.gov (United States)

    Divsalar, Dariush

    2006-01-01

    Recently LDPC codes with projected graph, or protograph structures have been proposed. In this paper, finite length ensemble weight enumerators for LDPC codes with protograph structures are obtained. Asymptotic results are derived as the block size goes to infinity. In particular we are interested in obtaining ensemble average weight enumerators for protograph LDPC codes which have minimum distance that grows linearly with block size. As with irregular ensembles, linear minimum distance property is sensitive to the proportion of degree-2 variable nodes. In this paper the derived results on ensemble weight enumerators show that linear minimum distance condition on degree distribution of unstructured irregular LDPC codes is a sufficient but not a necessary condition for protograph LDPC codes.

  5. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kent, Stephen [University of Chicago

    2012-07-20

    The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

  6. Enumeration of Rectangles in a Tableau Shape

    Science.gov (United States)

    Mingus, Tabitha T. Y.; Grassl, Richard M.; Diaz, Ricardo; Andrew, Lane; Parker, Frieda

    2010-01-01

    This article analyzes the challenge of counting the number of rectangles of all sizes in the n-tableau and to provide a combinatorial reason for the answer. The authors present a solution on enumerating rectangles in the n-tableau using Grassl and Mingus results. The authors demonstrate their conjecture for the n-tableau and attempt to apply their…

  7. Sensitive enumeration of Listeria monocytogenes and other Listeria species in various naturally contaminated matrices using a membrane filtration method.

    Science.gov (United States)

    Barre, Léna; Brasseur, Emilie; Doux, Camille; Lombard, Bertrand; Besse, Nathalie Gnanou

    2015-06-01

    For the enumeration of Listeria monocytogenes (L. monocytogenes) in food, a sensitive enumeration method has been recently developed. This method is based on a membrane filtration of the food suspension followed by transfer of the filter on a selective medium to enumerate L. monocytogenes. An evaluation of this method was performed with several categories of foods naturally contaminated with L. monocytogenes. The results obtained with this technique were compared with those obtained from the modified reference EN ISO 11290-2 method for the enumeration of L. monocytogenes in food, and are found to provide more precise results. In most cases, the filtration method enabled to examine a greater quantity of food thus greatly improving the sensitivity of the enumeration. However, it was hardly applicable to some food categories because of filtration problems and background microbiota interference. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Impact of Roadway Stormwater Runoff on Microbial Contamination in the Receiving Stream.

    Science.gov (United States)

    Wyckoff, Kristen N; Chen, Si; Steinman, Andrew J; He, Qiang

    2017-09-01

    Stormwater runoff from roadways has increasingly become a regulatory concern for water pollution control. Recent work has suggested roadway stormwater runoff as a potential source of microbial pollutants. The objective of this study was to determine the impact of roadway runoff on the microbiological quality of receiving streams. Microbiological quality of roadway stormwater runoff and the receiving stream was monitored during storm events with both cultivation-dependent fecal bacteria enumeration and cultivation-independent high-throughput sequencing techniques. Enumeration of total coliforms as a measure of fecal microbial pollution found consistently lower total coliform counts in roadway runoff than those in the stream water, suggesting that roadway runoff was not a major contributor of microbial pollutants to the receiving stream. Further characterization of the microbial community in the stormwater samples by 16S ribosomal RNA gene-based high-throughput amplicon sequencing revealed significant differences in the microbial composition of stormwater runoff from the roadways and the receiving stream. The differences in microbial composition between the roadway runoff and stream water demonstrate that roadway runoff did not appear to have a major influence on the stream in terms of microbiological quality. Thus, results from both fecal bacteria enumeration and high-throughput amplicon sequencing techniques were consistent that roadway stormwater runoff was not the primary contributor of microbial loading to the stream. Further studies of additional watersheds with distinct characteristics are needed to validate these findings. Understanding gained in this study could support the development of more effective strategies for stormwater management in sensitive watersheds. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  9. Identification of bacteria used for microbial enhanced oil recovery process by fluorescence in situ hybridization technique

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, K.; Tanaka, S.; Otsuka, M. [Kansai Research Institute, Kyoto (Japan). Lifescience Lab.; Yonebayashi, H. [Japan National Oil Corp., Chiba (Japan). Tech. Research Center; Enomoto, H. [Tohoku University, Sendai (Japan). Dept. of Geoscience and Tech.

    2000-01-01

    A fluorescence in situ hybridization (FISH) technique using 16S rRNA-targeted oligonucleotide probes was developed for rapid detection of microorganisms for use in the microbial enhancement of oil recovery (MEOR) process. Two microorganisms, Enterobacter cloacae TRC-322 and Bacillus licheniformis TRC-18-2-a, were selected from a collection of Enterobacter sp. and Bacillus sp. which were screened in previous studies as candidate microorganisms for injection, and were used for this experiment. Oligonucleotide probes, design based on specific sequences in the 16S rRNA gene were labeled with either fluorescein isothiocyanate (FITC), or 6-car-boxy-X-rhodamine (ROX), and were allowed to hybridize with fixed cells of the two microorganisms noted above. The fluorescence signal emitted from each microorganism cells could clearly be detected by an epifluorescence microscope. Moreover, E. cloacae TRC-322 and B, licheniformis TRC-18-2-a, suspended in actual reservoir brine, including inorganic salts, oil and aboriginal cells of the reservoir brine, could be detected directly by this hybridization method, without the need for cultivation and isolation. (author)

  10. Perceptual grouping affects haptic enumeration over the fingers

    NARCIS (Netherlands)

    Overvliet, K.E.; Plaisier, M.A.

    2016-01-01

    Spatial arrangement is known to influence enumeration times in vision. In haptic enumeration, it has been shown that dividing the total number of items over the two hands can speed up enumeration. Here we investigated how spatial arrangement of items and non-items presented to the individual fingers

  11. Circulating Tumor Cells, Enumeration and Beyond

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Jian-Mei [Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); Krebs, Matthew [Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); Christie Hospital Foundation NHS Trust, Manchester M20 4BX (United Kingdom); Ward, Tim; Morris, Karen; Sloane, Robert [Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); Blackhall, Fiona [Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); School of Cancer and Enabling Sciences, University of Manchester, Manchester Cancer Research Centre, Manchester Academic Health Sciences Centre, Manchester M20 4BX (United Kingdom); Christie Hospital Foundation NHS Trust, Manchester M20 4BX (United Kingdom); Dive, Caroline, E-mail: cdive@picr.man.ac.uk [Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); School of Cancer and Enabling Sciences, University of Manchester, Manchester Cancer Research Centre, Manchester Academic Health Sciences Centre, Manchester M20 4BX (United Kingdom)

    2010-06-09

    The detection and enumeration of circulating tumor cells (CTCs) has shown significant clinical utility with respect to prognosis in breast, colorectal and prostate cancers. Emerging studies show that CTCs can provide pharmacodynamic information to aid therapy decision making. CTCs as a ‘virtual and real-time biopsy’ have clear potential to facilitate exploration of tumor biology, and in particular, the process of metastasis. The challenge of profiling CTC molecular characteristics and generating CTC signatures using current technologies is that they enrich rather than purify CTCs from whole blood; we face the problem of looking for the proverbial ‘needle in the haystack’. This review summarizes the current methods for CTC detection and enumeration, focuses on molecular characterization of CTCs, unveils some aspects of CTC heterogeneity, describes attempts to purify CTCs and scans the horizon for approaches leading to comprehensive dissection of CTC biology.

  12. Circulating Tumor Cells, Enumeration and Beyond

    International Nuclear Information System (INIS)

    Hou, Jian-Mei; Krebs, Matthew; Ward, Tim; Morris, Karen; Sloane, Robert; Blackhall, Fiona; Dive, Caroline

    2010-01-01

    The detection and enumeration of circulating tumor cells (CTCs) has shown significant clinical utility with respect to prognosis in breast, colorectal and prostate cancers. Emerging studies show that CTCs can provide pharmacodynamic information to aid therapy decision making. CTCs as a ‘virtual and real-time biopsy’ have clear potential to facilitate exploration of tumor biology, and in particular, the process of metastasis. The challenge of profiling CTC molecular characteristics and generating CTC signatures using current technologies is that they enrich rather than purify CTCs from whole blood; we face the problem of looking for the proverbial ‘needle in the haystack’. This review summarizes the current methods for CTC detection and enumeration, focuses on molecular characterization of CTCs, unveils some aspects of CTC heterogeneity, describes attempts to purify CTCs and scans the horizon for approaches leading to comprehensive dissection of CTC biology

  13. Circulating Tumor Cells, Enumeration and Beyond

    Directory of Open Access Journals (Sweden)

    Jian-Mei Hou

    2010-06-01

    Full Text Available The detection and enumeration of circulating tumor cells (CTCs has shown significant clinical utility with respect to prognosis in breast, colorectal and prostate cancers. Emerging studies show that CTCs can provide pharmacodynamic information to aid therapy decision making. CTCs as a ‘virtual and real-time biopsy’ have clear potential to facilitate exploration of tumor biology, and in particular, the process of metastasis. The challenge of profiling CTC molecular characteristics and generating CTC signatures using current technologies is that they enrich rather than purify CTCs from whole blood; we face the problem of looking for the proverbial ‘needle in the haystack’. This review summarizes the current methods for CTC detection and enumeration, focuses on molecular characterization of CTCs, unveils some aspects of CTC heterogeneity, describes attempts to purify CTCs and scans the horizon for approaches leading to comprehensive dissection of CTC biology.

  14. A state enumeration of the foil knot

    OpenAIRE

    Ramaharo, Franck; Rakotondrajao, Fanja

    2017-01-01

    We split the crossings of the foil knot and enumerate the resulting states with a generating polynomial. Unexpectedly, the number of such states which consist of two components are given by the lazy caterer's sequence. This sequence describes the maximum number of planar regions that is obtained with a given number of straight lines. We then establish a bijection between this partition of the plane and the concerned foil splits sequence.

  15. Enumeration of connected Catalan objects by type

    OpenAIRE

    Rhoades, Brendon

    2010-01-01

    Noncrossing set partitions, nonnesting set partitions, Dyck paths, and rooted plane trees are four classes of Catalan objects which carry a notion of type. There exists a product formula which enumerates these objects according to type. We define a notion of `connectivity' for these objects and prove an analogous product formula which counts connected objects by type. Our proof of this product formula is combinatorial and bijective. We extend this to a product formula which counts objects wit...

  16. Enumeration of Enterobacter cloacae after chloramine exposure.

    OpenAIRE

    Watters, S K; Pyle, B H; LeChevallier, M W; McFeters, G A

    1989-01-01

    Growth of Enterobacter cloacae on various media was compared after disinfection. This was done to examine the effects of monochloramine and chlorine on the enumeration of coliforms. The media used were TLY (nonselective; 5.5% tryptic soy broth, 0.3% yeast extract, 1.0% lactose, and 1.5% Bacto-Agar), m-T7 (selective; developed to recover injured coliforms), m-Endo (selective; contains sodium sulfite), TLYS (TLY with sodium sulfite), and m-T7S (m-T7 with sodium sulfite). Sodium sulfite in any m...

  17. Dense module enumeration in biological networks

    Science.gov (United States)

    Tsuda, Koji; Georgii, Elisabeth

    2009-12-01

    Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

  18. Dense module enumeration in biological networks

    International Nuclear Information System (INIS)

    Tsuda, Koji; Georgii, Elisabeth

    2009-01-01

    Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

  19. Enumeration of small collections violates Weber's law.

    Science.gov (United States)

    Choo, H; Franconeri, S L

    2014-02-01

    In a phenomenon called subitizing, we can immediately generate exact counts of small collections (one to three objects), in contrast to larger collections, for which we must either create rough estimates or serially count. A parsimonious explanation for this advantage for small collections is that noisy representations of small collections are more tolerable, due to the larger relative differences between consecutive numbers (e.g., 2 vs. 3 is a 50 % increase, but 10 vs. 11 is only a 10 % increase). In contrast, the advantage could stem from the fact that small-collection enumeration is more precise, relying on a unique mechanism. Here, we present two experiments that conclusively showed that the enumeration of small collections is indeed "superprecise." Participants compared numerosity within either small or large visual collections in conditions in which the relative differences were controlled (e.g., performance for 2 vs. 3 was compared with performance for 20 vs. 30). Small-number comparison was still faster and more accurate, across both "more-fewer" judgments (Exp. 1), and "same-different" judgments (Exp. 2). We then reviewed the remaining potential mechanisms that might underlie this superprecision for small collections, including the greater diagnostic value of visual features that correlate with number and a limited capacity for visually individuating objects.

  20. Algebraic computability and enumeration models recursion theory and descriptive complexity

    CERN Document Server

    Nourani, Cyrus F

    2016-01-01

    This book, Algebraic Computability and Enumeration Models: Recursion Theory and Descriptive Complexity, presents new techniques with functorial models to address important areas on pure mathematics and computability theory from the algebraic viewpoint. The reader is first introduced to categories and functorial models, with Kleene algebra examples for languages. Functorial models for Peano arithmetic are described toward important computational complexity areas on a Hilbert program, leading to computability with initial models. Infinite language categories are also introduced to explain descriptive complexity with recursive computability with admissible sets and urelements. Algebraic and categorical realizability is staged on several levels, addressing new computability questions with omitting types realizably. Further applications to computing with ultrafilters on sets and Turing degree computability are examined. Functorial models computability is presented with algebraic trees realizing intuitionistic type...

  1. Assessment of N and P in organic fertilizer using the missing element technique and a microbial bioassay

    International Nuclear Information System (INIS)

    Salas, E.; Ramirez, C.

    2002-01-01

    Assessment of N and P in organic fertilizers using the missing element technique and a microbial bioassay.Through a greenhouse bioassay, using sorghum (Sorghum vulgare) as a test plant, and a microbial assay the availability of N and P in 6 substrates was determined, namely: soil alone and in combination with several organic amendments 10% W/W of chicken manure (CM), compost (C), bocashi (B), vermicompost (V) and coffe hulls (Br). In the microbial assay a complete randomized design with 6 replicates was used; the microbial biomass (BM) was determined 2 days after the glucose amendment of each treatment. In both bioassays a 2 X 2 factorial (N and P fertilization) was establish and the following combinations resulted: +N, +P, +P+N and -P-N (control). For the greenhouse experiment, a complete randomized design with 4 replicates was used. Above-ground plant material of sorghum was harvested 34 days after showing to determine plant dry weight (PS) and content of N and P. Both assays showed a response to the soil amendment with N and P. Soil treatments with CM, C and B showed the highest values of PS and BM. Soil treatment with CM amended with N, P or both did not showed a response in PS or BM, in C and B there was a response to N addition but not to P. In treatments with V and Br, the lowest values for PS and BM were obtained, and there was a growth response to N and P. Both bioassays were able to pinpoint N and P defficiencies in the soil as well in some of the mixtures of soil with organic amendments. A high correlation was encountered between the greenhouse assay and the microbial bioassay (r= 0.86, P=0.0001). Therefore, the microbial bioassay can be a cheaper alternative to the plant bioassay not only to evaluate the nutritional quality of compost but also to identify nutrient deficiencies in soils as well as in substrates amended with organic fertilizers. (Author) [es

  2. Evaluation of the Efficacy of Different Mixing Techniques and Disinfection on Microbial Colonization of Polyether Impression Materials: A Comparative Study.

    Science.gov (United States)

    Singla, Youginder; Pachar, Renu B; Poriya, Sangeeta; Mishra, Aalok; Sharma, Rajni; Garg, Anshu

    2018-03-01

    This study aims to determine the role of mixing techniques of polyether impression materials and efficacy of disinfection on microbial colonization of these impression materials. Polyether impression material was mixed using two methods: First by hand mixing (group I) and second using an automixer (group II) with a total of 100 samples. Four microbial strains were studied, which included Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. After incubation, the bacterial colonies were counted, and then, disinfectant solution was applied. The effect of disinfection solution was evaluated for each specimen. The surface of polyether impression materials mixed with an automixer has less number of voids and overall a smoother surface as compared with the hand-mixed ones. On comparing the disinfection procedures, i.e., specimens without any disinfection and specimens after disinfection, statistically highly significant difference was seen between all the groups. We can conclude that impression mixing procedures are important in determining the surface characteristics of the impression and ultimately the colonization of bacteria and also determine the importance of disinfection on microbial colonization. This study emphasises the deleterious role of nosocomial infections and specific measures that should be taken regarding the prevention of such diseases. Dental impressions are proved to be a source of such infections and may lead to transmission of such diseases. Thus, proper measures should be taken right from the first step of impression taking to minimizing and preventing such kind of contaminations in clinical practice.

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  4. [Effect of Long-Term Application of Agrotechnical Techniques and Crops on Soil Microbial Communities].

    Science.gov (United States)

    Korvigo, I O; Pershina, E V; Ivanova, E A; Matyuk, N S; Savos'kina, O A; Chirak, E L; Provorov, N A; Andronov, E E

    2016-01-01

    Effects of long-term application ofvarious fertilizers and crops on soil microbiomes an a long-term field experiment were investigated using the library of the 16S rRNA gene sequences obtained by high-throughput sequencing of the total DNA. The communities exhibited high diversity, with 655 microbial genera belonging to 34 phyla detected (31 bacterial and 3 archaeal ones). For analysis of the effect of the studied factors on community structure, a linear model was developed in order to simplify interpretation of the data of high-throughput sequencing and to obtain biologically important information. Liming was shown to modulate the effect of mineral fertilizers on the structure of microbial populations. The differences in the structure and alpha-diversity of microbial communities were shown to depend more on the crops and liming, rather than on the fertilizers applied. Interaction between the crop factor and liming expressed as an ambiguous effect of liming on the microbiome in the presence of different plants was reliably demonstrated. Thus, in the case of barley and clover, liming resulted in increased taxonomic diversity of the community, while in the case of potato and flax it had an opposite effect.

  5. Development of a Centrifugal Technique for the Microbial Bioburden Analysis of Freon (CFC-11)

    Science.gov (United States)

    Benardini, James N.; Koukol, Robert C.; Kazarians, Gayane A.; Morales, Fabian

    2013-01-01

    NASA Procedural Requirement 8020.12C entitled "Planetary Protection Provisions for Robotic Extraterrestrial Missions" states that the source-specific encapsulated microbial density for encapsulated organisms (div(0)) in nonmetallic materials ranges from 1-30 spores/cubic cm. The standard laboratory procedure, NASA Standard Procedures for the Microbial Examination of Space Hardware, NHB 5340.1B, does not provide any direction into the methodologies to understand the bioburden within such a fluid as CFC-11 (Freon). This general specification value for the Freon would be applicable to the Freon charged within the Mars Science Laboratory fs (MSL fs) Heat Rejection System. Due to the large volume required to fill this system, MSL could not afford to conservatively allocate 55.8% of the total spore budget of the entire laboratory system (rover, descent stage, cruise stage, and aeroshell) of 5.00 X 10(exp 5) spores at launch. A novel filtration approach was developed to analyze the Freon employing a 50 kDa molecular weight cutoff (MCO) filter, followed by 0.22-micron pore-size filter to establish a calculated microbial bioburden.

  6. Enumeration of Enterobacter cloacae after chloramine exposure.

    Science.gov (United States)

    Watters, S K; Pyle, B H; LeChevallier, M W; McFeters, G A

    1989-01-01

    Growth of Enterobacter cloacae on various media was compared after disinfection. This was done to examine the effects of monochloramine and chlorine on the enumeration of coliforms. The media used were TLY (nonselective; 5.5% tryptic soy broth, 0.3% yeast extract, 1.0% lactose, and 1.5% Bacto-Agar), m-T7 (selective; developed to recover injured coliforms), m-Endo (selective; contains sodium sulfite), TLYS (TLY with sodium sulfite), and m-T7S (m-T7 with sodium sulfite). Sodium sulfite in any medium improved the recovery of chloramine-treated E. cloacae. However, sodium sulfite in TLYS and m-T7S did not significantly improve the detection of chlorine-treated E. cloacae, and m-Endo was the least effective medium for recovering chlorinated bacteria. Differences in recovery of chlorine- and chloramine-treated E. cloacae are consistent with mechanistic differences between the disinfectants. PMID:2619309

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

    Science.gov (United States)

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

    2006-07-01

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

  8. Microbial structures in an Alpine Thermal Spring - Microscopic techniques for the examination of Biofilms in a Subsurface Environment

    Science.gov (United States)

    Dornmayr-Pfaffenhuemer, Marion; Pierson, Elisabeth; Janssen, Geert-Jan; Stan-Lotter, Helga

    2010-05-01

    The research into extreme environments hast important implications for biology and other sciences. Many of the organisms found there provide insights into the history of Earth. Life exists in all niches where water is present in liquid form. Isolated environments such as caves and other subsurface locations are of interest for geomicrobiological studies. And because of their "extra-terrestrial" conditions such as darkness and mostly extreme physicochemical state they are also of astrobiological interest. The slightly radioactive thermal spring at Bad Gastein (Austria) was therefore examined for the occurrence of subsurface microbial communities. The surfaces of the submerged rocks in this warm spring were overgrown by microbial mats. Scanning electron microscopy (SEM) performed by the late Dr. Wolfgang Heinen revealed an interesting morphological diversity in biofilms found in this environment (1, 2). Molecular analysis of the community structure of the radioactive subsurface thermal spring was performed by Weidler et al. (3). The growth of these mats was simulated using sterile glass slides which were exposed to the water stream of the spring. Those mats were analysed microscopically. Staining, using fluorescent dyes such as 4',6-Diamidino-2-phenylindol (DAPI), gave an overview of the microbial diversity of these biofilms. Additional SEM samples were prepared using different fixation protocols. Scanning confocal laser microscopy (SCLM) allowed a three dimensional view of the analysed biofilms. This work presents some electron micrographs of Dr. Heinen and additionally new microscopic studies of the biofilms formed on the glass slides. The appearances of the new SEM micrographs were compared to those of Dr. Heinen that were done several years ago. The morphology and small-scale distribution in the microbial mat was analyzed by fluorescence microscopy. The examination of natural biomats and biofilms grown on glass slides using several microscopical techniques

  9. The effect of starch, inulin, and degradable protein on ruminal fermentation and microbial growth in rumen simulation technique

    Directory of Open Access Journals (Sweden)

    Xiang H. Zhao

    2014-03-01

    Full Text Available A rumen simulation technique apparatus with eight 800 mL fermentation vessels was used to investigate the effects of rumen degradable protein (RDP level and non-fibre carbohydrate (NFC type on ruminal fermentation, microbial growth, and populations of ruminal cellulolytic bacteria. Treatments consisted of two NFC types (starch and inulin supplemented with 0 g/d (low RDP or 1.56 g/d (high RDP sodium caseinate. No significant differences existed among dietary treatments in the apparent disappearance of dietary nutrients except for dietary N, which increased with increased dietary RDP (P<0.001. Compared with starch, inulin treatments reduced the molar proportion of acetate (P<0.001, the acetate:propionate ratio (P<0.001, and methane production (P=0.006, but increased the butyrate proportion (P<0.001. Increased dietary RDP led to increases in production of total volatile fatty acid (P=0.014 and methane (P=0.050, various measures of N (P≤0.046, and 16s rDNA copy numbers of Ruminococcus flavefaciens (P≤0.010. Non-fibre carbohydrate source did not affect daily microbial N flow regardless of dietary RDP, but ammonia N production was lower for inulin than for starch treatments under high RDP conditions (P<0.001. Compared with starch treatments, inulin depressed the copy numbers of Fibrobacter succinogenes in solid fraction (P=0.023 and R. flavefaciens in liquid (P=0.017 and solid fractions (P=0.007, but it increased the carboxymethylcellulase activity in solid fraction (P=0.045. Current results suggest that starch and inulin differ in ruminal volatile fatty acid fermentation but have similar effects on ruminal digestion and microbial synthesis in vitro, although inulin suppressed the growth of partial ruminal cellulolytic bacteria.

  10. Selection of bioindicators to detect lead pollution in Ebro delta microbial mats, using high-resolution microscopic techniques

    International Nuclear Information System (INIS)

    Maldonado, J.; Sole, A.; Puyen, Z.M.; Esteve, I.

    2011-01-01

    Lead (Pb) is a metal that is non-essential to any metabolic process and, moreover, highly deleterious to life. In microbial mats - benthic stratified ecosystems - located in coastal areas, phototrophic microorganisms (algae and oxygenic phototrophic bacteria) are the primary producers and they are exposed to pollution by metals. In this paper we describe the search for bioindicators among phototrophic populations of Ebro delta microbial mats, using high-resolution microscopic techniques that we have optimized in previous studies. Confocal laser scanning microscopy coupled to a spectrofluorometric detector (CLSM-λscan) to determine in vivo sensitivity of different cyanobacteria to lead, and scanning electron microscopy (SEM) and transmission electron microscopy (TEM), both coupled to energy dispersive X-ray microanalysis (EDX), to determine the extra- and intracellular sequestration of this metal in cells, were the techniques used for this purpose. Oscillatoria sp. PCC 7515, Chroococcus sp. PCC 9106 and Spirulina sp. PCC 6313 tested in this paper could be considered bioindicators for lead pollution, because all of these microorganisms are indigenous, have high tolerance to high concentrations of lead and are able to accumulate this metal externally in extracellular polymeric substances (EPS) and intracellularly in polyphosphate (PP) inclusions. Experiments made with microcosms demonstrated that Phormidium-like and Lyngbya-like organisms selected themselves at the highest concentrations of lead assayed. In the present study it is shown that all cyanobacteria studied (both in culture and in microcosms) present PP inclusions in their cytoplasm and that these increase in number in lead polluted cultures and microcosms. We believe that the application of these microscopic techniques open up broad prospects for future studies of metal ecotoxicity.

  11. Selection of bioindicators to detect lead pollution in Ebro delta microbial mats, using high-resolution microscopic techniques

    Energy Technology Data Exchange (ETDEWEB)

    Maldonado, J.; Sole, A.; Puyen, Z.M. [Departament de Genetica i Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, Edifici C, Campus de la UAB, Cerdanyola del Valles, Bellaterra (Spain); Esteve, I., E-mail: isabel.esteve@uab.cat [Departament de Genetica i Microbiologia, Facultat de Biociencies, Universitat Autonoma de Barcelona, Edifici C, Campus de la UAB, Cerdanyola del Valles, Bellaterra (Spain)

    2011-07-15

    Lead (Pb) is a metal that is non-essential to any metabolic process and, moreover, highly deleterious to life. In microbial mats - benthic stratified ecosystems - located in coastal areas, phototrophic microorganisms (algae and oxygenic phototrophic bacteria) are the primary producers and they are exposed to pollution by metals. In this paper we describe the search for bioindicators among phototrophic populations of Ebro delta microbial mats, using high-resolution microscopic techniques that we have optimized in previous studies. Confocal laser scanning microscopy coupled to a spectrofluorometric detector (CLSM-{lambda}scan) to determine in vivo sensitivity of different cyanobacteria to lead, and scanning electron microscopy (SEM) and transmission electron microscopy (TEM), both coupled to energy dispersive X-ray microanalysis (EDX), to determine the extra- and intracellular sequestration of this metal in cells, were the techniques used for this purpose. Oscillatoria sp. PCC 7515, Chroococcus sp. PCC 9106 and Spirulina sp. PCC 6313 tested in this paper could be considered bioindicators for lead pollution, because all of these microorganisms are indigenous, have high tolerance to high concentrations of lead and are able to accumulate this metal externally in extracellular polymeric substances (EPS) and intracellularly in polyphosphate (PP) inclusions. Experiments made with microcosms demonstrated that Phormidium-like and Lyngbya-like organisms selected themselves at the highest concentrations of lead assayed. In the present study it is shown that all cyanobacteria studied (both in culture and in microcosms) present PP inclusions in their cytoplasm and that these increase in number in lead polluted cultures and microcosms. We believe that the application of these microscopic techniques open up broad prospects for future studies of metal ecotoxicity.

  12. Selection of bioindicators to detect lead pollution in Ebro delta microbial mats, using high-resolution microscopic techniques.

    Science.gov (United States)

    Maldonado, J; Solé, A; Puyen, Z M; Esteve, I

    2011-07-01

    Lead (Pb) is a metal that is non-essential to any metabolic process and, moreover, highly deleterious to life. In microbial mats - benthic stratified ecosystems - located in coastal areas, phototrophic microorganisms (algae and oxygenic phototrophic bacteria) are the primary producers and they are exposed to pollution by metals. In this paper we describe the search for bioindicators among phototrophic populations of Ebro delta microbial mats, using high-resolution microscopic techniques that we have optimized in previous studies. Confocal laser scanning microscopy coupled to a spectrofluorometric detector (CLSM-λscan) to determine in vivo sensitivity of different cyanobacteria to lead, and scanning electron microscopy (SEM) and transmission electron microscopy (TEM), both coupled to energy dispersive X-ray microanalysis (EDX), to determine the extra- and intracellular sequestration of this metal in cells, were the techniques used for this purpose. Oscillatoria sp. PCC 7515, Chroococcus sp. PCC 9106 and Spirulina sp. PCC 6313 tested in this paper could be considered bioindicators for lead pollution, because all of these microorganisms are indigenous, have high tolerance to high concentrations of lead and are able to accumulate this metal externally in extracellular polymeric substances (EPS) and intracellularly in polyphosphate (PP) inclusions. Experiments made with microcosms demonstrated that Phormidium-like and Lyngbya-like organisms selected themselves at the highest concentrations of lead assayed. In the present study it is shown that all cyanobacteria studied (both in culture and in microcosms) present PP inclusions in their cytoplasm and that these increase in number in lead polluted cultures and microcosms. We believe that the application of these microscopic techniques open up broad prospects for future studies of metal ecotoxicity. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. The microbial habitability of weathered volcanic glass inferred from continuous sensing techniques.

    Science.gov (United States)

    Bagshaw, Elizabeth A; Cockell, Charles S; Magan, Naresh; Wadham, Jemma L; Venugopalan, T; Sun, Tong; Mowlem, Matt; Croxford, Anthony J

    2011-09-01

    Basaltic glasses (hyaloclastite) are a widespread habitat for life in volcanic environments, yet their interior physical conditions are poorly characterized. We investigated the characteristics of exposed weathered basaltic glass from a surface outcrop in Iceland, using microprobes capable of continuous sensing, to determine whether the physical conditions in the rock interior are hospitable to microbial life. The material provided thermal protection from freeze-thaw and rapid temperature fluctuations, similar to data reported for other rock types. Water activity experiments showed that at moisture contents less than 13% wet weight, the glass and its weathering product, palagonite, had a water activity below levels suitable for bacterial growth. In pore spaces, however, these higher moisture conditions might be maintained for many days after a precipitation event. Gas exchange between the rock interior and exterior was rapid (< 10 min) when the rocks were dry, but when saturated with water, equilibration took many hours. During this period, we demonstrated the potential for low oxygen conditions within the rock caused by respiratory stimulation of the heterotrophic community within. These conditions might exist within subglacial environments during the formation of the rocks or in micro-environments in the interior of exposed rocks. The experiments showed that microbial communities at the site studied here could potentially be active for 39% of the year, if the depth of the community within the outcrop maintains a balance between access to liquid water and adequate protection from freezing. In the absence of precipitation, the interior of weathered basaltic glass is an extreme and life-limiting environment for microorganisms on Earth and other planets.

  14. Estimating rumen microbial protein supply for indigenous ruminants using nuclear and purine excretion techniques in Indonesia

    International Nuclear Information System (INIS)

    Soejono, M.; Yusiati, L.M.; Budhi, S.P.S.; Widyobroto, B.P.; Bachrudin, Z.

    1999-01-01

    The microbial protein supply to ruminants can be estimated based on the amount of purine derivatives (PD) excreted in the urine. Four experiments were conducted to evaluate the PD excretion method for Bali and Ongole cattle. In the first experiment, six male, two year old Bali cattle (Bos sondaicus) and six Ongole cattle (Bos indicus) of similar sex and age, were used to quantify the endogenous contribution to total PD excretion in the urine. In the second experiment, four cattle from each breed were used to examine the response of PD excretion to feed intake. 14 C-uric acid was injected in one single dose to define the partitioning ratio of renal:non-renal losses of plasma PD. The third experiment was conducted to examine the ratio of purine N:total N in mixed rumen microbial population. The fourth experiment measured the enzyme activities of blood, liver and intestinal tissues concerned with PD metabolism. The results of the first experiment showed that endogenous PD excretion was 145 ± 42.0 and 132 ± 20.0 μmol/kg W 0.75 /d, for Bali and Ongole cattle, respectively. The second experiment indicated that the proportion of plasma PD excreted in the urine of Bali and Ongole cattle was 0.78 and 0.77 respectively. Hence, the prediction of purine absorbed based on PD excretion can be stated as Y = 0.78 X + 0.145 W 0.75 and Y = 0.77 X + 0.132 W 0.75 for Bali and Ongole cattle, respectively. The third experiment showed that there were no differences in the ratio of purine N:total N in mixed rumen microbes of Bali and Ongole cattle (17% vs 18%). The last experiment, showed that intestinal xanthine oxidase activity of Bali cattle was lower than that of Ongole cattle (0.001 vs 0.015 μmol uric acid produced/min/g tissue) but xanthine oxidase activity in the blood and liver of Bali cattle was higher than that of Ongole cattle (3.48 vs 1.34 μmol/min/L plasma and 0.191 vs 0.131 μmol/min/g liver tissue). Thus, there was no difference in PD excretion between these two breeds

  15. Comparison of classical and molecular techniques for the determination of microbial biodiversity in Mediterranean crop soils

    Energy Technology Data Exchange (ETDEWEB)

    Munoz, A.; Lopez-Pineiro, A.; Ramirez, M.

    2009-07-01

    Soil microbe ecology has lately become increasingly important in the study of soil microbe populations. direct extraction of soil bacteria DNA allows PCR and DGGE analyses for the microorganism identification of these complex samples, avoiding the need for time-consuming culture-dependent techniques. The aim of the present study was to compare the two techniques (culture-dependent and molecular culture-independent) in four different plots of maize (Zea mays L.) crop under irrigation in south-western Spain. (Author)

  16. Optimisation of a direct plating method for the detection and enumeration of Alicyclobacillus acidoterrestris spores.

    Science.gov (United States)

    Henczka, Marek; Djas, Małgorzata; Filipek, Katarzyna

    2013-01-01

    A direct plating method for the detection and enumeration of Alicyclobacillus acidoterrestris spores has been optimised. The results of the application of four types of growth media (BAT agar, YSG agar, K agar and SK agar) regarding the recovery and enumeration of A. acidoterrestris spores were compared. The influence of the type of applied growth medium, heat shock conditions, incubation temperature, incubation time, plating technique and the presence of apple juice in the sample on the accuracy of the detection and enumeration of A. acidoterrestris spores was investigated. Among the investigated media, YSG agar was the most sensitive medium, and its application resulted in the highest recovery of A. acidoterrestris spores, while K agar and BAT agar were the least suitable media. The effect of the heat shock time on the recovery of spores was negligible. When there was a low concentration of spores in a sample, the membrane filtration method was superior to the spread plating method. The obtained results show that heat shock carried out at 80°C for 10 min and plating samples in combination with membrane filtration on YSG agar, followed by incubation at 46°C for 3 days provided the optimal conditions for the detection and enumeration of A. acidoterrestris spores. Application of the presented method allows highly efficient, fast and sensitive identification and enumeration of A. acidoterrestris spores in food products. This methodology will be useful for the fruit juice industry for identifying products contaminated with A. acidoterrestris spores, and its practical application may prevent economic losses for manufacturers. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Enzymatic studies on phosphorus availability from phosphate compounds by microbial activities using nuclear techniques

    International Nuclear Information System (INIS)

    Abou Seer, A.M.M.

    2002-01-01

    the present study aimed to evaluate to evaluate the of phosphate solubilizing bacteria (PSB) and vesicular arbuscular mycorrhizae(VAM) as microbiological mean to convert the sparingly soluble P into available from utilized by plant through excretion of acid and alkaline phosphatase. rock phosphate as natural and a cheap source of P- fertilizer was applied in the present study. To trace the effect of microbial activity and phosphatase enzymes on phosphate availability from its compounds , set of experiments were conducted either in the lab. or green house. The obtained results could be summarized as following:- 1- phosphate solubilizing bacteria(PSB) w isolated from samples of fertile soil, 16 colonies showed positive reaction were chosen .2- bacteria , which exhibited high phosphate clearing zone (PCZ) selected to detect their efficiencies for dissolving rock phospate and select the effective one (most potent) on the basis of highest production of phosphatase and phosphorus solubilization.3- identification of the most potent (pseudomonas aeruginosa) 4- effective environmental and nutritional factors on phosphatase production by pseudomonas aeruginosa were discussed.green-house experiment: inoculation of wheat (triticum aestivum cv.sakha 8) with either PSB and /or VAM with or without rock-P fertilization was under taken. dual inoculation with psb (pseudomonas aeruginosa) and VAM improved the dry matter yield and N and P uptake by wheat as compared to other treatments. application of psb as well as VAM increased the availability of rock phosphate to be utilized by wheat

  18. Immobilization of microbial cell and yeast cell and its application to biomass conversion using radiation techniques

    International Nuclear Information System (INIS)

    Kaetsu, Isao; Kumakura, Minoru; Fujimura, Takashi; Kasai, Noboru; Tamada, Masao

    1987-01-01

    The recent results of immobilization of cellulase-producing cells and ethanol-fermentation yeast by radiation were reported. The enzyme of cellulase produced by immobilized cells was used for saccharification of lignocellulosic wastes and immobilized yeast cells were used for fermentation reaction from glucose to ethanol. The wastes such as chaff and bagasse were treated by γ-ray or electron-beam irradiation in the presence of alkali and subsequent mechanical crushing, to form a fine powder less than 50 μm in diameter. On the other hand, Trichoderma reesei as a cellulase-producing microbial cell was immobilized on a fibrous carrier having a specific porous structure and cultured to produce cellulase. The enzymatic saccharification of the pretreated waste was carried out using the produced cellulase. The enhanced fermentation process to produce ethanol from glucose with the immobilized yeast by radiation was also studied. The ethanol productivity of immobilized growing yeast cells thus obtained was thirteen times that of free yeast cells in a 1:1 volume of liquid medium to immobilized yeast cells. (author)

  19. Biofilm removal technique using sands as a research tool for accessing microbial attachment on surface

    Directory of Open Access Journals (Sweden)

    Nathanon Trachoo

    2004-01-01

    Full Text Available Biofilms have profound impacts on improved survival of the constituent microorganisms in nature. Biofilms were believed to protect constituent microorganisms from sanitizer treatment, provide a more suitable habitat for microorganisms, and become a site for genetic material exchanges between microorganisms. As we realize more about the significance of biofilm, methods used for biofilm study should be consistently developed and evaluated. To determine microbial attachment on surfaces, usually biofilms are grown on substratum surfaces and removed by vortexing with glass beads or scraping. However, scraping is not as effective as vortexing with glass beads. Another approach is direct-agar overlaying which cannot be used with high density biofilm. In this experiment, we compared effectiveness of glass beads (298±28 μm in diameter and sands (width: 221±55 μm and length: 329±118 μm in removing biofilm of Pseudomonas aeruginosa by vortexing method. The results suggested that acid-washed sands, which are significantly less inexpensive than glass beads, were as effective as (P>0.05 analytical grade glass beads in Pseudomonas aeruginosa biofilm removal without inhibiting growth of the organism.

  20. Immobilization of microbial cell and yeast cell and its application to biomass conversion using radiation techniques

    Science.gov (United States)

    Kaetsu, Isao; Kumakura, Minoru; Fujimura, Takashi; Kasai, Noboru; Tamada, Masao

    The recent results of immobilization of cellulase-producing cells and ethanol-fermentation yeast by radiation were reported. The enzyme of cellulase produced by immobilized cells was used for saccharification of lignocellulosic wastes and immobilized yeast cells were used for fermentation reaction from glucose to ethanol. The wastes such as chaff and bagasse were treated by γ-ray or electron-beam irradiation in the presence of alkali and subsequent mechanical crushing, to form a fine powder less than 50 μm in diameter. On the other hand, Trichoderma reesei as a cellulase-producing microbial cell was immobilized on a fibrous carrier having a specific porous structure and cultured to produce cellulase. The enzymatic saccharification of the pretreated waste was carried out using the produced cellulase. The enhanced fermentation process to produce ethanol from glucose with the immobilized yeast by radiation was also studied. The ethanol productivity of immobilized growing yeast cells thus obtained was thirteen times that of free yeast cells in a 1:1 volume of liquid medium to immobilized yeast cells.

  1. Comparison of media for enumeration of Clostridium perfringens from foods

    NARCIS (Netherlands)

    Jong, A.E.I. de; Eijhusen, G.P.; Brouwer-Post, E.J.F.; Grand, M.; Johansson, T.; Kärkkäinen, T.; Marugg, J.; Veld, P.H. in 't; Warmerdam, F.H.M.; Wörner, G.; Zicavo, A.; Rombouts, F.M.; Beumer, R.R.

    2003-01-01

    Many media have been developed to enumerate Clostridium perfringens from foods. In this study, six media [iron sulfite (IS) agar, tryptose sulfite cycloserine (TSC) agar, Shahidi Ferguson perfringens (SFP) agar, sulfite cycloserine azide (SCA), differential clostridial agar (DCA), and oleandomycin

  2. Enumeration, isolation and identification of bacteria and fungi from ...

    African Journals Online (AJOL)

    Enumeration, isolation and identification of bacteria and fungi from soil contaminated with petroleum products ... dropping can be useful in the bioremediation of soil contaminated with petroleum products and possibly other oil polluted sites.

  3. Wipe-rinse technique for quantitating microbial contamination on large surfaces

    Science.gov (United States)

    Kirschner, L. E.; Puleo, J. R.

    1979-01-01

    The evaluation of an improved wipe-rinse technique for the bioassay of large areas was undertaken due to inherent inadequacies in the cotton swab-rinse technique to which assay of spacecraft is currently restricted. Four types of contamination control cloths were initially tested. A polyester-bonded cloth (PBC) was selected for further evaluation because of its superior efficiency and handling characteristics. Results from comparative tests with PBC and cotton swabs on simulated spacecraft surfaces indicated a significantly higher recovery efficiency for the PBC than for the cotton (90.4 versus 75.2%). Of the sampling area sites studied, PBC was found to be most effective on surface areas not exceeding 0.74 sq m (8.0 sq ft).

  4. Mississippi exploration field trials using microbial, radiometrics, free soil gas, and other techniques

    Energy Technology Data Exchange (ETDEWEB)

    Moody, J.S.; Brown, L.R.; Thieling, S.C.

    1995-12-31

    The Mississippi Office of Geology has conducted field trials using the surface exploration techniques of geomicrobial, radiometrics, and free soil gas. The objective of these trials is to determine if Mississippi oil and gas fields have surface hydrocarbon expression resulting from vertical microseepage migration. Six fields have been surveyed ranging in depth from 3,330 ft to 18,500 ft. The fields differ in trapping styles and hydrocarbon type. The results so far indicate that these fields do have a surface expression and that geomicrobial analysis as well as radiometrics and free soil gas can detect hydrocarbon microseepage from pressurized reservoirs. All three exploration techniques located the reservoirs independent of depth, hydrocarbon type, or trapping style.

  5. Survival of probiotic adjunct cultures in cheese and challenges in their enumeration using selective media.

    Science.gov (United States)

    Oberg, C J; Moyes, L V; Domek, M J; Brothersen, C; McMahon, D J

    2011-05-01

    Various selective media for enumerating probiotic and cheese cultures were screened, with 6 media then used to study survival of probiotic bacteria in full-fat and low-fat Cheddar cheese. Commercial strains of Lactobacillus acidophilus, Lactobacillus casei, Lactobacillus paracasei, or Bifidobacterium lactis were added as probiotic adjuncts. The selective media, designed to promote growth of certain lactic acid bacteria (LAB) over others or to differentiate between LAB, were used to detect individual LAB types during cheese storage. Commercial strains of Lactococcus, Lactobacillus, and Bifidobacterium spp. were initially screened on the 6 selective media along with nonstarter LAB (NSLAB) isolates. The microbial flora of the cheeses was analyzed during 9 mo of storage at 6°C. Many NSLAB were able to grow on media presumed selective for Lactococcus, Bifidobacterium spp., or Lb. acidophilus, which became apparent after 90 d of cheese storage, Between 90 and 120 d of storage, bacterial counts changed on media selective for Bifidobacterium spp., suggesting growth of NSLAB. Appearance of NSLAB on Lb. casei selective media [de man, Rogosa, and Sharpe (MRS)+vancomycin] occurred sooner (30 d) in low-fat cheese than in full-fat control cheeses. Differentiation between NSLAB and Lactococcus was achieved by counting after 18 to 24h when the NSLAB colonies were only pinpoint in size. Growth of NSLAB on the various selective media during aging means that probiotic adjunct cultures added during cheesemaking can only be enumerated with confidence on selective media for up to 3 or 4 mo. After this time, growth of NSLAB obfuscates enumeration of probiotic adjuncts. When adjunct Lb. casei or Lb. paracasei cultures are added during cheesemaking, they appear to remain at high numbers for a long time (9 mo) when counted on MRS+vancomycin medium, but a reasonable probability exists that they have been overtaken by NSLAB, which also grow readily on this medium. Enumeration using multiple

  6. RatBot: anti-enumeration peer-to-peer botnets

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Guanhua [Los Alamos National Laboratory; Eidenbenz, Stephan [Los Alamos National Laboratory; Chen, Songqing [GEORGE MASON UNIV.

    2010-01-01

    Botnets have emerged as one of the most severe cyber threats in recent years. To obtain high resilience against a single point of failure, the new generation of botnets have adopted the peer-to-peer (P2P) structure. One critical question regarding these P2P botnets is: how big are they indeed? To address this question, researchers have proposed both actively crawling and passively monitoring methods to enumerate existing P2P botnets. In this work, we go further to explore the potential strategies that botnets may have to obfuscate their true sizes. Towards this end, this paper introduces RatBot, a P2P botnet that applies some statistical techniques to defeat existing P2P botnet enumeration methods. The key ideas of RatBot are two-fold: (1) there exist a fraction of bots that are indistinguishable from their fake identities, which are spoofing IP addresses they use to hide themselves; (2) we use a heavy-tailed distribution to generate the number of fake identities for each of these bots so that the sum of observed fake identities converges only slowly and thus has high variation. We use large-scale high-fidelity simulation to quantify the estimation errors under diverse settings, and the results show that a naive enumeration technique can overestimate the sizes of P2P botnets by one order of magnitude. We believe that our work reveals new challenges of accurately estimating the sizes of P2P botnets, and hope that it will raise the awareness of security practitioners with these challenges. We further suggest a few countermeasures that can potentially defeat RatBot's anti-enumeration scheme.

  7. Sampling methods for rumen microbial counts by Real-Time PCR techniques

    Directory of Open Access Journals (Sweden)

    S. Puppo

    2010-02-01

    Full Text Available Fresh rumen samples were withdrawn from 4 cannulated buffalo females fed a fibrous diets in order to quantify bacteria concentration in the rumen by Real-Time PCR techniques. To obtain DNA of a good quality from whole rumen fluid, eight (M1-M8 different pre-filtration methods (cheese cloths, glass-fibre and nylon filter in combination with various centrifugation speeds (1000, 5000 and 14,000 rpm were tested. Genomic DNA extraction was performed either on fresh or frozen samples (-20°C. The quantitative bacteria analysis was realized according to Real-Time PCR procedure for Butyrivibrio fibrisolvens reported in literature. M5 resulted the best sampling procedure allowing to obtain a suitable genomic DNA. No differences were revealed between fresh and frozen samples.

  8. Preparation of a newly microbial polymer using ionizing radiation technique and its conductivity

    Energy Technology Data Exchange (ETDEWEB)

    KIm, Hwa Jung; Song, Aram; Kim, Dong Ho; Park, Hae Jun [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup (Korea, Republic of)

    2016-11-15

    Extracellular polymeric substance (EPS) is produced by microorganisms for a variety of purpose in response to environmental stresses. The EPS are heterogeneous mixture composed dominantly of polysaccharides and proteins, with nucleic acid and lipid as minor constituents. Application of a bacterial EPS is in mostly bioremediation in environment and it applied to pharmaceutical industries including indwelling medical devices. Furthermore, the EPS studies have mostly been performed in the only level of bacterial culture system. In this study, we have first investigated the structural modification of EPS using ionizing radiation technique. The extracted EPS solution from bacterial culture step was exposed to gamma-irradiation at room temperature. Especially, the EPS was given irradiation at various ranges of 0, 2, 10 and 30 kGy from {sup 60}Co gamma-ray source. The structural property and surface morphology were characterized by using Fourier-transform infrared (FTIR) and field emission-scanning electron microscopy (FE-SEM). Also, the conductivity of EPS was determined by using the Van der PauW method, and the polymeric substances turned out to have semi-conductivity (about 5.38*10{sup -7})

  9. Rumen Microbial Protein Production in Rumen-Simulating-Technique (RUSITEC) Using 15N-Urea Nitrogen, as Influenced By Hay and Barley Ratios in Feed

    International Nuclear Information System (INIS)

    Al-Masri, M. R.; Abel, HJ.; Steinberg, W.

    2004-01-01

    Metabolism of dietary nitrogen using labeled 15 N and the changes in the microbial protein mass and NH3-N were studied in five rumen-simulating-technique(RUSITEC)-fermenters, which were run simultaneously in three identically repeated experiments. Each experiment consisted of a 6-day adaptation period followed directly by a 3-day collection period. The feed of the fermenters (G1, G2, G3, G4 and G5) varied in the ratio of barley. The barley increased by 20% between the fermenters. Grass hay+barley (g/d) in the feed of the fermenters was 10+2 (G1), 8+4 (G2), 6+6 (G3), 4+8 (G4) and 2+10 (G5). The results indicated that there were no significant (P>0.05) changes in the amounts of microbial nitrogen (92-118 mg/d) and microbial mass syntheses which were (mg/d): 1154 (G1), 1063 (G2), 1152 (G3), 1127 (G4) and 1362 (G5). Increasing the proportion of barley in the fermenters (G4 and G5) decreased NH3-N amounts (G2 and G3) significantly (P<0.05). The energy was not efficiently used in G5 having a lower ratio of the microbial nitrogen and microbial mass to the total short chain fatty acids than that other fermenters. (authors)

  10. Enumeration of smallest intervention strategies in genome-scale metabolic networks.

    Directory of Open Access Journals (Sweden)

    Axel von Kamp

    2014-01-01

    Full Text Available One ultimate goal of metabolic network modeling is the rational redesign of biochemical networks to optimize the production of certain compounds by cellular systems. Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still lacking. In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal provide an exhaustive enumeration approach. However, their disadvantage is the combinatorial explosion in larger networks and the requirement to compute first the elementary modes (EMs which itself is impractical in genome-scale networks. We present MCSEnumerator, a new method for effective enumeration of the smallest MCSs (with fewest interventions in genome-scale metabolic network models. For this we combine two approaches, namely (i the mapping of MCSs to EMs in a dual network, and (ii a modified algorithm by which shortest EMs can be effectively determined in large networks. In this way, we can identify the smallest MCSs by calculating the shortest EMs in the dual network. Realistic application examples demonstrate that our algorithm is able to list thousands of the most efficient intervention strategies in genome-scale networks for various intervention problems. For instance, for the first time we could enumerate all synthetic lethals in E.coli with combinations of up to 5 reactions. We also applied the new algorithm exemplarily to compute strain designs for growth-coupled synthesis of different products (ethanol, fumarate, serine by E.coli. We found numerous new engineering strategies partially requiring less knockouts and guaranteeing higher product yields (even without the assumption of optimal growth than reported previously. The strength of the presented approach is that smallest intervention strategies can be

  11. Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

    Science.gov (United States)

    Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

    2017-08-16

    Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

  12. Prospective randomized investigation for evaluation of postoperative changes in the microbial climate of paranasal mucosa by the use of different dissoluting techniques during postoperative care.

    Science.gov (United States)

    Maune, S; Johannssen, V; Sahly, H; Werner, J A; Salhy, H

    1999-09-01

    Endonasal dissolution by the use of NaCl-solution is a common postoperative treatment of the nasal mucosa after endonasal surgery. These procedure involve for example endonasal shower and sterilized solutions. The contamination of nasal shower in case of unprofessional cleaning after treatment was an argument against this technique in earlier discussions. The danger of such an infection should be avoided by the use of sterilized solution. Therefore the dependence of nasal microbial climate on different nasal dissoluting techniques was investigated by the use of such named endonasal shower (Siemens und Co, Bad Ems, Germany) in comparison with sterilized solution (Rhinomer, Zyma SA, Nyon, France). Microbial cultures were investigated of 80 patients after endonasal surgery (53 m, 27 f; 31 +/- 21 age). Surgery was done for the treatment of chronic polypous sinusitis. Pre-, intra- and postoperative samples were taken in 640 cases to proceed microbial cultures. Material was transferred with the use of a Port-A-Cul-transport medium and preparation of the microbial cultures was done during the first four hours. As a result 895 bacterial clones were cultivated. These consisted of 87% aerob and 13% anaerob bacteria. Staphylococcus aureus (39%) and members of the family of Enterobactericae (30%) were the most common microbes. There was neither an evidence for postoperative microbes on the nasal mucosa nor a correlation between the dissoluting technique and the postoperative outcome. The use of sterilized solutions for the postoperative care of endonasal mucosa does not cause an additional worthful effect on neither the postoperative microbial climate nor the outcome in comparison to endonasal shower.

  13. Development, standardization and validation of purine excretion technique for measuring microbial protein supply for Yerli Kara cross-breed cattle

    International Nuclear Information System (INIS)

    Cetinkaya, N.; Ozdemir, H.; Gucus, A.I.; Ozcan, H.; Sogut, A.; Yaman, S.

    2002-01-01

    Three experiments were conducted to evaluate of the developed techniques for uric acid, allantoin and creatinine in Yerli Kara cross-breed cattle on farm at different feeding level locally available feed resources and linking the observed information to feed intake and to assess of protein nutrition status of Yerli Kara cross-breed dairy cattle using urinary PD and creatinine excretion. In Experiment I. Response of daily PD excretion to feed intake in Yerli Kara cross-breed on state farm was measured. Animals were fed a mixed diet containing 30 % wheat straw and 70 % compounded feed. The diet contained 90 % DM, its N and OM contents were 124 and 950 g/kg DM, respectively. In Experiment II. Spot urine sampling techniques was applied at state farm. Four Yerli Kara cross-breed bulls live weight with a mean of 211±41.3 kg were used. Experimental design, feeding and diet were the same as in Experiment I. The treatments were [located according to a 4x4 Latin Square design. In Experiment III. Spot urine sampling techniques was applied at smallholder farms. Compound feed containing 65 % barley, 25 % bran, 6 % sunflower seed meal, 3 % manner dust and 1 % mineral and vitamin mixture (120 g/kg DM-Crude Protein and 950 g/kg DM-Organic Matter)- was offered total in between 2 to 3 kg in two parts one in the morning (07:30 h) and one in the afternoon (17:00 h). Compound feed ingredients were similar given to all animals but Groups I, II and III animals were receiving 1 to 2 kg/d of straw (30 g CP/kg DM, 93Og OM/kg DM), grass hay (70g CP/kg DM, 915 g OM/kg DM), straw and grass hay respectively. There were significant correlations (R 2 =0.99) between PD excretion (mmol/d) and DOMI (kg/d) for YK-C cattle. PD execration (mmol/L) was plotted against PD: Creatinine W 0.75 to obtain slope and use as constant for the estimation of daily PD excretion from spot sampling from animals held by small holders. The equation could be expressed as: PD (mmol/d)=8.27+0.960 (PD:CxW 0.75 ). The

  14. CLEVER: Clique-Enumerating Variant Finder

    NARCIS (Netherlands)

    Marschall, T.; Costa, I.; Canzar, S.; bauer, m; Klau, G.W.; Schliep, A.; Schönhuth, A.

    2012-01-01

    Motivation: Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most

  15. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On; Chung, Hong Chun; Yang, Jiangke; Wang, Yong; Dash, Swagatika; Wang, Hao; Qian, Pei-Yuan

    2014-01-01

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members

  16. Dose-response effects of dietary pequi oil on fermentation characteristics and microbial population using a rumen simulation technique (Rusitec).

    Science.gov (United States)

    Duarte, Andrea Camacho; Durmic, Zoey; Vercoe, Philip E; Chaves, Alexandre V

    2017-12-01

    The effect of increasing the concentration of commercial pequi (Caryocar brasiliense) oil on fermentation characteristics and abundance of methanogens and fibrolityc bacteria was evaluated using the rumen simulation technique (Rusitec). In vitro incubation was performed over 15 days using a basal diet consisting of ryegrass, maize silage and concentrate in equal proportions. Treatments consisted of control diet (no pequi oil inclusion, 0 g/kg DM), pequi dose 1 (45 g/kg DM), and pequi dose 2 (91 g/kg DM). After a 7 day adaptation period, samples for fermentation parameters (total gas, methane, and VFA production) were taken on a daily basis. Quantitative real time PCR (q-PCR) was used to evaluate the abundance of the main rumen cellulolytic bacteria, as well as abundance of methanogens. Supplementation with pequi oil did not reduce overall methane production (P = 0.97), however a tendency (P = 0.06) to decrease proportion of methane in overall microbial gas was observed. Increasing addition of pequi oil was associated with a linear decrease (P < 0.01) in dry matter disappearance of maize silage. The abundance of total methanogens was unchanged by the addition of pequi oil, but numbers of those belonging to Methanomassiliicoccaceae decreased in liquid-associated microbes (LAM) samples (P < 0.01) and solid-associated microbes (SAM) samples (P = 0.09) respectively, while Methanobrevibacter spp. increased (P < 0.01) only in SAM samples. Fibrobacter succinogenes decreased (P < 0.01) in both LAM and SAM samples when substrates were supplemented with pequi oil. In conclusion, pequi oil was ineffective in mitigating methane emissions and had some adverse effects on digestibility and selected fibrolytic bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Mupirocin-mucin agar for selective enumeration of Bifidobacterium bifidum

    Czech Academy of Sciences Publication Activity Database

    Pechar, R.; Rada, V.; Parafati, L.; Musilová, S.; Bunešová, V.; Vlková, E.; Killer, Jiří; Mrázek, Jakub; Kmeť, V.; Svejštil, R.

    2014-01-01

    Roč. 191, č. 1 (2014), s. 32-35 ISSN 0168-1605 R&D Projects: GA ČR GA13-08803S Institutional support: RVO:67985904 Keywords : probiotics * Bifidobacterium bifidum * selective enumeration Subject RIV: EE - Microbiology, Virology Impact factor: 3.082, year: 2014

  18. Enumeration and estimation of insect attack fruits of some cultivars ...

    African Journals Online (AJOL)

    In this study, five cultivars of Punica granatum identified (two of which are endemic, while the other three are new) were grown in certain farms at Al-Taif, Saudi Arabia. Enumeration to the insects attack its' fruits illustrated that, there are three insects, namely, Virchola livia, Ectomyelois ceratonia and Pseudococcus maitimus ...

  19. Immunophenotypic enumeration of CD4 + T-lymphocyte values in ...

    African Journals Online (AJOL)

    Background: The enumeration of CD4+ T-lymphocytes in Human Immunodeficiency Virus (HIV)-infected individuals is an essential tool for staging HIV disease, to make decisions for initiation of anti-retroviral therapy (ART), for monitoring response to ART and to initiate chemoprophylaxis against opportunistic infections.

  20. A combinatorial enumeration problem of RNA secondary structures

    African Journals Online (AJOL)

    use

    2011-12-21

    Dec 21, 2011 ... interesting combinatorial questions (Chen et al., 2005;. Liu, 2006; Schmitt and Waterman 1994; Stein and. Waterman 1978). The research on the enumeration of. RNA secondary structures becomes one of the hot topics in Computational Molecular Biology. An RNA molecule is described by its sequences of.

  1. A review of gastrointestinal microbiology with special emphasis on molecular microbial ecology approaches

    International Nuclear Information System (INIS)

    Mackie, R.I.; Cann, I.K.O.

    2005-01-01

    All animals, including humans, are adapted to life in a microbial world. Large populations of micro-organisms inhabit the gastrointestinal tract of all animals and form a closely integrated ecological unit with the host. This complex, mixed, microbial culture can be considered the most metabolically adaptable and rapidly renewable organ of the body, which plays a vital role in the normal nutritional, physiological, immunological and protective functions of the host animal. Bacteria have traditionally been classified mainly on the basis of phenotypic properties. Despite the vast amount of knowledge generated for ruminal and other intestinal ecosystems using traditional techniques, the basic requisites for ecological studies, namely, enumeration and identification of all community members, have limitations. The two major problems faced by microbial ecologists are bias introduced by culture-based enumeration and characterization techniques, and the lack of a phylogenetically-based classification scheme. Modem molecular ecology techniques based on sequence comparisons of nucleic acids (DNA or RNA) can be used to provide molecular characterization while at the same time providing a classification scheme that predicts natural evolutionary relationships. These molecular methods provide results that are independent of growth conditions and media used. Also, using these techniques, bacteria can be classified and identified before they can be grown in pure culture. These nucleic acid-based techniques will enable gut microbiologists to answer the most difficult question in microbial ecology: namely, describing the exact role or function a specific bacterium plays in its natural environment and its quantitative contribution to the whole. However, rather than replacing the classical culture-based system, the new molecular-based techniques can be used in combination with the classical approach to improve cultivation, speciation and evaluation of diversity. The study of microbial

  2. Estimation of microbial protein supply of lactating dairy cows under smallholder farms in north-east Thailand using urinary purine derivative technique

    International Nuclear Information System (INIS)

    Pimpa, O.; Liang, J.B.

    2004-01-01

    Two experiments were conducted to examine the potential of urinary purine derivative (PD) as a predictive index of microbial protein supply in ruminant livestock under farm conditions. Results of Experiment 1 indicated that diurnal variation in the PDC index ( [mmol/L PD]/[mmol/L creatinine] kgW 0.75 ) in spot urine samples of zebu cattle was small and highly correlated with the daily PD output, suggesting that spot urine samples could be used to derive an index for estimating microbial protein supply of cattle under farm conditions. However, the PDC index for buffaloes was poorly correlated to daily urinary PD output, therefore the use of spot urine samples appeared to be unsuitable for buffaloes. Based on the above results, spot urine samples were used to estimate the microbial protein supply of lactating dairy cows under farm conditions in a follow-up experiment. The study was conducted using 24 lactating cows in 6 smallholder dairy farms situated in Khon Kaen province of Northeast Thailand. The study was conducted over two climatic seasons (raining and dry), where the animals were fed 5 kg of farm-mixed concentrate feed supplemented either with green grass (cut or grazing) or rice straw as roughage source during the raining and dry seasons, respectively. The results indicated that microbial protein supply was not significantly different and therefore, the nutritional status of the lactating cows was not significantly different between the two seasons. The absence of differences in milk yield between seasons seems to support our findings. We conclude that urinary PD technique could be used to estimate rumen microbial protein production for dairy cattle under farm conditions. (author)

  3. An insight into the isolation, enumeration and molecular detection of Listeria monocytogenes in food

    Directory of Open Access Journals (Sweden)

    Jodi Woan-Fei Law

    2015-11-01

    Full Text Available Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria Enrichment Broth (BLEB, Fraser broth and University of Vermont Medium (UVM Listeria enrichment broth are recommended by regulatory agencies such as FDA-BAM, USDA-FSIS and ISO. Many plating media are available for the isolation of L. monocytogenes, for instance, PALCAM, Oxford and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. MPN technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction (PCR, multiplex polymerase chain reaction (mPCR, real-time/quantitative polymerase chain reaction (qPCR, nucleic acid sequence-based amplification (NASBA, loop-mediated isothermal amplification (LAMP, DNA microarray and Next Generation Sequencing (NGS technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labour-saving. In future, there are chances for the development of new techniques for the detection and identification of foodborne with improved features.

  4. An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food

    Science.gov (United States)

    Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

    2015-01-01

    Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are

  5. Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC).

    Science.gov (United States)

    Zhao, X H; Liu, C J; Liu, Y; Li, C Y; Yao, J H

    2013-12-01

    A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N. © 2012 Blackwell Verlag GmbH.

  6. Enumeration of self-avoiding walks on the square lattice

    International Nuclear Information System (INIS)

    Jensen, Iwan

    2004-01-01

    We describe a new algorithm for the enumeration of self-avoiding walks on the square lattice. Using up to 128 processors on a HP Alpha server cluster we have enumerated the number of self-avoiding walks on the square lattice to length 71. Series for the metric properties of mean-square end-to-end distance, mean-square radius of gyration and mean-square distance of monomers from the end points have been derived to length 59. An analysis of the resulting series yields accurate estimates of the critical exponents γ and ν confirming predictions of their exact values. Likewise we obtain accurate amplitude estimates yielding precise values for certain universal amplitude combinations. Finally we report on an analysis giving compelling evidence that the leading non-analytic correction-to-scaling exponent Δ 1 = 3/2

  7. Probiotic bacteria: selective enumeration and survival in dairy foods.

    Science.gov (United States)

    Shah, N P

    2000-04-01

    A number of health benefits have been claimed for probiotic bacteria such as Lactobacillus acidophilus, Bifidobacterium spp., and Lactobacillus casei. Because of the potential health benefits, these organisms are increasingly incorporated into dairy foods. However, studies have shown low viability of probiotics in market preparations. In order to assess viability of probiotic bacteria, it is important to have a working method for selective enumeration of these probiotic bacteria. Viability of probiotic bacteria is important in order to provide health benefits. Viability of probiotic bacteria can be improved by appropriate selection of acid and bile resistant strains, use of oxygen impermeable containers, two-step fermentation, micro-encapsulation, stress adaptation, incorporation of micronutrients such as peptides and amino acids and by sonication of yogurt bacteria. This review will cover selective enumeration and survival of probiotic bacteria in dairy foods.

  8. Enumeration of minimal stoichiometric precursor sets in metabolic networks.

    Science.gov (United States)

    Andrade, Ricardo; Wannagat, Martin; Klein, Cecilia C; Acuña, Vicente; Marchetti-Spaccamela, Alberto; Milreu, Paulo V; Stougie, Leen; Sagot, Marie-France

    2016-01-01

    What an organism needs at least from its environment to produce a set of metabolites, e.g. target(s) of interest and/or biomass, has been called a minimal precursor set. Early approaches to enumerate all minimal precursor sets took into account only the topology of the metabolic network (topological precursor sets). Due to cycles and the stoichiometric values of the reactions, it is often not possible to produce the target(s) from a topological precursor set in the sense that there is no feasible flux. Although considering the stoichiometry makes the problem harder, it enables to obtain biologically reasonable precursor sets that we call stoichiometric. Recently a method to enumerate all minimal stoichiometric precursor sets was proposed in the literature. The relationship between topological and stoichiometric precursor sets had however not yet been studied. Such relationship between topological and stoichiometric precursor sets is highlighted. We also present two algorithms that enumerate all minimal stoichiometric precursor sets. The first one is of theoretical interest only and is based on the above mentioned relationship. The second approach solves a series of mixed integer linear programming problems. We compared the computed minimal precursor sets to experimentally obtained growth media of several Escherichia coli strains using genome-scale metabolic networks. The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr.

  9. Planar articulated mechanism design by graph theoretical enumeration

    DEFF Research Database (Denmark)

    Kawamoto, A; Bendsøe, Martin P.; Sigmund, Ole

    2004-01-01

    This paper deals with design of articulated mechanisms using a truss-based ground-structure representation. By applying a graph theoretical enumeration approach we can perform an exhaustive analysis of all possible topologies for a test example for which we seek a symmetric mechanism. This guaran....... This guarantees that one can identify the global optimum solution. The result underlines the importance of mechanism topology and gives insight into the issues specific to articulated mechanism designs compared to compliant mechanism designs....

  10. The application of fluorescence in situ hybridization (FISH technique for studying the microbial communities in intestinal tissues of white shrimp (Penaeus vannamei

    Directory of Open Access Journals (Sweden)

    Supamattaya, K.

    2005-02-01

    Full Text Available Fluorescence in situ hybridization technique is very useful for the evaluation of microbial communities in various environments. It is possible to apply this technique to study the intestinal microflora in white shrimp (Penaeus vannamei. Different fixatives and storage temperature were tested in this technique. It was found that fixation with 10% buffered formalin for 12 hours and changed to 70% ethanol shown positive results when compared to the fixation with Davidson's fixative or RF fixative. The best signaling was obtainedfrom the samples which were stored in -20ºC. By using the DNA probe targeted to the Eubacteria domain (EUB338 probe, 5′-GCT GCC TCC CGT AGG AGT-3′ labeled with fluorescein as a hybridizing probe, it was found that most intestinal microflora were aggregated with the intestinal contents, or dispersed in the lumen. There was not evidence of the attachment of the microflora with the intestinal epithelium in this study.

  11. Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

    Directory of Open Access Journals (Sweden)

    Anna Gałązka

    2018-01-01

    Full Text Available Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS, reduced tillage (RT, full tillage (FT, and crop rotation (CR. Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation. The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895, genus level (P = 0.026, F = 3.313 and on the species level (P = 0.033, F = 2.718. This study has shown that: (1 fungal diversity was changed

  12. Multicentre evaluation of stable reference whole blood for enumeration of lymphocyte subsets by flow cytometry.

    Science.gov (United States)

    Edwards, Cherry; Belgrave, Danielle; Janossy, George; Bradley, Nicholas J; Stebbings, Richard; Gaines-Das, Rose; Thorpe, Robin; Sawle, Alex; Arroz, Maria Jorge; Brando, Bruno; Gratama, Jan Willem; Orfao de Matos, Alberto; Papa, Stephano; Papamichail, Michael; Lenkei, Rodica; Rothe, Gregor; Barnett, David

    2005-06-22

    BACKGROUND: Clinical indications for lymphocyte subset enumeration by flow cytometry include monitoring of disease progression and timing of therapeutic intervention in infection with human immunodeficiency virus. Until recently international standardisation has not been possible due to a lack of suitable stable reference material. METHODS: This study consisted of two trials of a stabilised whole blood preparation. Eleven participants were sent two standard protocols for staining plus gating strategy and asked to report absolute counts for lymphocyte subsets. RESULTS: No significant difference was detected between the two methods when results from the two assays and all partners were pooled. Significant differences in results from the different partners were observed. However, representative mean counts were obtained for geometric means, geometric coefficient of variation, and 95% confidence interval for CD3 910 cells/mul, 9%, and 888 to 933, respectively), CD4 (495 cells/mul, 12%, and 483 to 507), and CD8 (408 cells/mul, 13%, and 393 to 422). CONCLUSION: We have introduced a stabilised blood preparation and a well-characterized biological standard. The availability of this reference material greatly simplifies the validation of new techniques for CD4(+) T-cell enumeration and the expansion of external quality assurance programmes for clinical laboratories, including those that operate in resource-restricted environments. (c) 2005 Wiley-Liss, Inc.

  13. Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R. [University of Massachusetts, Amherst

    2012-11-28

    The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities in a diversity of soils and sediments.

  14. Influence of Inoculation, Nitrogen and Phosphorus Levels on Wheat Growth and Soil Microbial Biomass-N Using 15N Techniques

    International Nuclear Information System (INIS)

    Galal, Y.G.; El-Ghandour, I.A.; Abdel Raouf, A.M.; Osman, M.E.

    2003-01-01

    Pot experiment was carried out with wheat that cultivated in virgin sandy soil and inoculated with Rhizobium (Rh), mycorrhizea (VAM) and mixture of both. The objective of this work was to verify the potential of these inoculum on wheat production, nutrient acquisition and microbial biomass N (MBN) contribution as affected by N and P fertilizers levels. MBN was detected through the fumigation-extraction method. Nitrogen and phosphorus fertilizers were applied at three levels, 0; 25 ppm N and 3.3 ppm P and 50 ppm N and 6.6 ppm P in the form of ( 15 NH 4 ) 2 SO 4 , 5% atom excess and super-phosphate, respectively. The effect of inoculation and chemical fertilizers on dry matter (DM), N and P uptake (shoot and grain) and MBN were traced. The obtained data revealed that the highest DM and N uptake by wheat shoot were recorded with the dual inoculation (Rh + VAM) at the highest level of N and P fertilizers. The highest grain yield was detected with single inoculum of AM fungi while N and P uptake were with dual inoculation at the same rate of fertilizers. Inoculation with Rh either alone or in combination with VAM have a positive and stimulative effect on wheat growth and N and P uptake indicating the possibilities of extending the use of symbiotic microorganisms to be applied with cereals. The fluctuation in the soil microbial biomass N did not gave a chance to recognize, exactly, the impact of inoculation and/or fertilization levels

  15. Microbial deterioration of vacuum-packaged chilled beef cuts and techniques for microbiota detection and characterization: a review

    Directory of Open Access Journals (Sweden)

    Maria Lucila Hernández-Macedo

    2011-03-01

    Full Text Available Gas production from microbial deterioration in vacuum-packs of chilled meat leads to pack distension, which is commonly referred as blown pack. This phenomenon is attributed to some psychrophilic and psychrotrophic Clostridium species, as well as Enterobacteria. The ability of these microorganisms to grow at refrigeration temperatures makes the control by the meat industry a challenge. This type of deterioration has been reported in many countries including some plants in the Midwestern and Southeastern regions of Brazil. In addition to causing economic losses, spoilage negatively impacts the commercial product brand, thereby impairing the meat industry. In the case of strict anaerobes species they are difficult to grow and isolate using culture methods in conventional microbiology laboratories. Furthermore, conventional culture methods are sometimes not capable of distinguishing species or genera. DNA-based molecular methods are alternative strategies for detecting viable and non-cultivable microorganisms and strict anaerobic microorganisms that are difficult to cultivate. Here, we review the microorganisms and mechanisms involved in the deterioration of vacuum-packaged chilled meat and address the use of molecular methods for detecting specific strict anaerobic microorganisms and microbial communities in meat samples.

  16. Simple method for correct enumeration of Staphylococcus aureus

    DEFF Research Database (Denmark)

    Haaber, J.; Cohn, M. T.; Petersen, A.

    2016-01-01

    culture. When grown in such liquid cultures, the human pathogen Staphylococcus aureus is characterized by its aggregation of single cells into clusters of variable size. Here, we show that aggregation during growth in the laboratory standard medium tryptic soy broth (TSB) is common among clinical...... and laboratory S. aureus isolates and that aggregation may introduce significant bias when applying standard enumeration methods on S. aureus growing in laboratory batch cultures. We provide a simple and efficient sonication procedure, which can be applied prior to optical density measurements to give...

  17. Microbial and molecular techniques to evaluate and to implement in-situ biodegradation potential and activity at sites contaminated with aromatic and chlorinated hydrocarbons

    International Nuclear Information System (INIS)

    Karg, F.; Henkler, Ch.

    2005-01-01

    Intrinsic bio-remediation harnesses the ability of indigenous microorganisms to degrade contaminants that are present in soil and groundwater. Over the past decade many environmental regulatory agencies especially in Europe have come to recognize the importance of these natural processes in contaminant attenuation. In order to use in-situ bio-remediation to clean up a site successfully it is necessary to investigate the indigenous microbial population and its potential activity to degrade the contaminants of concern (COCs). The evaluation of naturally-occurring degradative activity in initial screening of soil and groundwater samples using recently developed molecular and microbial methods may allow for the implementation of a contaminant reduction and management program without the need for fully engineered remediation intervention. Limited engineering approaches (nutrient delivery etc.) can be implemented to support naturally-occurring bio-restoration processes to achieve a controlled, dynamic attenuation of COCs. Techniques for monitoring pollutant-degrading microorganisms were previously limited to standard culturing techniques. More recently, techniques based upon detection of genetic elements and metabolic activities have been developed in collaboration with university partners Europe, especially in France. The modern techniques are more sensitive for monitoring microbial populations, metabolic activity and the genetic potential to degrade the COCs, and avoid the need for cultivation of microbes under artificial conditions in the laboratory. Especially the application of PCR-Tests (Polymerase Chain Reaction) are able to quantify the Genetic Potential of Pollutant Microbiological Degradation on a contaminated site. This enables to use very economic in-situ site rehabilitation strategies as for example (Dynamic Natural Attenuation). For this modern application of these new strategies PLANREAL created with HPC Envirotec and together with a French University

  18. Alternative microbial methods: An overview and selection criteria.

    NARCIS (Netherlands)

    Jasson, V.; Jacxsens, L.; Luning, P.A.; Rajkovic, A.; Uyttendaele, M.

    2010-01-01

    This study provides an overview and criteria for the selection of a method, other than the reference method, for microbial analysis of foods. In a first part an overview of the general characteristics of rapid methods available, both for enumeration and detection, is given with reference to relevant

  19. Anthropogenic Pollution Impact on Microbial Contamination of Lake ...

    African Journals Online (AJOL)

    Indicator bacteria were enumerated by membrane filtration while pathogenic bacteria were recovered by broth enrichment of water samples. Microbial load did not differ significantly with season and locations but fecal coliform (FC) had positive significant correlation (r = 0.36*; P < 0.05) with season. Mean total coliform (TC) ...

  20. Microbial flora of Clarias Gariepinus in the early stages of ...

    African Journals Online (AJOL)

    A study was carried out to establish the microbial flora in farmed Clarias gariepinus hatchery systems. Enumeration of total aerobic heterotrophic bacteria and fungi, total coliforms, Salmonella spp. Vibrio spp. and Aeromonas hydrophila from eggs (fertilized and unfertilized), larvae, fry, fry feed and tank water showed that ...

  1. Soil Microbes and soil microbial proteins: interactions with clay minerals

    International Nuclear Information System (INIS)

    Spence, A.; Kelleher, B. P.

    2009-01-01

    Bacterial enumeration in soil environments estimates that the population may reach approximately 10 1 0 g - 1 of soil and comprise up to 90% of the total soil microbial biomass. Bacteria are present in soils as single cells or multicell colonies and often strongly adsorb onto mineral surfaces such as sand and clay. The interactions of microbes and microbial biomolecules with these minerals have profound impacts on the physical, chemical and biological properties of soils. (Author)

  2. Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario.

    Science.gov (United States)

    Blanco, Yolanda; Gallardo-Carreño, Ignacio; Ruiz-Bermejo, Marta; Puente-Sánchez, Fernando; Cavalcante-Silva, Erika; Quesada, Antonio; Prieto-Ballesteros, Olga; Parro, Víctor

    2017-10-01

    The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing. Key Words: Planetary exploration-Life detection-Microbial mat-Life detector chip-Thermogravimetry-Raman spectroscopy-NIR-DRIFTS. Astrobiology 17, 984-996.

  3. MacWilliams Identity for M-Spotty Weight Enumerator

    Science.gov (United States)

    Suzuki, Kazuyoshi; Fujiwara, Eiji

    M-spotty byte error control codes are very effective for correcting/detecting errors in semiconductor memory systems that employ recent high-density RAM chips with wide I/O data (e.g., 8, 16, or 32bits). In this case, the width of the I/O data is one byte. A spotty byte error is defined as random t-bit errors within a byte of length b bits, where 1 le t ≤ b. Then, an error is called an m-spotty byte error if at least one spotty byte error is present in a byte. M-spotty byte error control codes are characterized by the m-spotty distance, which includes the Hamming distance as a special case for t =1 or t = b. The MacWilliams identity provides the relationship between the weight distribution of a code and that of its dual code. The present paper presents the MacWilliams identity for the m-spotty weight enumerator of m-spotty byte error control codes. In addition, the present paper clarifies that the indicated identity includes the MacWilliams identity for the Hamming weight enumerator as a special case.

  4. Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

    Science.gov (United States)

    Deepak, Akshay; Fernández-Baca, David

    2014-01-01

    A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.

  5. Enumerating all maximal frequent subtrees in collections of phylogenetic trees

    Science.gov (United States)

    2014-01-01

    Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474

  6. HEMATOPOIETIC PROGENITOR CELLS AS A PREDICTIVE OF CD34+ ENUMERATION PRIOR TO PERIPHERAL BLOOD STEM CELLS HARVESTING

    Directory of Open Access Journals (Sweden)

    Z. Zulkafli

    2014-09-01

    Full Text Available Background: To date, the CD34+ cell enumeration has relied predominantly on flow cytometry technique. However, flow cytometry is time consuming and operator dependent. The application of the hematopoietic progenitor cells (HPCs channel in Sysmex XE-2100, a fully automated hematology analyzer offers an alternative approach, which is with minimal sample manipulation and less operator dependent. This study evaluates the utility of HPC counts as a predictive of CD34+ enumeration prior to peripheral blood stem cells harvesting. Materials and methods: HPC, CD34+, white blood cell (WBC, reticulocytes (retic, immature platelet fraction (IPF and immature reticulocyte fraction (IRF were determined in 61 samples from 19 patients with hematological malignancies (15 lymphoma and 4 multiple myeloma patients at Hospital Universiti Sains Malaysia (Hospital USM who had received granulocyte-colony stimulating factor (G-CSF and planned for autologous transplantation. Results: CD34+ count showed strong and significant correlation with HPC. The receiver operating characteristics (ROC curve analysis revealed that HPC count > 21.5 x 106 / L can predicts a pre harvest CD34+ count of >20 x 106 / L with sensitivity of 77%, specificity of 64% and area under the curve (AUC of 0.802. Conclusion: We concluded that HPC count can be a useful potential parameter in optimizing timing for CD34+ enumeration prior to leukapheresis.

  7. Rumen microbial protein synthesis and nitrogen efficiency as affected by tanniferous and non-tanniferous forage legumes incubated individually or together in Rumen Simulation Technique.

    Science.gov (United States)

    Grosse Brinkhaus, Anja; Bee, Giuseppe; Schwarm, Angela; Kreuzer, Michael; Dohme-Meier, Frigga; Zeitz, Johanna O

    2018-03-01

    A limited availability of microbial protein can impair productivity in ruminants. Ruminal nitrogen efficiency might be optimised by combining high-quality forage legumes such as red clover (RC), which has unfavourably high ruminal protein degradability, with tanniferous legumes like sainfoin (SF) and birdsfoot trefoil (BT). Silages from SF and from BT cultivars [Bull (BB) and Polom (BP)] were incubated singly or in combination with RC using the Rumen Simulation Technique (n = 6). The tanniferous legumes, when compared to RC, changed the total short-chain fatty acid profile by increasing propionate proportions at the expense of butyrate. Silage from SF contained the most condensed tannins (CTs) (136 g CT kg -1 dry matter) and clearly differed in various traits from the BT and RC silages. The apparent nutrient degradability (small with SF), microbial protein synthesis, and calculated content of potentially utilisable crude protein (large with SF) indicated that SF had the greatest efficiency in ruminal protein synthesis. The effects of combining SF with RC were mostly linear. The potential of sainfoin to improve protein supply, demonstrated either individually or in combination with a high-performance forage legume, indicates its potential usefulness in complementing protein-deficient ruminant diets and high-quality forages rich in rumen-degradable protein. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  8. Automatic Slide-Loader Fluorescence Microscope for Discriminative Enumeration of Subseafloor Life

    Directory of Open Access Journals (Sweden)

    Fumio Inagaki

    2010-04-01

    Full Text Available The marine subsurface environment is considered the potentially largest ecosystem on Earth, harboring one-tenth of all living biota (Whitman et al., 1998 and comprising diverse microbial components (Inagaki et al., 2003, 2006; Teske, 2006; Inagaki and Nakagawa, 2008. In deep marine sediments, the discrimination of life is significantly more difficult than in surface sediments and terrestrial soils because buried cells generally have extremely low metabolic activities (D’Hondt et al., 2002, 2004, and a highly consolidated sediment matrix produces auto-fluorescence fromdiatomaceous spicules and other mineral particles (Kallmeyer et al., 2008. The cell abundance in marine subsurface sediments has conventionally been evaluated by acridine orange direct count (AODC; Cragg et al., 1995; Parkes et al., 2000 down to 1613 meters below the seafloor (mbsf (Roussel et al., 2008. Since the cell-derived AOsignals often fade out in a short exposure time, recognizing and counting cells require special training. Hence, such efforts to enumerate AO-stained cells from the subseafloor on photographic images have been difficult, and a verification of counts by other methods has been impossible. In addition, providing mean statistical values from low biomass sedimentary habitats has been complicated byphysical and time limitations, yet these habitats are considered critical for understanding the Earth’s biosphere close to the limits of habitable zones (Hoehler, 2004; D’Hondt et al., 2007.

  9. Evaluation of dispersion methods for enumeration of microorganisms from peat and activated carbon biofilters treating volatile organic compounds.

    Science.gov (United States)

    Khammar, Nadia; Malhautier, Luc; Degrange, Valérie; Lensi, Robert; Fanlo, Jean-Louis

    2004-01-01

    To enumerate microorganisms having colonized biofilters treating volatile organic compounds, it is necessary firstly to evaluate dispersion methods. Crushing, shaking and sonication were then tested for the removal of microflora from biofilters packing materials (peat and activated carbon). Continuous or discontinuous procedures, and addition of glass beads had no effect on the number of microorganisms removed from peat particles. The duration of treatment also had no effect for shaking and crushing, but the number of microorganisms after 60 min of treatment with ultrasound was significantly higher than that obtained after 0.5 min. The comparison between these methods showed that crushing was the most efficient for the removal of microorganisms from both peat and activated carbon. The comparison between three chemical dispersion agents showed that 1% Na-pyrophosphate was less efficient, compared with 200 mM phosphate buffer or 1% Na-hexametaphosphate. To optimize the cultivation of microorganisms, three different agar media were compared. Tryptic soy agar tenfold diluted (TSA 1/10) was the most suitable medium for the culture of microflora from a peat biofilter. For the activated carbon biofilter, there was no significant difference between Luria Bertoni, TSA 1/10, and plate count agar. The optimized extraction and enumeration protocols were used to perform a quantitative characterization of microbial populations in an operating laboratory activated carbon biofilter and in two parallel peat biofilters.

  10. Automated Mobile System for Accurate Outdoor Tree Crop Enumeration Using an Uncalibrated Camera

    OpenAIRE

    Thuy Tuong Nguyen; David C. Slaughter; Bradley D. Hanson; Andrew Barber; Amy Freitas; Daniel Robles; Erin Whelan

    2015-01-01

    This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera) and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration) required to obtain robust performance in a natural outdoor environment. The enumeration system uses a t...

  11. Nuclear techniques to determine microbial protein synthesis and productive performance of barki lambs fed rations containing some medicinal plants

    International Nuclear Information System (INIS)

    Mohamed, M.M.S.

    2009-01-01

    This study included two experiments, the first experiment was carried out in vitro to evaluate the effect of adding two levels of Lemongrass or Rosemary in ruminant rations on microbial protein synthesis using radio active sulfur S 35 . While, the second experiment was to study the effect of Lemongrass (CC) and Rosemary (RO) as feed additives in rations of lambs on feed intake, nutrient digestibility, some parameters of blood and rumen activity. Meanwhile, body weight and economical efficiency were studied. Twenty five of Barki male lambs with average body weight of 19.8 kg ± 1 kg and 3- 4 months of age were divided into 5 similar groups (5 lambs each). The first group (control) (R1) was fed on a concentrate feed mixture (CFM) plus rice straw (RS). While, R2 and R3 were fed as R1 ration supplemented with 100 or 200 mg Lemongrass /kg LBW/d respectively. Meantime, R4 and R5 were fed as R1 ration supplemented with 100 or 200 mg Rosemary /kg LBW/d respectively.The results indicated that more microbial protein synthesis was noticed with 4 mg of Lemongrass followed by 2 mg Rosemary, 2 mg Lemongrass and control which was higher than 4 mg Rosemary/ 0.5 g concentrate mixture. The differences were not statistically significant. The dry matter intake (DMI) was not significantly different for R4 and R3 when compared with R1 (control) and it significantly decreased in R5 and R2 compared with R1. The digestibilities of DM, OM, CP, EE and NFE in the supplemented groups were not significantly differing compared with R1. The digestibility of CF was significantly increased in R2 and R4 compared with R1 and there were no significant differences for R3 and R5 compared with R1. There were no significant differences in nutritive values as TDN, DCP and SV among all supplemented groups compared with R1. Rumen liquor TVFA,s was not significantly differ at zero time, but it decreased at 3 h and 6 h with all additives compared with the control with no significant differences among all

  12. The association of color memory and the enumeration of multiple spatially overlapping sets.

    Science.gov (United States)

    Poltoratski, Sonia; Xu, Yaoda

    2013-07-09

    Using dot displays, Halberda, Sires, and Feigenson (2006) showed that observers could simultaneously encode the numerosity of two spatially overlapping sets and the superset of all items at a glance. With the brief display and the masking used in Halberda et al., the task required observers to encode the colors of each set in order to select and enumerate all the dots in that set. As such, the observed capacity limit for set enumeration could reflect a limit in visual short-term memory (VSTM) capacity for the set color rather than a limit in set enumeration per se. Here, we largely replicated Halberda et al. and found successful enumeration of approximately two sets (the superset was not probed). We also found that only about two and a half colors could be remembered from the colored dot displays whether or not the enumeration task was performed concurrently with the color VSTM task. Because observers must remember the color of a set prior to enumerating it, the under three-item VSTM capacity for color necessarily dictates that set enumeration capacity in this paradigm could not exceed two sets. Thus, the ability to enumerate multiple spatially overlapping sets is likely limited by VSTM capacity to retain the discriminating feature of these sets. This relationship suggests that the capacity for set enumeration cannot be considered independently from the capacity for the set's defining features.

  13. Anti-microbial surfaces: An approach for deposition of ZnO nanoparticles on PVA-Gelatin composite film by screen printing technique

    Energy Technology Data Exchange (ETDEWEB)

    Meshram, J.V.; Koli, V.B.; Phadatare, M.R.; Pawar, S.H., E-mail: shpawar1946@gmail.com

    2017-04-01

    Initially micro-organisms get exposed to the surfaces, this demands development of anti-microbial surfaces to inhibit their proliferation. Therefore, herein, we attempt screen printing technique for development of PVA-GE/ZnO nanocomposite (PG/ZnO) films. The synthesis of PG/ZnO nanocomposite includes two steps as: (i) Coating of Zinc Oxide nanoparticles (ZnO NPs) by poly ethylene glycol in order to be compatible with organic counterparts. (ii) Deposition of coated nanoparticles on the PG film surface. The results suggest the enhancement in anti-microbial activity of PG/ZnO nanocomposite over pure ZnO NPs against both Gram positive Bacillus subtilis and Gram negative Escherichia coli from zone of inhibition. The uniformity in deposition is further confirmed by scanning electron microscopy (SEM) images. The phase identification of ZnO NPs and formation of PG/ZnO nanocomposite has been confirmed by X-ray diffraction (XRD) analysis and UV–vis spectroscopy (UV–vis). The Attenuated total reflection Spectroscopy (ATR) analysis indicates the ester bond between PVA and gelatin molecules. The thermal stability of nanocomposite is studied by thermogravimetric analysis (TGA) revealing increase in crystallinity due to ZnO NPs which could be utilized to inhibit the growth of micro-organisms. The tensile strength is found to be higher and percent elongation is double of PG/ZnO nanocomposite than PG composite film. - Highlights: • Synthesis of PG/ZnO nanocomposite by screen printing technique • Antimicrobial activity is due presence of ZnO nanoparticles on PG composite. • Improved tensile strength due to ZnO nanoparticles.

  14. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    KAUST Repository

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  15. Microbial water diversion technique-designed for near well treatment in low temperature sandstone reservoirs in the North Sea

    Energy Technology Data Exchange (ETDEWEB)

    Paulsen, J.E.; Vatland, A. [RF-Rogaland Research, Stavanger (Norway); Sorheim, R. [SINTEF, Oslo (Norway)] [and others

    1995-12-31

    A Norwegian Research Program on Improved Oil Recovery (IOR) in North Sea reservoirs was launched in 1992. Microbial methods, applied in this context, is a part of this program. The scope, the methodological approach, and results from the three first years are presented. Water profile control, using biomass to block high permeable zones of a reservoir, has been investigated using nitrate-reducing bacteria in the injected sea water as plugging agents. Emphasis has been put on developing a process that does not have disadvantages secondary to the process itself, such as souring and impairment of the overall injectivity of the field. Data from continuous culture studies indicate that souring may successfully be mitigated by adding nitrite to the injected seawater. The morphology and size of generic-nitrate-reducing seawater bacteria have been investigated. Screening of growth-promoting nutrients has been carried out, and some sources were detected as favorable. Transport and penetration of bacteria in porous media have been given special attention. Investigations with sand packs, core models, and pore micromodels have been carried out. The inherent problems connected with permeability contrasts and flow patterns, versus bacterial behavior, are believed to be critical for the success of this technology. Data from the transport and blocking experiments with the porous matrices confirm this concern. The technology is primarily being developed for temperatures less than 40{degrees}C.

  16. Evaluation of pre-PCR processing approaches for enumeration of Salmonella enterica in naturally contaminated animal feed

    DEFF Research Database (Denmark)

    Schelin, Jenny; Andersson, Gunnar; Vigre, Håkan

    2014-01-01

    Three pre‐PCR processing strategies for the detection and/or quantification of Salmonella in naturally contaminated soya bean meal were evaluated. Methods included: (i) flotation‐qPCR [enumeration of intact Salmonella cells prior to quantitative PCR (qPCR)], (ii) MPN‐PCR (modified most probable...... be due to the presence of nonculturable Salmonella and/or a heterogeneous distribution of Salmonella in the material. The evaluated methods provide different possibilities to assess the prevalence of Salmonella in feed, together with the numbers of culturable, as well as nonculturable cells, and can...... be applied to generate data to allow more accurate quantitative microbial risk assessment for Salmonella in the feed chain....

  17. Silage review: Using molecular approaches to define the microbial ecology of silage.

    Science.gov (United States)

    McAllister, T A; Dunière, L; Drouin, P; Xu, S; Wang, Y; Munns, K; Zaheer, R

    2018-05-01

    Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors

  18. Quantitative comparison of the in situ microbial communities in different biomes

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C. [Tennessee Univ., Knoxville, TN (United States)]|[Oak Ridge National Lab., TN (United States); Ringelberg, D.B.; Palmer, R.J. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

    1995-12-31

    A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/

  19. Comparison of two non-invasive methods of microbial analysis in surgery practice: incision swabbing and the indirect imprint technique.

    Science.gov (United States)

    Chovanec, Zdenek; Veverkova, Lenka; Votava, Miroslav; Svoboda, Jiri; Jedlicka, Vaclav; Capov, Ivan

    2014-12-01

    A variety of methods exist to take samples from surgical site infections for cultivation; however, an unambiguous and suitable method has not yet been defined. The aim of our retrospective non-randomized study was to compare two non-invasive techniques of sampling material for microbiologic analysis in surgical practice. We compared bacteria cultured from samples obtained with the use of the swab technique, defined in our study as the gold standard, with the indirect imprint technique. A cotton-tipped swab (Copan, Brescia, Italy) was used; the imprints were taken using Whatman no. 4 filter paper (Macherey-Nagal, Duren, Germany) cut into 5×5 cm pieces placed on blood agar in a Petri dish. To culture the microorganisms in the microbiology laboratory, we used blood agar, UriSelect 4 medium (Bio-Rad, Marnes-la-Coquette, France), and a medium with sodium chloride (blood agar with salt). After careful debridement, a sample was taken from the incision surface by swab and subsequently the same area of the surface was imprinted onto filter paper. The samples were analyzed in the microbiology laboratory under standard safety precautions. The cultivation results of the two techniques were processed statistically using contingency tables and the McNemar test. Those samples that were simultaneously cultivation-positive by imprint and -negative by swabbing were processed in greater detail. Over the period between October 2008 and March 2013, 177 samples from 70 patients were analyzed. Sampling was carried out from 42 males and 28 females. One hundred forty-six samples were from incisions after operations (21 samples from six patients after operation on the thoracic cavity, 73 samples from 35 patients after operation on the abdominal cavity combined with the gastrointestinal tract, 52 samples from 19 patients with other surgical site infections not included above) and 31 samples from 11 patients with no post-operative infection. One patient had a sample taken both from a post

  20. Strategies for enumeration of circulating microvesicles on a conventional flow cytometer: Counting beads and scatter parameters.

    Science.gov (United States)

    Alkhatatbeh, Mohammad J; Enjeti, Anoop K; Baqar, Sara; Ekinci, Elif I; Liu, Dorothy; Thorne, Rick F; Lincz, Lisa F

    2018-01-01

    Enumeration of circulating microvesicles (MVs) by conventional flow cytometry is accomplished by the addition of a known amount of counting beads and calculated from the formula: MV/μl = (MV count/bead count) × final bead concentration. We sought to optimize each variable in the equation by determining the best parameters for detecting 'MV count' and examining the effects of different bead preparations and concentrations on the final calculation. Three commercially available bead preparations (TruCount, Flow-Count and CountBright) were tested, and MV detection on a BD FACSCanto was optimized for gating by either forward scatter (FSC) or side scatter (SSC); the results were compared by calculating different subsets of MV on a series of 74 typical patient plasma samples. The relationship between the number of beads added to each test and the number of beads counted by flow cytometry remained linear over a wide range of bead concentrations ( R 2 ≥ 0.997). However, TruCount beads produced the most consistent (concentration variation = 3.8%) calculated numbers of plasma CD41 + /Annexin V + MV, which were significantly higher from that calculated using either Flow-Count or CountBright ( p beads by FSC and 0.16 μm beads by SSC, but there were significantly more background events using SSC compared with FSC (3113 vs. 470; p = 0.008). In general, sample analysis by SSC resulted in significantly higher numbers of MV ( p beads provided linear results at concentrations ranging from 6 beads/μl to 100 beads/μl, but TruCount was the most consistent. Using SSC to gate MV events produced high background which negatively affected counting bead enumeration and overall MV calculations. Strategies to reduce SSC background should be employed in order to reliably use this technique.

  1. Characterizing Microbial Mat Morphology with Structure from Motion Techniques in Ice-Covered Lake Joyce, McMurdo Dry Valleys, Antarctica

    Science.gov (United States)

    Mackey, T. J.; Leidman, S. Z.; Allen, B.; Hawes, I.; Lawrence, J.; Jungblut, A. D.; Krusor, M.; Coleman, L.; Sumner, D. Y.

    2015-12-01

    Structure from Motion (SFM) techniques can provide quantitative morphological documentation of otherwise inaccessible benthic ecosystems such as microbial mats in Lake Joyce, a perennially ice-covered lake of the Antarctic McMurdo Dry Valleys (MDV). Microbial mats are a key ecosystem of MDV lakes, and diverse mat morphologies like pinnacles emerge from interactions among microbial behavior, mineralization, and environmental conditions. Environmental gradients can be isolated to test mat growth models, but assessment of mat morphology along these gradients is complicated by their inaccessibility: the Lake Joyce ice cover is 4-5 m thick, water depths containing diverse pinnacle morphologies are 9-14 m, and relevant mat features are cm-scale. In order to map mat pinnacle morphology in different sedimentary settings, we deployed drop cameras (SeaViewer and GoPro) through 29 GPS referenced drill holes clustered into six stations along a transect spanning 880 m. Once under the ice cover, a boom containing a second GoPro camera was unfurled and rotated to collect oblique images of the benthic mats within dm of the mat-water interface. This setup allowed imaging from all sides over a ~1.5 m diameter area of the lake bottom. Underwater lens parameters were determined for each camera in Agisoft Lens; images were reconstructed and oriented in space with the SFM software Agisoft Photoscan, using the drop camera axis of rotation as up. The reconstructions were compared to downward facing images to assess accuracy, and similar images of an object with known geometry provided a test for expected error in reconstructions. Downward facing images identify decreasing pinnacle abundance in higher sedimentation settings, and quantitative measurements of 3D reconstructions in KeckCAVES LidarViewer supplement these mat morphological facies with measurements of pinnacle height and orientation. Reconstructions also help isolate confounding variables for mat facies trends with measurements

  2. A note on the complexity of finding and enumerating elementary modes.

    NARCIS (Netherlands)

    Acuna, V.; Marchetti-Spaccamela, A.; Sagot, M.-F.; Stougie, L.

    2010-01-01

    In the context of the study into elementary modes of metabolic networks, we prove two complexity results. Enumerating elementary modes containing a specific reaction is hard in an enumeration complexity sense. The decision problem if there exists an elementary mode containing two specific reactions

  3. 21 CFR 866.4700 - Automated fluorescence in situ hybridization (FISH) enumeration systems.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated fluorescence in situ hybridization (FISH... Laboratory Equipment and Reagents § 866.4700 Automated fluorescence in situ hybridization (FISH) enumeration... Hybridization (FISH) Enumeration Systems.” See § 866.1(e) for the availability of this guidance document. [70 FR...

  4. Evaluation of optimum roughage to concentrate ratio in maize stover based complete rations for efficient microbial biomass production using in vitro gas production technique

    Directory of Open Access Journals (Sweden)

    Y. Ramana Reddy

    2016-06-01

    Full Text Available Aim: A study was undertaken to evaluate the optimum roughage to concentrate ratio in maize stover (MS based complete diets for efficient microbial biomass production (EMBP using in vitro gas production technique. Materials and Methods: MS based complete diets with roughage to concentrate ratio of 100:0, 90:10, 80:20, 70:30, 60:40, 50:50, 40:60, and 30:70 were formulated, and 200 mg of oven-dried sample was incubated in water bath at 39°C along with media (rumen liquor [RL] - buffer in in vitro gas syringes to evaluate the gas production. The gas produced was recorded at 8 and 24 h of inc ubation. In vitro organic matter digestibility (IVOMD, metabolizable energy (ME, truly digestible organic matter (TDOM, partitioning factor (PF, and EMBP were calculated using appropriate formulae. Ammonia nitrogen and total volatile fatty acids (TVFAs production were analyzed in RL fluid-media mixture after 24 h of incubation. Results: In vitro gas production (ml at 24 h incubation, IVOMD, ME, TDOM, TVFA concentration, and ammonia nitrogen production were increased (p<0.01 in proportion to the increase in the level of concentrate in the diet. Significantly (p<0.01 higher PF and EMBP was noticed in total mixed ration with roughage to concentrate ratio of 60:40 and 50:50 followed by 70:30 and 40:60. Conclusion: Based on the results, it was concluded that the MS can be included in complete rations for ruminants at the level of 50-60% for better microbial biomass synthesis which in turn influences the performance of growing sheep.

  5. Evaluation of optimum roughage to concentrate ratio in maize stover based complete rations for efficient microbial biomass production using in vitro gas production technique.

    Science.gov (United States)

    Reddy, Y Ramana; Kumari, N Nalini; Monika, T; Sridhar, K

    2016-06-01

    A study was undertaken to evaluate the optimum roughage to concentrate ratio in maize stover (MS) based complete diets for efficient microbial biomass production (EMBP) using in vitro gas production technique. MS based complete diets with roughage to concentrate ratio of 100:0, 90:10, 80:20, 70:30, 60:40, 50:50, 40:60, and 30:70 were formulated, and 200 mg of oven-dried sample was incubated in water bath at 39°C along with media (rumen liquor [RL] - buffer) in in vitro gas syringes to evaluate the gas production. The gas produced was recorded at 8 and 24 h of incubation. In vitro organic matter digestibility (IVOMD), metabolizable energy (ME), truly digestible organic matter (TDOM), partitioning factor (PF), and EMBP were calculated using appropriate formulae. Ammonia nitrogen and total volatile fatty acids (TVFAs) production were analyzed in RL fluid-media mixture after 24 h of incubation. In vitro gas production (ml) at 24 h incubation, IVOMD, ME, TDOM, TVFA concentration, and ammonia nitrogen production were increased (p<0.01) in proportion to the increase in the level of concentrate in the diet. Significantly (p<0.01) higher PF and EMBP was noticed in total mixed ration with roughage to concentrate ratio of 60:40 and 50:50 followed by 70:30 and 40:60. Based on the results, it was concluded that the MS can be included in complete rations for ruminants at the level of 50-60% for better microbial biomass synthesis which in turn influences the performance of growing sheep.

  6. Inactivation of viable Ascaris eggs by reagents during enumeration.

    Science.gov (United States)

    Nelson, K L; Darby, J L

    2001-12-01

    Various reagents commonly used to enumerate viable helminth eggs from wastewater and sludge were evaluated for their potential to inactivate Ascaris eggs under typical laboratory conditions. Two methods were used to enumerate indigenous Ascaris eggs from sludge samples. All steps in the methods were the same except that in method I a phase extraction step with acid-alcohol (35% ethanol in 0.1 N H(2)SO(4)) and diethyl ether was used whereas in method II the extraction step was avoided by pouring the sample through a 38-microm-mesh stainless steel sieve that retained the eggs. The concentration of eggs and their viability were lower in the samples processed by method I than in the samples processed by method II by an average of 48 and 70%, respectively. A second set of experiments was performed using pure solutions of Ascaris suum eggs to elucidate the effect of the individual reagents and relevant combination of reagents on the eggs. The percentages of viable eggs in samples treated with acid-alcohol alone and in combination with diethyl ether or ethyl acetate were 52, 27, and 4%, respectively, whereas in the rest of the samples the viability was about 80%. Neither the acid nor the diethyl ether alone caused any decrease in egg viability. Thus, the observed inactivation was attributed primarily to the 35% ethanol content of the acid-alcohol solution. Inactivation of the eggs was prevented by limiting the direct exposure to the extraction reagents to 30 min and diluting the residual concentration of acid-alcohol in the sample by a factor of 100 before incubation. Also, the viability of the eggs was maintained if the acid-alcohol solution was replaced with an acetoacetic buffer. None of the reagents used for the flotation step of the sample cleaning procedure (ZnSO(4), MgSO(4), and NaCl) or during incubation (0.1 N H(2)SO(4) and 0.5% formalin) inactivated the Ascaris eggs under the conditions studied.

  7. Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario

    Science.gov (United States)

    Blanco, Yolanda; Gallardo-Carreño, Ignacio; Ruiz-Bermejo, Marta; Puente-Sánchez, Fernando; Cavalcante-Silva, Erika; Quesada, Antonio; Prieto-Ballesteros, Olga; Parro, Víctor

    2017-10-01

    The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing.

  8. Microbial Removal Efficiency of UV in Tehran Shahid Mahallati Wastewater Treatment Plant

    Directory of Open Access Journals (Sweden)

    Reza Dabbagh

    2009-03-01

    Full Text Available Shahid Mahallati Wastewater Treatment Plant was selected for installing a UV disinfection unit to investigate its germicidal effect on microbial removal. Low pressure mercury lamps were used to generate germicidal ultraviolet radiation (UV-C. The UV system was operated over a period of 6 months that included both warm and cold seasons. A maximum UV disinfection efficiency of 14.4m3/h was recorded for the system on the basis of design criteria within turbidity ranges of 9 to 32 NTU. The minimum UV dose applied in the UV unit was 40000 µW.s/cm2 and the highest bacterial density in the UV unit influent was 5.6*107. Effluent total coliform or fecal coliform enumeration after exposure to UV ray showed the microbial density decreasing from four logs, or 99.99%, to as high as six logs, or 99.9999% removal efficiency, under different conditions. Effluent microbial densities in terms of total and fecal coliforms were below 1000MPN/100mL and 400MPN/100mL, respectively. These values comply with wastewater discharge or agricultural irrigation standards according to Iran Department of Environment. From our results, it is concluded that UV disinfection may be an effective technique for wastewater disinfection in Iranian wastewater treatment plants.

  9. Using pattern enumeration to accelerate process development and ramp yield

    Science.gov (United States)

    Zhuang, Linda; Pang, Jenny; Xu, Jessy; Tsai, Mengfeng; Wang, Amy; Zhang, Yifan; Sweis, Jason; Lai, Ya-Chieh; Ding, Hua

    2016-03-01

    During a new technology node process setup phase, foundries do not initially have enough product chip designs to conduct exhaustive process development. Different operational teams use manually designed simple test keys to set up their process flows and recipes. When the very first version of the design rule manual (DRM) is ready, foundries enter the process development phase where new experiment design data is manually created based on these design rules. However, these IP/test keys contain very uniform or simple design structures. This kind of design normally does not contain critical design structures or process unfriendly design patterns that pass design rule checks but are found to be less manufacturable. It is desired to have a method to generate exhaustive test patterns allowed by design rules at development stage to verify the gap of design rule and process. This paper presents a novel method of how to generate test key patterns which contain known problematic patterns as well as any constructs which designers could possibly draw based on current design rules. The enumerated test key patterns will contain the most critical design structures which are allowed by any particular design rule. A layout profiling method is used to do design chip analysis in order to find potential weak points on new incoming products so fab can take preemptive action to avoid yield loss. It can be achieved by comparing different products and leveraging the knowledge learned from previous manufactured chips to find possible yield detractors.

  10. Taking a(c)count of eye movements: Multiple mechanisms underlie fixations during enumeration.

    Science.gov (United States)

    Paul, Jacob M; Reeve, Robert A; Forte, Jason D

    2017-03-01

    We habitually move our eyes when we enumerate sets of objects. It remains unclear whether saccades are directed for numerosity processing as distinct from object-oriented visual processing (e.g., object saliency, scanning heuristics). Here we investigated the extent to which enumeration eye movements are contingent upon the location of objects in an array, and whether fixation patterns vary with enumeration demands. Twenty adults enumerated random dot arrays twice: first to report the set cardinality and second to judge the perceived number of subsets. We manipulated the spatial location of dots by presenting arrays at 0°, 90°, 180°, and 270° orientations. Participants required a similar time to enumerate the set or the perceived number of subsets in the same array. Fixation patterns were systematically shifted in the direction of array rotation, and distributed across similar locations when the same array was shown on multiple occasions. We modeled fixation patterns and dot saliency using a simple filtering model and show participants judged groups of dots in close proximity (2°-2.5° visual angle) as distinct subsets. Modeling results are consistent with the suggestion that enumeration involves visual grouping mechanisms based on object saliency, and specific enumeration demands affect spatial distribution of fixations. Our findings highlight the importance of set computation, rather than object processing per se, for models of numerosity processing.

  11. Detection and enumeration of Coliforms and Escherichia coli in water

    African Journals Online (AJOL)

    Water samples from eighteen different sources in Nairobi were analyzed for coliform and E. coli content using three microbiological techniques, namely: Multiple tube or Most Probable Number (MPN) technique, Defined Substrate Technique (DST) or Colilert technique and Petrifilm(TM) Plate Count Techniques. All the three ...

  12. Rapid evaluation technique to differentiate mushroom disease-related moulds by detecting microbial volatile organic compounds using HS-SPME-GC-MS.

    Science.gov (United States)

    Radványi, Dalma; Gere, Attila; Jókai, Zsuzsa; Fodor, Péter

    2015-01-01

    Headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS) was used to analyse microbial volatile organic compounds (MVOCs) of mushroom disease-related microorganisms. Mycogone perniciosa, Lecanicillum fungicola var. fungicola, and Trichoderma aggressivum f. europaeum species, which are typically harmful in mushroom cultivation, were examined, and Agaricus bisporus (bisporic button mushroom) was also examined as a control. For internal standard, a mixture of alkanes was used; these were introduced as the memory effect of primed septa in the vial seal. Several different marker compounds were found in each sample, which enabled us to distinguish the different moulds and the mushroom mycelium from each other. Monitoring of marker compounds enabled us to investigate the behaviour of moulds. The records of the temporal pattern changes were used to produce partial least squares regression (PLS-R) models that enabled determination of the exact time of contamination (the infection time of the media). Using these evaluation techniques, the presence of mushroom disease-related fungi can be easily detected and monitored via their emitted MVOCs.

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

    Science.gov (United States)

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

    2015-12-23

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

  14. Microbial impacts on geothermometry temperature predictions

    Energy Technology Data Exchange (ETDEWEB)

    Yoshiko Fujita; David W. Reed; Kaitlyn R. Nowak; Vicki S. Thompson; Travis L. McLing; Robert W. Smith

    2013-02-01

    Conventional geothermometry approaches assume that the composition of a collected water sample originating in a deep geothermal reservoir still reflects chemical equilibration of the water with the deep reservoir rocks. However, for geothermal prospecting samples whose temperatures have dropped to <120°C, temperature predictions may be skewed by the activity of microorganisms; microbial metabolism can drastically and rapidly change the water’s chemistry. We hypothesize that knowledge of microbial impacts on exploration sample geochemistry can be used to constrain input into geothermometry models and thereby improve the reliability of reservoir temperature predictions. To evaluate this hypothesis we have chosen to focus on sulfur cycling, because of the significant changes in redox state and pH associated with sulfur chemistry. Redox and pH are critical factors in defining the mineral-fluid equilibria that form the basis of solute geothermometry approaches. Initially we are developing assays to detect the process of sulfate reduction, using knowledge of genes specific to sulfate reducing microorganisms. The assays rely on a common molecular biological technique known as quantitative polymerase chain reaction (qPCR), which allows estimation of the number of target organisms in a particular sample by enumerating genes specific to the organisms rather than actually retrieving and characterizing the organisms themselves. For quantitation of sulfate reducing genes using qPCR, we constructed a plasmid (a piece of DNA) containing portions of two genes (known as dsrA and dsrB) that are directly involved with sulfate reduction and unique to sulfate reducing microorganisms. Using the plasmid as well as DNA from other microorganisms known to be sulfate reducers or non-sulfate reducers, we developed qPCR protocols and showed the assay’s specificity to sulfate reducers and that a qPCR standard curve using the plasmid was linear over >5 orders of magnitude. As a first test

  15. Introducing the fit-criteria assessment plot - A visualisation tool to assist class enumeration in group-based trajectory modelling.

    Science.gov (United States)

    Klijn, Sven L; Weijenberg, Matty P; Lemmens, Paul; van den Brandt, Piet A; Lima Passos, Valéria

    2017-10-01

    Background and objective Group-based trajectory modelling is a model-based clustering technique applied for the identification of latent patterns of temporal changes. Despite its manifold applications in clinical and health sciences, potential problems of the model selection procedure are often overlooked. The choice of the number of latent trajectories (class-enumeration), for instance, is to a large degree based on statistical criteria that are not fail-safe. Moreover, the process as a whole is not transparent. To facilitate class enumeration, we introduce a graphical summary display of several fit and model adequacy criteria, the fit-criteria assessment plot. Methods An R-code that accepts universal data input is presented. The programme condenses relevant group-based trajectory modelling output information of model fit indices in automated graphical displays. Examples based on real and simulated data are provided to illustrate, assess and validate fit-criteria assessment plot's utility. Results Fit-criteria assessment plot provides an overview of fit criteria on a single page, placing users in an informed position to make a decision. Fit-criteria assessment plot does not automatically select the most appropriate model but eases the model assessment procedure. Conclusions Fit-criteria assessment plot is an exploratory, visualisation tool that can be employed to assist decisions in the initial and decisive phase of group-based trajectory modelling analysis. Considering group-based trajectory modelling's widespread resonance in medical and epidemiological sciences, a more comprehensive, easily interpretable and transparent display of the iterative process of class enumeration may foster group-based trajectory modelling's adequate use.

  16. Multicanonical simulation of the Domb-Joyce model and the Gō model: new enumeration methods for self-avoiding walks

    International Nuclear Information System (INIS)

    Shirai, Nobu C; Kikuchi, Macoto

    2013-01-01

    We develop statistical enumeration methods for self-avoiding walks using a powerful sampling technique called the multicanonical Monte Carlo method. Using these methods, we estimate the numbers of the two dimensional N-step self-avoiding walks up to N = 256 with statistical errors. The developed methods are based on statistical mechanical models of paths which include self-avoiding walks. The criterion for selecting a suitable model for enumerating self-avoiding walks is whether or not the configuration space of the model includes a set for which the number of the elements can be exactly counted. We call this set a scale fixing set. We selected the following two models which satisfy the criterion: the Gō model for lattice proteins and the Domb-Joyce model for generalized random walks. There is a contrast between these two models in the structures of the configuration space. The configuration space of the Gō model is defined as the universal set of self-avoiding walks, and the set of the ground state conformation provides a scale fixing set. On the other hand, the configuration space of the Domb-Joyce model is defined as the universal set of random walks which can be used as a scale fixing set, and the set of the ground state conformation is the same as the universal set of self-avoiding walks. From the perspective of enumeration performance, we conclude that the Domb-Joyce model is the better of the two. The reason for the performance difference is partly explained by the existence of the first-order phase transition of the Gō model

  17. Method to enumerate oocysts of cryptosporidium and cysts of Giardia in water

    International Nuclear Information System (INIS)

    Briancesco, R.; Bonadonna, L.

    2000-01-01

    Cryptosporidium and Giardia have been recognized as etiological agents of gastrointestinal illness in humans with severe consequences on children and immunocompromised individuals. Water seems to be vehicle of infection. In last years many efforts have been done to evaluate a method to enumerate oocysts of Cryptosporidium and cysts of Giardia in waters. Throughout filtration and concentration steps, the two procedures proposed allow to enumerate oocysts and cysts belonging to the two genera of protozoa [it

  18. Comparison of culture media, simplate, and petrifilm for enumeration of yeasts and molds in food.

    Science.gov (United States)

    Taniwaki, M H; Silva, N; Banhe, A A; Iamanaka, B T

    2001-10-01

    The efficacy of three culture media, dichloran rose bengal chloramphenicol (DRBC), dichloran 18% glycerol agar (DG18), and potato dextrose agar (PDA) supplemented with two antibiotics, were compared with the Simplate and Petrifilm techniques for mold and yeast enumeration. The following foods were analyzed: corn meal, wheat flour, cassava flour, bread crumbs, whole meal, sliced bread, ground peanuts, mozzarella cheese, grated parmesan cheese, cheese rolls, orange juice, pineapple pulp, pineapple cake, and mushroom in conserve. Correlation coefficients of DRBC versus PDA and DG18 for recovering total mold and yeast counts from the composite of 14 foods indicated that the three media were generally equivalent. Correlation coefficients for Petrifilm versus culture media were acceptable, although not as good as between culture media. Correlation coefficients of Simplate versus DRBC, DG18, PDA, and Petrifilm for recovering total yeasts and molds from a composite of 11 foods demonstrated that there was no equivalence between the counts obtained by Simplate and other culture media and Petrifilm, with significant differences observed for the most foods analyzed.

  19. COMPETITION BETWEEN ANOXYGENIC PHOTOTROPHIC BACTERIA AND COLORLESS SULFUR BACTERIA IN A MICROBIAL MAT

    NARCIS (Netherlands)

    VISSCHER, PT; VANDENENDE, FP; SCHAUB, BEM; VANGEMERDEN, H

    The populations of chemolithoautotrophic (colorless) sulfur bacteria and anoxygenic phototrophic bacteria were enumerated in a marine microbial mat. The highest population densities were found in the 0-5 mm layer of the mat: 2.0 X 10(9) cells CM-3 sediment, and 4.0 X 10(7) cells cm-3 sediment for

  20. Microbially produced phytotoxins and plant disease management ...

    African Journals Online (AJOL)

    Nowadays, these evaluation techniques are becoming an important complement to classical breeding methods. The knowledge of the inactivation of microbial toxins has led to the use of microbial enzymes to inactivate phytotoxins thereby reducing incidence and severity of disease induced by microbial toxins. Considering ...

  1. Template-based combinatorial enumeration of virtual compound libraries for lipids.

    Science.gov (United States)

    Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

    2012-09-25

    A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

  2. Detection and enumeration of Salmonella enteritidis in homemade ice cream associated with an outbreak: comparison of conventional and real-time PCR methods.

    Science.gov (United States)

    Seo, K H; Valentin-Bon, I E; Brackett, R E

    2006-03-01

    Salmonellosis caused by Salmonella Enteritidis (SE) is a significant cause of foodborne illnesses in the United States. Consumption of undercooked eggs and egg-containing products has been the primary risk factor for the disease. The importance of the bacterial enumeration technique has been enormously stressed because of the quantitative risk analysis of SE in shell eggs. Traditional enumeration methods mainly depend on slow and tedious most-probable-number (MPN) methods. Therefore, specific, sensitive, and rapid methods for SE quantitation are needed to collect sufficient data for risk assessment and food safety policy development. We previously developed a real-time quantitative PCR assay for the direct detection and enumeration of SE and, in this study, applied it to naturally contaminated ice cream samples with and without enrichment. The detection limit of the real-time PCR assay was determined with artificially inoculated ice cream. When applied to the direct detection and quantification of SE in ice cream, the real-time PCR assay was as sensitive as the conventional plate count method in frequency of detection. However, populations of SE derived from real-time quantitative PCR were approximately 1 log higher than provided by MPN and CFU values obtained by conventional culture methods. The detection and enumeration of SE in naturally contaminated ice cream can be completed in 3 h by this real-time PCR method, whereas the cultural enrichment method requires 5 to 7 days. A commercial immunoassay for the specific detection of SE was also included in the study. The real-time PCR assay proved to be a valuable tool that may be useful to the food industry in monitoring its processes to improve product quality and safety.

  3. Microbial functional diversity of a shrubland soil experimentally burned and treated with two post-fire stabilization techniques (straw mulch and seeding

    Directory of Open Access Journals (Sweden)

    M.T. Fonturbel

    2013-01-01

    Full Text Available The study examined the effect of two post-fire stabilization treatments (seeding and mulching on microbial diversity of a shrubland area of Galicia after an experimental fire. The soil was a Leptosol developed over granite with a slope of 38-54% and the soil microbial functional diversity was assessed using Biolog substrate utilization EcoPlates (Biolog Inc., Hayward, CA, USA. Soil samples were taken from the A horizon (0-5 cm depth at different sampling times over one year after the experimental fire. The results indicated that immediately after the fire there were significant differences in the categorized substrate utilization pattern between the microbial communities of the burnt soil treatments and the corresponding unburnt control. The burned soils exhibited significant higher values for the utilization of carboxylic acids, amino acids, carbohydrates and phenolic compounds, suggesting that the microbial community in the burned soils could be favoured by the increase in available C and nutrients following the experimental fire. These changes in the categorized substrate utilization pattern were attenuated with time; thus, one year after the fire, similar values for utilization of different C sources were observed for all unburned and burnt soils. With respect to post-fire treatments only the mulching showed an effect on the C utilization pattern.

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

    Science.gov (United States)

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

    2015-06-01

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

  5. The isolation, enumeration, and characterization of Rhizobium bacteria of the soil in Wamena Biological Garden

    Directory of Open Access Journals (Sweden)

    SRI PURWANINGSIH

    2005-04-01

    Full Text Available The eleven soil samples have been isolated and characterized. The aims of the study were to get the pure culture and some data which described about enumeration and especially their characters in relation to the acids and bases reaction in their growth. The isolation of the bacteria use Yeast Extract Mannitol Agar medium (YEMA while the characterization by using YEMA medium mixed with Brom Thymol Blue and Congo Red indicators respectively. The results showed that eighteen isolates have been isolated which consisted of three low growing and fifteen fast growing bacteria. Two isolates were not indicated Rhizobium and sixteen were Rhizobium. Density of Rhizobium enumeration was varied which related to soil organic matter content. The enumeration bacteria in YEMA medium were in the range of 0.6 x 105 and 11.6 x 105 CFU /g soil. The highest population was found in soil sample of Wieb vegetation.

  6. Microbial radio-resistance of Salmonella Typhimurium in egg increases due to repetitive irradiation with electron beam

    International Nuclear Information System (INIS)

    Tesfai, Adiam T.; Beamer, Sarah K.; Matak, Kristen E.; Jaczynski, Jacek

    2011-01-01

    Ionizing radiation improves food safety. However, foodborne pathogens develop increased resistance in response to sub-lethal stresses such as heat, pH, antibiotics, etc. Therefore, it is hypothesized that foodborne pathogens may develop increased radio-resistance to electron beam (e-beam) radiation. The objective was to determine if D 10 -value for Salmonella Typhimurium in de-shelled raw egg (egg white and yolk mixed together) increases due to repetitive processing with e-beam at sub-lethal doses. Survivors were enumerated on non-selective (TSA) and selective (XLD) media. Survivors from the highest dose were isolated and used in subsequent e-beam cycle. This process was repeated four times for a total of five e-beam cycles. D 10 -values for S. Typhimurium enumerated on TSA and XLD following each e-beam cycle were calculated as inverse reciprocal of the slope of survivor curves. D 10 -values for the ATCC strain were 0.59±0.031 and 0.46±0.022 kGy on TSA and XLD, respectively. However, following the fifth e-beam cycle, the respective D 10 -values increased (P 0.05) to develop radio-resistance faster on selective media, likely due to facilitated selection of radio-resistant cells within microbial population following each e-beam cycle. For all five e-beam cycles, S. Typhimurium had higher (P 10 -values on non-selective media, indicating that sub-lethal injury followed by cellular repair and recovery are important for radio-resistance and inactivation of this microorganism. This study demonstrated that e-beam efficiently inactivates S. Typhimurium in raw egg; however, similar to other inactivation techniques and factors affecting microbial growth, S. Typhimurium develops increased radio-resistance if repetitively processed with e-beam at sub-lethal doses.

  7. Summary of the Skookumchuck Creek bull trout enumeration project 2001.; TOPICAL

    International Nuclear Information System (INIS)

    Baxter, James S.; Baxter, Jeremy

    2002-01-01

    This report summarizes the second year of a bull trout (Salvelinus confluentus) enumeration project on Skookumchuck Creek in southeastern British Columbia. An enumeration fence and traps were installed on the creek from September 6th to October 12th 2001 to enable the capture of post-spawning bull trout emigrating out of the watershed. During the study period, a total of 273 bull trout were sampled through the enumeration fence. Length and weight were determined for all bull trout captured. In total, 39 fish of undetermined sex, 61 males and 173 females were processed through the fence. An additional 19 bull trout were observed on a snorkel survey prior to the fence being removed on October 12th. Coupled with the fence count, the total bull trout enumerated during this project was 292 fish. Several other species of fish were captured at the enumeration fence including westslope cutthroat trout (Oncorhynchus clarki lewisi), Rocky Mountain whitefish (Prosopium williamsoni), and kokanee (O. nerka). A total of 143 bull trout redds were enumerated on the ground in two different locations (river km 27.5-30.5, and km 24.0-25.5) on October 3rd. The majority of redds (n=132) were observed in the 3.0 km index section (river km 27.5-30.5) that has been surveyed over the past five years. The additional 11 redds were observed in a 1.5 km section (river km 24.0-25.5). Summary plots of water temperature for Bradford Creek, Sandown Creek, Buhl Creek, and Skookumchuck Creek at three locations suggested that water temperatures were within the temperature range preferred by bull trout for spawning, egg incubation, and rearing

  8. Rapid enumeration of low numbers of moulds in tea based drinks using an automated system.

    Science.gov (United States)

    Tanaka, Kouichi; Yamaguchi, Nobuyasu; Baba, Takashi; Amano, Norihide; Nasu, Masao

    2011-01-31

    Aseptically prepared cold drinks based on tea have become popular worldwide. Contamination of these drinks with harmful microbes is a potential health problem because such drinks are kept free from preservatives to maximize aroma and flavour. Heat-tolerant conidia and ascospores of fungi can survive pasteurization, and need to be detected as quickly as possible. We were able to rapidly and accurately detect low numbers of conidia and ascospores in tea-based drinks using fluorescent staining followed by an automated counting system. Conidia or ascospores were inoculated into green tea and oolong tea, and samples were immediately filtered through nitrocellulose membranes (pore size: 0.8 μm) to concentrate fungal propagules. These were transferred onto potato dextrose agar and incubated for 23 h at 28 °C. Fungi germinating on the membranes were fluorescently stained for 30 min. The stained mycelia were counted selectively within 90s using an automated counting system (MGS-10LD; Chuo Electric Works, Osaka, Japan). Very low numbers (1 CFU/100ml) of conidia or ascospores could be rapidly counted, in contrast to traditional labour intensive techniques. All tested mould strains were detected within 24h while conventional plate counting required 72 h for colony enumeration. Counts of slow-growing fungi (Cladosporium cladosporioides) obtained by automated counting and by conventional plate counting were close (r(2) = 0.986). Our combination of methods enables counting of both fast- and slow-growing fungi, and should be useful for microbiological quality control of tea-based and also other drinks. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Analyzing the behavior and reliability of voting systems comprising tri-state units using enumerated simulation

    International Nuclear Information System (INIS)

    Yacoub, Sherif

    2003-01-01

    Voting is a common technique used in combining results from peer experts, for multiple purposes, and in a variety of domains. In distributed decision making systems, voting mechanisms are used to obtain a decision by incorporating the opinion of multiple units. Voting systems have many applications in fault tolerant systems, mutual exclusion in distributed systems, and replicated databases. We are specifically interested in voting systems as used in decision-making applications. In this paper, we describe a synthetic experimental procedure to study the behavior of a variety of voting system configurations using a simulator to: analyze the state of each expert, apply a voting mechanism, and analyze the voting results. We introduce an enumerated-simulation approach and compare it to existing mathematical approaches. The paper studies the following behaviors of a voting system: (1) the reliability of the voting system, R; (2) the probability of reaching a consensus, P c ; (3) certainty index, T; and (4) the confidence index, C. The configuration parameters controlling the analysis are: (1) the number of participating experts, N, (2) the possible output states of an expert, and (3) the probability distribution of each expert states. We illustrate the application of this approach to a voting system that consists of N units, each has three states: correct (success), wrong (failed), and abstain (did not produce an output). The final output of the decision-making (voting) system is correct if a consensus is reached on a correct unit output, abstain if all units abstain from voting, and wrong otherwise. We will show that using the proposed approach, we can easily conduct studies to unleash several behaviors of a decision-making system with tri-state experts

  10. Impact of enumeration method on diversity of Escherichia coli genotypes isolated from surface water.

    Science.gov (United States)

    Martin, E C; Gentry, T J

    2016-11-01

    There are numerous regulatory-approved Escherichia coli enumeration methods, but it is not known whether differences in media composition and incubation conditions impact the diversity of E. coli populations detected by these methods. A study was conducted to determine if three standard water quality assessments, Colilert ® , USEPA Method 1603, (modified mTEC) and USEPA Method 1604 (MI), detect different populations of E. coli. Samples were collected from six watersheds and analysed using the three enumeration approaches followed by E. coli isolation and genotyping. Results indicated that the three methods generally produced similar enumeration data across the sites, although there were some differences on a site-by-site basis. The Colilert ® method consistently generated the least diverse collection of E. coli genotypes as compared to modified mTEC and MI, with those two methods being roughly equal to each other. Although the three media assessed in this study were designed to enumerate E. coli, the differences in the media composition, incubation temperature, and growth platform appear to have a strong selective influence on the populations of E. coli isolated. This study suggests that standardized methods of enumeration and isolation may be warranted if researchers intend to obtain individual E. coli isolates for further characterization. This study characterized the impact of three USEPA-approved Escherichia coli enumeration methods on observed E. coli population diversity in surface water samples. Results indicated that these methods produced similar E. coli enumeration data but were more variable in the diversity of E. coli genotypes observed. Although the three methods enumerate the same species, differences in media composition, growth platform, and incubation temperature likely contribute to the selection of different cultivable populations of E. coli, and thus caution should be used when implementing these methods interchangeably for

  11. Microbial biosensors

    International Nuclear Information System (INIS)

    Le Yu; Chen, Wilfred; Mulchandani, Ashok

    2006-01-01

    A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

  12. Comparative effects of application of coated and non-coated urea in clayey and sandy paddy soil microcosms examined by the 15N tracer technique. 2. Effects on soil microbial biomass N and microbial 15N immobilization

    International Nuclear Information System (INIS)

    Acquaye, Solomon; Inubushi, Kazuyuki

    2004-01-01

    Nitrogen fertilizer and soil types exert an impact on plant and soil microbial biomass (SMB). A 15 N tracer experiment was conducted to compare the effects of the application of controlled-release coated urea (CRCU) and urea on SMB in gley (clayey) and sandy paddy soils. The fertilizers were applied at the rate of 8 g N m -2 for CRCU as deep-side placement and 10 g N m -2 for urea mixed into soil or applied into floodwater. The soil type and soil layer (surface: few millimeter depth of surface soil to include benthic algae; subsurface: 1 to 20 cm depth), but not the fertilizer type, affected the amount of microbial biomass N (B N ). On an area basis, subsurface soil layers contained about 2-3 times the amount of B N in the surface layers. The seasonal average B N amount i.e. at 1 to 20 cm depth, in the gley soil was 1.67 g N m -2 , compared to 1.20 g N m -2 for the sandy soil. The proportion of B N in total soil N was significantly influenced by the soil type and soil layer, and was higher for the surface layers of both soils and subsurface layer of the sandy soil than for the subsurface layer of gley soil. Soil type, soil layer, and fertilizer type significantly influenced the amount of microbial biomass 15 N (B 15N ). Unlike B N , the amount of B 15N was significantly higher in the surface (11.9-177.3 mg N m -2 ) than in the subsurface soil layers (4.8-83.6 mg N m -2 ), especially with urea application between 60 and 120 DAT (days after transplanting). At 30 DAT, the subsurface layer of the sandy soil showed a higher B 15N (218 mg N m -2 ) amount than the surface layer (133.4 mg N m -2 ). Sandy soil (4.8-218 mg N m -2 ) and urea (6.2-218 mg N m -2 ) induced a larger increase of the amount of B 15 N than the gley soil (6.2-83.6 mg N m -2 ) and CRCU (4.8-40 mg Nm -2 ). Again, the sandy soil, surface soil layers, and urea induced a higher proportion (%) of B 15N in B N than the gley soil, subsurface soil layers, and CRCU, respectively. The soil type affected B N

  13. Enumeration versus Multiple Object Tracking: The Case of Action Video Game Players

    Science.gov (United States)

    Green, C. S.; Bavelier, D.

    2006-01-01

    Here, we demonstrate that action video game play enhances subjects' ability in two tasks thought to indicate the number of items that can be apprehended. Using an enumeration task, in which participants have to determine the number of quickly flashed squares, accuracy measures showed a near ceiling performance for low numerosities and a sharp drop…

  14. Miniaturized most probable number for the enumeration of Salmonella sp in artificially contaminated chicken meat

    Directory of Open Access Journals (Sweden)

    FL Colla

    2014-03-01

    Full Text Available Salmonella is traditionally identified by conventional microbiological tests, but the enumeration of this bacterium is not used on a routine basis. Methods such as the most probable number (MPN, which utilize an array of multiple tubes, are time-consuming and expensive, whereas miniaturized most probable number (mMPN methods, which use microplates, can be adapted for the enumeration of bacteria, saving up time and materials. The aim of the present paper is to assess two mMPN methods for the enumeration of Salmonella sp in artificially-contaminated chicken meat samples. Microplates containing 24 wells (method A and 96 wells (method B, both with peptone water as pre-enrichment medium and modified semi-solid Rappaport-Vassiliadis (MSRV as selective enrichment medium, were used. The meat matrix consisted of 25g of autoclaved ground chicken breast contaminated with dilutions of up to 10(6 of Salmonella Typhimurium (ST and Escherichia coli (EC. In method A, the dilution 10-5 of Salmonella Typhimurium corresponded to >57 MPN/mL and the dilution 10-6 was equal to 30 MPN/mL. There was a correlation between the counts used for the artificial contamination of the samples and those recovered by mMPN, indicating that the method A was sensitive for the enumeration of different levels of contamination of the meat matrix. In method B, there was no correlation between the inoculated dilutions and the mMPN results.

  15. Sieving for pseudosquares and pseudocubes in parallel using doubly-focused enumeration and wheel datastructures

    OpenAIRE

    Sorenson, Jonathan P.

    2010-01-01

    We extend the known tables of pseudosquares and pseudocubes, discuss the implications of these new data on the conjectured distribution of pseudosquares and pseudocubes, and present the details of the algorithm used to do this work. Our algorithm is based on the space-saving wheel data structure combined with doubly-focused enumeration, run in parallel on a cluster supercomputer.

  16. TEMA and Dot Enumeration Profiles Predict Mental Addition Problem Solving Speed Longitudinally.

    Science.gov (United States)

    Major, Clare S; Paul, Jacob M; Reeve, Robert A

    2017-01-01

    Different math indices can be used to assess math potential at school entry. We evaluated whether standardized math achievement (TEMA-2 performance), core number abilities (dot enumeration, symbolic magnitude comparison), non-verbal intelligence (NVIQ) and visuo-spatial working memory (VSWM), in combination or separately, predicted mental addition problem solving speed over time. We assessed 267 children's TEMA-2, magnitude comparison, dot enumeration, and VSWM abilities at school entry (5 years) and NVIQ at 8 years. Mental addition problem solving speed was assessed at 6, 8, and 10 years. Longitudinal path analysis supported a model in which dot enumeration performance ability profiles and previous mental addition speed predicted future mental addition speed on all occasions, supporting a componential account of math ability. Standardized math achievement and NVIQ predicted mental addition speed at specific time points, while VSWM and symbolic magnitude comparison did not contribute unique variance to the model. The implications of using standardized math achievement and dot enumeration ability to index math learning potential at school entry are discussed.

  17. Sample handling factors affecting the enumeration of lactobacilli and cellulolytic bacteria in equine feces

    Science.gov (United States)

    The objectives were to compare media types and evaluate the effects of fecal storage time and temperature on the enumeration of cellulolytic bacteria and lactobacilli from horses. Fecal samples were collected from horses (n = 3) and transported to the lab (CO2, 37 ºC, 0.5 h). The samples were assign...

  18. A comparison of test statistics for the recovery of rapid growth-based enumeration tests

    NARCIS (Netherlands)

    van den Heuvel, Edwin R.; IJzerman-Boon, Pieta C.

    This paper considers five test statistics for comparing the recovery of a rapid growth-based enumeration test with respect to the compendial microbiological method using a specific nonserial dilution experiment. The finite sample distributions of these test statistics are unknown, because they are

  19. Discontinuity in the Enumeration of Sequentially Presented Auditory and Visual Stimuli

    Science.gov (United States)

    Camos, Valerie; Tillmann, Barbara

    2008-01-01

    The seeking of discontinuity in enumeration was recently renewed because Cowan [Cowan, N. (2001). "The magical number 4 in short-term memory: A reconsideration of mental storage capacity." "Behavioral and Brain Sciences," 24, 87-185; Cowan, N. (2005). "Working memory capacity." Hove: Psychology Press] suggested that it allows evaluating the limit…

  20. Evaluation of culture media for selective enumeration of bifidobacteria and lactic acid bacteria

    Directory of Open Access Journals (Sweden)

    Judit Süle

    2014-09-01

    Full Text Available The purpose of this study was to test the suitability of Transgalactosylated oligosaccharides-mupirocin lithium salt (TOS-MUP and MRS-clindamycin-ciprofloxacin (MRS-CC agars, along with several other culture media, for selectively enumerating bifidobacteria and lactic acid bacteria (LAB species commonly used to make fermented milks. Pure culture suspensions of a total of 13 dairy bacteria strains, belonging to eight species and five genera, were tested for growth capability under various incubation conditions. TOS-MUP agar was successfully used for the selective enumeration of both Bifidobacterium animalis subsp. lactis BB-12 and B. breve M-16 V. MRS-CC agar showed relatively good selectivity for Lactobacillus acidophilus, however, it also promoted the growth of Lb. casei strains. For this reason, MRS-CC agar can only be used as a selective medium for the enumeration of Lb. acidophilus if Lb. casei is not present in a product at levels similar to or exceeding those of Lb. acidophilus. Unlike bifidobacteria and coccus-shaped LAB, all the lactobacilli strains involved in this work were found to grow well in MRS pH 5.4 agar incubated under anaerobiosis at 37 °C for 72 h. Therefore, this method proved to be particularly suitable for the selective enumeration of Lactobacillus spp.

  1. Comparison of selected methods for the enumeration of fecal coliforms and Escherichia coli in shellfish.

    Science.gov (United States)

    Grabow, W O; De Villiers, J C; Schildhauer, C I

    1992-09-01

    In a comparison of five selected methods for the enumeration of fecal coliforms and Escherichia coli in naturally contaminated and sewage-seeded mussels (Choromytilus spp.) and oysters (Ostrea spp.), a spread-plate procedure with mFC agar without rosolic acid and preincubation proved the method of choice for routine quality assessment.

  2. BACTERIOLOGICAL PROPERTIES OF MARINE WATER IN ADRIATIC FISH FARMS: ENUMERATION OF HETEROTROPHIC BACTERIA

    Directory of Open Access Journals (Sweden)

    Emin Teskeredžić

    2012-12-01

    Full Text Available Aquaculture is currently one of the fastest growing food production sectors in the world. Increase in nutrients and organic wastes lead to general deterioration of water quality. The problem of water quality is associated with both physical and chemical factors, as well as microbiological water quality. Heterotrophic bacteria play an important role in the process of decomposition of organic matter in water environment and indicate eutrophication process. Here we present our experience and knowledge on bacterial properties of marine water in the Adriatic fish farms with European sea bass (Dicentrarchus labrax L., 1758, with an emphasis on enumeration of heterotrophic bacteria in marine water. We applied two temperatures of incubation, as well as two methods for enumeration of heterotrophic bacteria: substrate SimPlate® test and spread plate method on conventional artificial media (Marine agar and Tryptic Soy agar with added NaCl. The results of analysis of bacteriological properties of marine water in the Adriatic fish farms showed that enumeration of heterotrophic bacteria in marine water depends on the applied incubation temperature and media for enumeration. At the same time, the incubation temperature of 22C favours more intense growth of marine heterotrophic bacteria, whereas a SimPlate test gives higher values of heterotrophic bacteria. Volatile values of heterotrophic bacteria during this research indicate a possible deterioration of microbiological water quality in the Adriatic fish farms and a need for regular monitoring of marine water quality.

  3. Enumeration of Mars years and seasons since the beginning of telescopic exploration

    Science.gov (United States)

    Piqueux, Sylvain; Byrne, Shane; Titus, Timothy N.; Hansen, Candice J.; Kieffer, Hugh H.

    2015-01-01

    A clarification for the enumeration of Mars Years prior to 1955 is presented, along with a table providing the Julian dates associated with Ls = 0° for Mars Years -183 (beginning of the telescopic study of Mars) to 100. A practical algorithm for computing Ls as a function of the Julian Date is provided. No new science results are presented

  4. Fluorogenic membrane overlays to enumerate total coliforms, Escherichia coli, and total Vibrionaceae in shellfish and seawater

    Science.gov (United States)

    Three assays were developed to enumerate total coliforms, Escherichia coli, and total Vibrionaceae in shellfish and other foods and in seawater and other environmental samples. Assays involve membrane overlays of overnight colonies on non-selective agar plates to detect ß-glucuronidase and lysyl am...

  5. Enumeration for spanning trees and forests of join graphs based on the combinatorial decomposition

    Directory of Open Access Journals (Sweden)

    Sung Sik U

    2016-10-01

    Full Text Available This paper discusses the enumeration for rooted spanning trees and forests of the labelled join graphs $K_m+H_n$ and $K_m+K_{n,p}$, where $H_n$ is a graph with $n$ isolated vertices. 

  6. Contaminant immobilization via microbial activity

    International Nuclear Information System (INIS)

    1991-11-01

    The aim of this study was to search the literature to identify biological techniques that could be applied to the restoration of contaminated groundwaters near uranium milling sites. Through bioremediation it was hypothesized that the hazardous heavy metals could be immobilized in a stable, low-solubility form, thereby halting their progress in the migrating groundwater. Three basic mechanisms were examined: reduction of heavy metals by microbially produced hydrogen sulfide; direct microbial mediated reduction; and biosorption

  7. Microbial glycoproteomics

    DEFF Research Database (Denmark)

    Halim, Adnan; Anonsen, Jan Haug

    2017-01-01

    Mass spectrometry-based "-omics" technologies are important tools for global and detailed mapping of post-translational modifications. Protein glycosylation is an abundant and important post translational modification widespread throughout all domains of life. Characterization of glycoproteins...... and research in this area is rapidly accelerating. Here, we review recent developments in glycoproteomic technologies with a special focus on microbial protein glycosylation....

  8. Rapid and quantitative detection of the microbial spoilage in milk using Fourier transform infrared spectroscopy and chemometrics.

    Science.gov (United States)

    Nicolaou, Nicoletta; Goodacre, Royston

    2008-10-01

    Microbiological safety plays a very significant part in the quality control of milk and dairy products worldwide. Current methods used in the detection and enumeration of spoilage bacteria in pasteurized milk in the dairy industry, although accurate and sensitive, are time-consuming. FT-IR spectroscopy is a metabolic fingerprinting technique that can potentially be used to deliver results with the same accuracy and sensitivity, within minutes after minimal sample preparation. We tested this hypothesis using attenuated total reflectance (ATR), and high throughput (HT) FT-IR techniques. Three main types of pasteurized milk - whole, semi-skimmed and skimmed - were used and milk was allowed to spoil naturally by incubation at 15 degrees C. Samples for FT-IR were obtained at frequent, fixed time intervals and pH and total viable counts were also recorded. Multivariate statistical methods, including principal components-discriminant function analysis and partial least squares regression (PLSR), were then used to investigate the relationship between metabolic fingerprints and the total viable counts. FT-IR ATR data for all milks showed reasonable results for bacterial loads above 10(5) cfu ml(-1). By contrast, FT-IR HT provided more accurate results for lower viable bacterial counts down to 10(3) cfu ml(-1) for whole milk and, 4 x 10(2) cfu ml(-1) for semi-skimmed and skimmed milk. Using FT-IR with PLSR we were able to acquire a metabolic fingerprint rapidly and quantify the microbial load of milk samples accurately, with very little sample preparation. We believe that metabolic fingerprinting using FT-IR has very good potential for future use in the dairy industry as a rapid method of detection and enumeration.

  9. Enumeration and characterization of microorganisms associated with the uranium ore deposit at Cigar Lake, Canada. Informal report

    International Nuclear Information System (INIS)

    Francis, A.J.; Joshi-Tope, G.; Gillow, J.B.; Dodge, C.J.

    1994-03-01

    The high-grade uranium deposit at Cigar Lake, Canada, is being investigated as a natural analog for the disposal of nuclear fuel waste. Geochemical aspects of the site have been studied in detail, but the microbial ecology has not been fully investigated. Microbial populations in an ore sample and in groundwater samples from the vicinity of the ore zone were examined to determine their effect on uranium mobility. Counts of the total number of bacteria and of respiring bacteria were obtained by direct microscopy, and the viable aerobic and anaerobic bacteria were assessed as colony forming units (CFUs) by the dilution plating technique. In addition, the population distribution of denitrifiers, fermenters, iron- and sulfur-oxidizers, iron- and sulfate-reducers, and methanogens was determined by the most probable number (MPN) technique

  10. Microbial ecology-based engineering of Microbial Electrochemical Technologies.

    Science.gov (United States)

    Koch, Christin; Korth, Benjamin; Harnisch, Falk

    2018-01-01

    Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  11. Comparative assessment of antibiotic susceptibility of coagulase-negative staphylococci in biofilm versus planktonic culture as assessed by bacterial enumeration or rapid XTT colorimetry.

    Science.gov (United States)

    Cerca, Nuno; Martins, Silvia; Cerca, Filipe; Jefferson, Kimberly K; Pier, Gerald B; Oliveira, Rosário; Azeredo, Joana

    2005-08-01

    To quantitatively compare the antibiotic susceptibility of biofilms formed by the coagulase-negative staphylococci (CoNS) Staphylococcus epidermidis and Staphylococcus haemolyticus with the susceptibility of planktonic cultures. Several CoNS strains were grown planktonically or as biofilms to determine the effect of the mode of growth on the level of susceptibility to antibiotics with different mechanisms of action. The utility of a new, rapid colorimetric method that is based on the reduction of a tetrazolium salt (XTT) to measure cell viability was tested by comparison with standard bacterial enumeration techniques. A 6 h kinetic study was performed using dicloxacillin, cefazolin, vancomycin, tetracycline and rifampicin at the peak serum concentration of each antibiotic. In planktonic cells, inhibitors of cell wall synthesis were highly effective over a 3 h period. Biofilms were much less susceptible than planktonic cultures to all antibiotics tested, particularly inhibitors of cell wall synthesis. The susceptibility to inhibitors of protein and RNA synthesis was affected by the biofilm phenotype to a lesser degree. Standard bacterial enumeration techniques and the XTT method produced equivalent results both in biofilms and planktonic assays. This study provides a more accurate comparison between the antibiotic susceptibilities of planktonic versus biofilm populations, because the cell densities in the two populations were similar and because we measured the concentration required to inhibit bacterial metabolism rather than to eradicate the entire bacterial population. While the biofilm phenotype is highly resistant to antibiotics that target cell wall synthesis, it is fairly susceptible to antibiotics that target RNA and protein synthesis.

  12. Enumeration of Vibrio parahaemolyticus in the viable but nonculturable state using direct plate counts and recognition of individual gene fluorescence in situ hybridization.

    Science.gov (United States)

    Griffitt, Kimberly J; Noriea, Nicholas F; Johnson, Crystal N; Grimes, D Jay

    2011-05-01

    Vibrio parahaemolyticus is a gram-negative, halophilic bacterium indigenous to marine and estuarine environments and it is capable of causing food and water-borne illness in humans. It can also cause disease in marine animals, including cultured species. Currently, culture-based techniques are used for quantification of V. parahaemolyticus in environmental samples; however, these can be misleading as they fail to detect V. parahaemolyticus in a viable but nonculturable (VBNC) state which leads to an underestimation of the population density. In this study, we used a novel fluorescence visualization technique, called recognition of individual gene fluorescence in situ hybridization (RING-FISH), which targets chromosomal DNA for enumeration. A polynucleotide probe labeled with Cyanine 3 (Cy3) was created corresponding to the ubiquitous V. parahaemolyticus gene that codes for thermolabile hemolysin (tlh). When coupled with the Kogure method to distinguish viable from dead cells, RING-FISH probes reliably enumerated total, viable V. parahaemolyticus. The probe was tested for sensitivity and specificity against a pure culture of tlh(+), tdh(-), trh(-)V. parahaemolyticus, pure cultures of Vibrio vulnificus, Vibrio harveyi, Vibrio alginolyticus and Vibrio fischeri, and a mixed environmental sample. This research will provide additional tools for a better understanding of the risk these environmental organisms pose to human health. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Development of an enumeration method for arsenic methylating bacteria from mixed culture samples.

    Science.gov (United States)

    Islam, S M Atiqul; Fukushi, Kensuke; Yamamoto, Kazuo

    2005-12-01

    Bacterial methylation of arsenic converts inorganic arsenic into volatile and non-volatile methylated species. It plays an important role in the arsenic cycle in the environment. Despite the potential environmental significance of AsMB, an assessment of their population size and activity remains unknown. This study has now established a protocol for enumeration of AsMB by means of the anaerobic-culture-tube, most probable number (MPN) method. Direct detection of volatile arsenic species is then done by GC-MS. This method is advantageous as it can simultaneously enumerate AsMB and acetate and formate-utilizing methanogens. The incubation time for this method was determined to be 6 weeks, sufficient time for AsMB growth.

  14. Spatial working memory load affects counting but not subitizing in enumeration.

    Science.gov (United States)

    Shimomura, Tomonari; Kumada, Takatsune

    2011-08-01

    The present study investigated whether subitizing reflects capacity limitations associated with two types of working memory tasks. Under a dual-task situation, participants performed an enumeration task in conjunction with either a spatial (Experiment 1) or a nonspatial visual (Experiment 2) working memory task. Experiment 1 showed that spatial working memory load affected the slope of a counting function but did not affect subitizing performance or subitizing range. Experiment 2 showed that nonspatial visual working memory load affected neither enumeration efficiency nor subitizing range. Furthermore, in both spatial and nonspatial memory tasks, neither subitizing efficiency nor subitizing range was affected by amount of imposed memory load. In all the experiments, working memory load failed to influence slope, subitizing range, or overall reaction time. These findings suggest that subitizing is performed without either spatial or nonspatial working memory. A possible mechanism of subitizing with independent capacity of working memory is discussed.

  15. Performance of mycological media in enumerating desiccated food spoilage yeasts: an interlaboratory study.

    Science.gov (United States)

    Beuchat, L R; Frandberg, E; Deak, T; Alzamora, S M; Chen, J; Guerrero, A S; López-Malo, A; Ohlsson, I; Olsen, M; Peinado, J M; Schnurer, J; de Siloniz, M I; Tornai-Lehoczki, J

    2001-10-22

    Dichloran 18% glycerol agar (DG18) was originally formulated to enumerate nonfastidious xerophilic moulds in foods containing rapidly growing Eurotium species. Some laboratories are now using DG18 as a general purpose medium for enumerating yeasts and moulds, although its performance in recovering yeasts from dry foods has not been evaluated. An interlaboratory study compared DG18 with dichloran rose bengal chloramphenicol agar (DRBC), plate count agar supplemented with chloramphenicol (PCAC), tryptone glucose yeast extract chloramphenicol agar (TGYC), acidified potato dextrose agar (APDA), and orange serum agar (OSA) for their suitability to enumerate 14 species of lyophilized yeasts. The coefficient of variation for among-laboratories repeatability within yeast was 1.39% and reproducibility of counts among laboratories was 7.1%. The order of performance of media for recovering yeasts was TGYC > PCAC = OSA > APDA > DRBC > DG 18. A second study was done to determine the combined effects of storage time and temperature on viability of yeasts and suitability of media for recovery. Higher viability was retained at -18 degrees C than at 5 degrees C or 25 degrees C for up to 42 weeks, although the difference in mean counts of yeasts stored at -18 degrees C and 25 degrees C was only 0.78 log10 cfu/ml of rehydrated suspension. TGYC was equal to PCAC and superior to the other four media in recovering yeasts stored at -18 degrees C, 5 degrees C, or 25 degrees C for up to 42 weeks. Results from both the interlaboratory study and the storage study support the use of TGYC for enumerating desiccated yeasts. DG18 is not recommended as a general purpose medium for recovering yeasts from a desiccated condition.

  16. Separating the Classes of Recursively Enumerable Languages Based on Machine Size

    Czech Academy of Sciences Publication Activity Database

    van Leeuwen, J.; Wiedermann, Jiří

    2015-01-01

    Roč. 26, č. 6 (2015), s. 677-695 ISSN 0129-0541 R&D Projects: GA ČR GAP202/10/1333 Grant - others:GA ČR(CZ) GA15-04960S Institutional support: RVO:67985807 Keywords : recursively enumerable languages * RE hierarchy * finite languages * machine size * descriptional complexity * Turing machines with advice Subject RIV: IN - Informatics, Computer Science Impact factor: 0.467, year: 2015

  17. Comparison of methods for detection and enumeration of airborne microorganisms collected by liquid impingement.

    OpenAIRE

    Terzieva, S; Donnelly, J; Ulevicius, V; Grinshpun, S A; Willeke, K; Stelma, G N; Brenner, K P

    1996-01-01

    Bacterial agents and cell components can be spread as bioaerosols, producing infections and asthmatic problems. This study compares four methods for the detection and enumeration of aerosolized bacteria collected in an AGI-30 impinger. Changes in the total and viable concentrations of Pseudomonas fluorescens in the collection fluid with respect to time of impingement were determined. Two direct microscopic methods (acridine orange and BacLight) and aerodynamic aerosol-size spectrometry (Aeros...

  18. The Enumeration Structure of 爾雅 Ěryǎ's "Semantic Lists"

    Science.gov (United States)

    Teboul (戴明德), Michel

    Modern linguistic enumeration theory is applied to a study of 爾雅 Ěryǎ's Semantic Lists, leading to an in-depth analysis of the work's first three sections without any recourse to the traditional methods of Chinese classical philology. It is hoped that an extension of the same method can lead to a better understanding of the remaining 16 sections.

  19. An information theory criteria based blind method for enumerating active users in DS-CDMA system

    Science.gov (United States)

    Samsami Khodadad, Farid; Abed Hodtani, Ghosheh

    2014-11-01

    In this paper, a new and blind algorithm for active user enumeration in asynchronous direct sequence code division multiple access (DS-CDMA) in multipath channel scenario is proposed. The proposed method is based on information theory criteria. There are two main categories of information criteria which are widely used in active user enumeration, Akaike Information Criterion (AIC) and Minimum Description Length (MDL) information theory criteria. The main difference between these two criteria is their penalty functions. Due to this difference, MDL is a consistent enumerator which has better performance in higher signal-to-noise ratios (SNR) but AIC is preferred in lower SNRs. In sequel, we propose a SNR compliance method based on subspace and training genetic algorithm to have the performance of both of them. Moreover, our method uses only a single antenna, in difference to the previous methods which decrease hardware complexity. Simulation results show that the proposed method is capable of estimating the number of active users without any prior knowledge and the efficiency of the method.

  20. Media for the isolation and enumeration of bifidobacteria in dairy products.

    Science.gov (United States)

    Roy, D

    2001-09-28

    Bifidobacteria are commonly used for the production of fermented milks, alone or in combination with other lactic acid bacteria. Bifidobacteria populations in fermented milks should be over 10(6) bifidobacteria/g at the time of consumption of strain added to the product. Hence, rapid and reliable methods are needed to routinely determine the initial inoculum and to estimate the storage time period bifidobacteria remain viable. Plate count methods are still preferable for quality control measurements in dairy products. It is, therefore, necessary to have a medium that selectively promotes the growth of bifidobacteria, whereas other bacteria are suppressed. The present paper is an overview of media and methods including summaries of published comparisons between different selective media. Culture media for bifidobacteria may be divided into basal, elective, differential and selective culture medium. Non-selective media are useful for routine enumeration of bifidobacteria when present in non-fermented milks. Reinforced Clostridial Agar and De Man Rogosa Sharpe (MRS) supplemented with cysteine and agar available commercially are the media of choice for industrial quality control laboratories. Several media for selective or differential isolation have been described for enumeration of bifidobacteria from other lactic acid bacteria. From the large number of selective media available, it can be concluded that there is no standard medium for the detection of bifidobacteria. However, Columbia agar base media supplemented with lithium chloride and sodium propionate and MRS medium supplemented with neomycin, paromomycin, nalidixic acid and lithium chloride can be recommended for selective enumeration of bifidobacteria in dairy products.

  1. Natural product-like virtual libraries: recursive atom-based enumeration.

    Science.gov (United States)

    Yu, Melvin J

    2011-03-28

    A new molecular enumerator is described that allows chemically and architecturally diverse sets of natural product-like and drug-like structures to be generated from a core structure as simple as a single carbon atom or as complex as a polycyclic ring system. Integrated with a rudimentary machine-learning algorithm, the enumerator has the ability to assemble biased virtual libraries enriched in compounds predicted to meet target criteria. The ability to dynamically generate relatively small focused libraries in a recursive manner could reduce the computational time and infrastructure necessary to construct and manage extremely large static libraries. Depending on enumeration conditions, natural product-like structures can be produced with a wide range of heterocyclic and alicyclic ring assemblies. Because natural products represent a proven source of validated structures for identifying and designing new drug candidates, mimicking the structural and topological diversity found in nature with a dynamic set of virtual natural product-like compounds may facilitate the creation of new ideas for novel, biologically relevant lead structures in areas of uncharted chemical space.

  2. Automated Mobile System for Accurate Outdoor Tree Crop Enumeration Using an Uncalibrated Camera

    Directory of Open Access Journals (Sweden)

    Thuy Tuong Nguyen

    2015-07-01

    Full Text Available This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration required to obtain robust performance in a natural outdoor environment. The enumeration system uses a three-step image analysis process based upon: (1 an orthographic plant projection method integrating a perspective transform with automatic parameter estimation; (2 a plant counting method based on projection histograms; and (3 a double-counting avoidance method based on a homography transform. Experimental results demonstrate the ability to count large numbers of plants automatically with no human effort. Results show that, for tree seedlings having a height up to 40 cm and a within-row tree spacing of approximately 10 cm, the algorithms successfully estimated the number of plants with an average accuracy of 95.2% for trees within a single image and 98% for counting of the whole plant population in a large sequence of images.

  3. Automated Mobile System for Accurate Outdoor Tree Crop Enumeration Using an Uncalibrated Camera.

    Science.gov (United States)

    Nguyen, Thuy Tuong; Slaughter, David C; Hanson, Bradley D; Barber, Andrew; Freitas, Amy; Robles, Daniel; Whelan, Erin

    2015-07-28

    This paper demonstrates an automated computer vision system for outdoor tree crop enumeration in a seedling nursery. The complete system incorporates both hardware components (including an embedded microcontroller, an odometry encoder, and an uncalibrated digital color camera) and software algorithms (including microcontroller algorithms and the proposed algorithm for tree crop enumeration) required to obtain robust performance in a natural outdoor environment. The enumeration system uses a three-step image analysis process based upon: (1) an orthographic plant projection method integrating a perspective transform with automatic parameter estimation; (2) a plant counting method based on projection histograms; and (3) a double-counting avoidance method based on a homography transform. Experimental results demonstrate the ability to count large numbers of plants automatically with no human effort. Results show that, for tree seedlings having a height up to 40 cm and a within-row tree spacing of approximately 10 cm, the algorithms successfully estimated the number of plants with an average accuracy of 95.2% for trees within a single image and 98% for counting of the whole plant population in a large sequence of images.

  4. Microbial xanthophylls.

    Science.gov (United States)

    Bhosale, Prakash; Bernstein, Paul S

    2005-09-01

    Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

  5. Microbial Energy Conversion

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, Merry [American Society for Microbiology (ASM), Washington, DC (United States); Wall, Judy D. [Univ. of Missouri, Columbia, MO (United States)

    2006-10-01

    The American Academy of Microbiology convened a colloquium March 10-12, 2006, in San Francisco, California, to discuss the production of energy fuels by microbial conversions. The status of research into various microbial energy technologies, the advantages and disadvantages of each of these approaches, research needs in the field, and education and training issues were examined, with the goal of identifying routes for producing biofuels that would both decrease the need for fossil fuels and reduce greenhouse gas emissions. Currently, the choices for providing energy are limited. Policy makers and the research community must begin to pursue a broader array of potential energy technologies. A diverse energy portfolio that includes an assortment of microbial energy choices will allow communities and consumers to select the best energy solution for their own particular needs. Funding agencies and governments alike need to prepare for future energy needs by investing both in the microbial energy technologies that work today and in the untested technologies that will serve the world’s needs tomorrow. More mature bioprocesses, such as ethanol production from starchy materials and methane from waste digestors, will find applications in the short term. However, innovative techniques for liquid fuel or biohydrogen production are among the longer term possibilities that should also be vigorously explored, starting now. Microorganisms can help meet human energy needs in any of a number of ways. In their most obvious role in energy conversion, microorganisms can generate fuels, including ethanol, hydrogen, methane, lipids, and butanol, which can be burned to produce energy. Alternatively, bacteria can be put to use in microbial fuel cells, where they carry out the direct conversion of biomass into electricity. Microorganisms may also be used some day to make oil and natural gas technologies more efficient by sequestering carbon or by assisting in the recovery of oil and

  6. [Prokaryotic community of subglacial bottom sediments of Antarctic Lake Untersee: detection by cultural and direct microscopic techniques].

    Science.gov (United States)

    Muliukin, A L; Demkina, E V; Manucharova, N A; Akimov, V N; Andersen, D; McKay, C; Gal'chenko, V F

    2014-01-01

    The heterotrophic mesophilic component was studied in microbial communities of the samples of frozen regolith collected from the glacier near Lake Untersee collected in 2011 during the joint Russian-American expedition to central Dronning Maud Land (Eastern Antarctica). Cultural techniques revealed high bacterial numbers in the samples. For enumeration of viable cells, the most probable numbers (MPN) method proved more efficient than plating on agar media. Fluorescent in situ hybridization with the relevant oligonucleotide probes revealed members of the groups Eubacteria (Actinobacteria, Firmicutes) and Archaea. Application of the methods of cell resuscitation, such as the use of diluted media and prevention of oxidative stress, did not result in a significant increase in the numbers of viable cells retrieved form subglacial sediment samples. Our previous investigations demonstrated the necessity for special procedures for efficient reactivation of the cells from microbial communities of preserved fossil soil and permafrost samples collected in the Arctic zone. The differences in response to the special resuscitation procedures may reflect the differences in the physiological and morphological state of bacterial cells in microbial communities subject to continuous or periodic low temperatures and dehydration.

  7. Microbial effects

    International Nuclear Information System (INIS)

    Sharpe, V.J.

    1985-10-01

    The long term safety and integrity of radioactive waste disposal sites proposed for use by Ontario Hydro may be affected by the release of radioactive gases. Microbes mediate the primary pathways of waste degradation and hence an assessment of their potential to produce gaseous end products from the breakdown of low level waste was performed. Due to a number of unknown variables, assumptions were made regarding environmental and waste conditions that controlled microbial activity; however, it was concluded that 14 C and 3 H would be produced, albeit over a long time scale of about 1500 years for 14 C in the worst case situation

  8. Monitoring Microbially Influenced Corrosion

    DEFF Research Database (Denmark)

    Hilbert, Lisbeth Rischel

    and diffusional effects and unreliable corrosion rates, when biofilm and ferrous sulphide corrosion products cover the steel surface. Corrosion rates can be overestimated by a factor of 10 to 100 by electrochemical techniques. Weight loss coupons and ER are recommended as necessary basic monitoring techniques......Abstract Microbially influenced corrosion (MIC) of carbon steel may occur in media with microbiological activity of especially sulphate-reducing bacteria (SRB). The applicability and reliability of a number of corrosion monitoring techniques for monitoring MIC has been evaluated in experiments....... EIS might be used for detection of MIC as the appearance of very large capacitances can be attributed to the combined ferrous sulphide and biofilm formation. Capacitance correlates directly with sulphide concentration in sterile sulphide media. Keywords: Corrosion monitoring, carbon steel, MIC, SRB...

  9. Evaluation of the Level of air Microbial Contamination in some ...

    African Journals Online (AJOL)

    The level of air microbial contamination in some teaching hospitals waste dump site in South Eastern Nigeria was evaluated using the standard microbiological techniques. Passive air sampling was performed using settle plates. The microbial load of the air around the hospitals waste dumpsite, showed high microbial load ...

  10. Techniques for the microbial community study in wastewater systems; Tecnicas utilizadas en el estudio de la comunidad microbiologica en sistemas de depuracion

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Gonzalez, M. C.; Fdez-Polanco, F.; Garcia Encina, P. A. [Universidad de Valladolid (Spain); Becares Mantecon, E. [Universidad de Leon (Spain)

    2003-07-01

    Activated sludge is community by an heterogenic organisms community, such as protozoa, metazoa, alga fungus and bacteria. Among these organisms bacteria are very important due to their rule in the nutrient (phosphate and nitrogen) and organic matter removal. so is important the study and knowledge of them, in order to understand how the wastewater systems works. To achieve this studies is necessary the characterization of the diverse bacterial groups (nitrifies, sulfate reducing, methanogenics etc.), thus it is essential the application of a rapid, reliable and precise method, like the molecular techniques that are commonly used in the wastewater studies. Among these techniques are F. I. S. H. (Florescence In Situ Hybridization). (Author) 27 refs.

  11. Microbial community structure in the gut of the New Zealand insect Auckland tree weta (Hemideina thoracica).

    Science.gov (United States)

    Waite, David W; Dsouza, Melissa; Biswas, Kristi; Ward, Darren F; Deines, Peter; Taylor, Michael W

    2015-05-01

    The endemic New Zealand weta is an enigmatic insect. Although the insect is well known by its distinctive name, considerable size, and morphology, many basic aspects of weta biology remain unknown. Here, we employed cultivation-independent enumeration techniques and rRNA gene sequencing to investigate the gut microbiota of the Auckland tree weta (Hemideina thoracica). Fluorescence in situ hybridisation performed on different sections of the gut revealed a bacterial community of fluctuating density, while rRNA gene-targeted amplicon pyrosequencing revealed the presence of a microbial community containing high bacterial diversity, but an apparent absence of archaea. Bacteria were further studied using full-length 16S rRNA gene sequences, with statistical testing of bacterial community membership against publicly available termite- and cockroach-derived sequences, revealing that the weta gut microbiota is similar to that of cockroaches. These data represent the first analysis of the weta microbiota and provide initial insights into the potential function of these microorganisms.

  12. Nutritional evaluation of leaves of some salt-tolerant tree species by assessing, in vitro, the ruminal microbial nitrogen and fermentation characteristics utilizing "1"5N tracer and gas production techniques

    International Nuclear Information System (INIS)

    Al-Masri, M.R.

    2014-04-01

    Leaves of some salt-tolerant tree species (Tamarix articulata Vahl., Tamarix aphylla (L) Karst, Acacia ampliceps Maslin, Casuarina equisetifolia L, Parkinsonia aculeate L, Eucaliptus camaldulensis Dahnhard) were evaluated in terms of microbial nitrogen (MN) and biomass (MBM) production after incubation with rumen fluid and 15N-tracer for 96 h in the absence or presence of polyethylene glycol (PEG, 6000). The characteristics of fermentation (initial gas produced from soluble fraction; a, gas production during incubation which produced from insoluble but fermentable fraction; b, potential gas production; a + b, fractional rate of gas production per hour; c) were assessed using an in vitro incubation technique with rumen fluid. Effective degradability (ED), short chain fatty acids (SCFA) and predicted daily intake (Y) were also estimated in leaves of the experimental tree species.The a + b values (mL/g DM) were highest (P<0.05) in A. ampliceps (191), lowest in T. articulate and C. equisetifolia (119), and intermediate in T. aphylla, E. camaldulensis and P. aculeate (158). E. camaldulensis, A. ampliceps and P. aculeate had higher (P<0.05) fractional rate of gas production (0.080/h) than other species (0.061/h). There was a positive correlation between SCFA concentrations and c and a + b values. The ratios of MN and MBM to effective degraded substrate and the values of MN and MBM were significantly higher (P<0.05) in P. aculeate and A. ampliceps compared with other species. Microbial nitrogen and MBM production were positively correlated with a + b, ED and SCFA.The addition of PEG to the plant samples incubated with rumen fluid at a ratio of 2:1 PEG: substrate increased the values of gas production, characteristics of fermentation, MN, MBM, SCFA, ED and Y. The response of leaves of the experimental tree species to PEG treatment in terms of increased gas production varied between species and tended to decline as incubation progressed, with the highest increase during the

  13. Use of LH-PCR as a DNA fingerprint technique to trace sediment-associated microbial communities from various land uses

    Science.gov (United States)

    Joe-Strack, J. A.; Petticrew, E. L.

    2012-04-01

    The search for new techniques to effectively and efficiently trace sediment from its source along catchment pathways continues, with a range of new methods being developed and tested annually. A relatively recent approach marries genetic techniques to sediment analysis in order to characterize and differentiate the bacterial populations associated with soil and/or sediment originating from specific locations. Here we present the preliminary results of DNA fingerprint profiles of soil and sediment-associated bacterial communities in and around two different industrial land uses in the central interior of British Columbia, a feedlot and a copper/gold mining site. We assessed the naturally varying 16S rDNA gene using amplicon length heterogeneity-polymerase chain reaction (LH-PCR). Statistical differences between bacterial community profiles were investigated using a suite of methods of which non-metric multidimensional scaling (NMS) and indicator species analysis (ISA) were the most useful. Stronger statistical results were observed for the feedlot data set with spatial differences observed from the source location and within the adjacent creek. Results from the mine site were more difficult to assess although responses were detected in downstream waterways. While bacterial DNA fingerprinting of soil and sediment appears to be a promising tracing technique issues of scale and transferability may limit its use. Lessons learned from this preliminary study will be presented.

  14. Enumeration of virtual libraries of combinatorial modular macrocyclic (bracelet, necklace) architectures and their linear counterparts.

    Science.gov (United States)

    Taniguchi, Masahiko; Du, Hai; Lindsey, Jonathan S

    2013-09-23

    A wide variety of cyclic molecular architectures are built of modular subunits and can be formed combinatorially. The mathematics for enumeration of such objects is well-developed yet lacks key features of importance in chemistry, such as specifying (i) the structures of individual members among a set of isomers, (ii) the distribution (i.e., relative amounts) of products, and (iii) the effect of nonequal ratios of reacting monomers on the product distribution. Here, a software program (Cyclaplex) has been developed to determine the number, identity (including isomers), and relative amounts of linear and cyclic architectures from a given number and ratio of reacting monomers. The program includes both mathematical formulas and generative algorithms for enumeration; the latter go beyond the former to provide desired molecular-relevant information and data-mining features. The program is equipped to enumerate four types of architectures: (i) linear architectures with directionality (macroscopic equivalent = electrical extension cords), (ii) linear architectures without directionality (batons), (iii) cyclic architectures with directionality (necklaces), and (iv) cyclic architectures without directionality (bracelets). The program can be applied to cyclic peptides, cycloveratrylenes, cyclens, calixarenes, cyclodextrins, crown ethers, cucurbiturils, annulenes, expanded meso-substituted porphyrin(ogen)s, and diverse supramolecular (e.g., protein) assemblies. The size of accessible architectures encompasses up to 12 modular subunits derived from 12 reacting monomers or larger architectures (e.g. 13-17 subunits) from fewer types of monomers (e.g. 2-4). A particular application concerns understanding the possible heterogeneity of (natural or biohybrid) photosynthetic light-harvesting oligomers (cyclic, linear) formed from distinct peptide subunits.

  15. Enumeration of an extremely high particle-to-PFU ratio for Varicella-zoster virus.

    Science.gov (United States)

    Carpenter, John E; Henderson, Ernesto P; Grose, Charles

    2009-07-01

    Varicella-zoster virus (VZV) is renowned for its low titers. Yet investigations to explore the low infectivity are hampered by the fact that the VZV particle-to-PFU ratio has never been determined with precision. Herein, we accomplish that task by applying newer imaging technology. More than 300 images were taken of VZV-infected cells on 4 different samples at high magnification. We enumerated the total number of viral particles within 25 cm(2) of the infected monolayer at 415 million. Based on these numbers, the VZV particle:PFU ratio was approximately 40,000:1 for a cell-free inoculum.

  16. Specific dot-immunobinding assay for detection and enumeration of Thiobacillus ferrooxidans

    International Nuclear Information System (INIS)

    Arredondo, R.; Jerez, C.A.

    1989-01-01

    A specific and very sensitive dot-immunobinding assay for the detection and enumeration of the bioleaching microorganism Thiobacillus ferrooxidans was developed. Nitrocellulose spotted with samples was incubated with polyclonal antisera against whole T. ferrooxidans cells and then in 125 I-labeled protein A or 125 I-labeled goat antirabbit immunoglobulin G; incubation was followed by autoradiography. Since a minimum of 10 3 cells per dot could be detected, the method offers the possibility of simultaneous processing of numerous samples in a short time to monitor the levels of T. ferrooxidans in bioleaching operations

  17. Enumeration and stability analysis of simple periodic orbits in β-Fermi Pasta Ulam lattice

    International Nuclear Information System (INIS)

    Sonone, Rupali L.; Jain, Sudhir R.

    2014-01-01

    We study the well-known one-dimensional problem of N particles with a nonlinear interaction. The special case of quadratic and quartic interaction potential among nearest neighbours is the β-Fermi-Pasta-Ulam model. We enumerate and classify the simple periodic orbits for this system and find the stability zones, employing Floquet theory. Such stability analysis is crucial to understand the transition of FPU lattice from recurrences to globally chaotic behavior, energy transport in lower dimensional system, dynamics of optical lattices and also its impact on shape parameter of bio-polymers such as DNA and RNA

  18. Enumeration and stability analysis of simple periodic orbits in β-Fermi Pasta Ulam lattice

    Energy Technology Data Exchange (ETDEWEB)

    Sonone, Rupali L., E-mail: vaidehisonone@gmail.com; Jain, Sudhir R., E-mail: vaidehisonone@gmail.com [Department of Physics, University of Pune, Pune-411007, India and Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai - 400085 (India)

    2014-04-24

    We study the well-known one-dimensional problem of N particles with a nonlinear interaction. The special case of quadratic and quartic interaction potential among nearest neighbours is the β-Fermi-Pasta-Ulam model. We enumerate and classify the simple periodic orbits for this system and find the stability zones, employing Floquet theory. Such stability analysis is crucial to understand the transition of FPU lattice from recurrences to globally chaotic behavior, energy transport in lower dimensional system, dynamics of optical lattices and also its impact on shape parameter of bio-polymers such as DNA and RNA.

  19. Specificity for field enumeration of Escherichia coli in tropical surface waters

    DEFF Research Database (Denmark)

    Jensen, Peter Kjær Mackie; Aalbaek, B; Aslam, R

    2001-01-01

    In remote rural areas in developing countries, bacteriological monitoring often depends on the use of commercial field media. This paper evaluates a commercial field medium used for the enumeration of Escherichia coli in different surface waters under primitive field conditions in rural Pakistan....... In order to verify the field kit, 117 presumptive E. coli isolates have been tested, finding a specificity of only 40%. By excluding some strains based on colony colours, the calculated specificity could be increased to 65%. Thus, it is suggested that prior to use in a tropical environment, the specificity...... of any commercial medium used should be tested with representative tropical isolates, in order to increase the specificity....

  20. Impact of microbial count distributions on human health risk estimates

    DEFF Research Database (Denmark)

    Ribeiro Duarte, Ana Sofia; Nauta, Maarten

    2015-01-01

    Quantitative microbiological risk assessment (QMRA) is influenced by the choice of the probability distribution used to describe pathogen concentrations, as this may eventually have a large effect on the distribution of doses at exposure. When fitting a probability distribution to microbial...... enumeration data, several factors may have an impact on the accuracy of that fit. Analysis of the best statistical fits of different distributions alone does not provide a clear indication of the impact in terms of risk estimates. Thus, in this study we focus on the impact of fitting microbial distributions...... on risk estimates, at two different concentration scenarios and at a range of prevalence levels. By using five different parametric distributions, we investigate whether different characteristics of a good fit are crucial for an accurate risk estimate. Among the factors studied are the importance...

  1. Fitting a distribution to microbial counts: Making sense of zeroes

    DEFF Research Database (Denmark)

    Ribeiro Duarte, Ana Sofia; Stockmarr, Anders; Nauta, Maarten

    2015-01-01

    The accurate estimation of true prevalence and concentration of microorganisms in foods is an important element of quantitative microbiological risk assessment (QMRA). This estimation is often based on microbial detection and enumeration data. Among such data are artificial zero counts, that orig......The accurate estimation of true prevalence and concentration of microorganisms in foods is an important element of quantitative microbiological risk assessment (QMRA). This estimation is often based on microbial detection and enumeration data. Among such data are artificial zero counts......, that originated by chance from contaminated food products. When these products are not differentiated from uncontaminated products that originate true zero counts, the estimates of true prevalence and concentration may be inaccurate. This inaccuracy is especially relevant in situations where highly pathogenic...... bacteria are involved and where growth can occur along the food pathway. Our aim was to develop a method that provides accurate estimates of concentration parameters and differentiates between artificial and true zeroes, thus also accurately estimating true prevalence. We first show the disadvantages...

  2. Microbial-influenced cement degradation: Literature review

    International Nuclear Information System (INIS)

    Rogers, R.D.; Hamilton, M.A.; McConnell, J.W. Jr.

    1993-03-01

    The Nuclear Regulatory Commission stipulates that disposed low-level radioactive waste (LLW) be stabilized. Because of apparent ease of use and normal structural integrity, cement has been widely used as a binder to solidify LLW. However, the resulting waste forms are sometimes susceptible to failure due to the actions of waste constituents, stress, and environment. This report reviews literature which addresses the effect of microbiologically influenced chemical attack on cement-solidified LLW. Groups of microorganisms are identified, which are capable of metabolically converting organic and inorganic substrates into organic and mineral acids. Such acids aggressively react with concrete and can ultimately lead to structural failure. Mechanisms inherent in microbial-influenced degradation of cement-based material are the focus of this report. This report provides sufficient evidence of the potential for microbial-influenced deterioration of cement-solidified LLW to justify the enumeration of the conditions necessary to support the microbiological growth and population expansion, as well as the development of appropriate tests necessary to determine the resistance of cement-solidified LLW to microbiological-induced degradation that could impact the stability of the waste form

  3. Microbial radio-resistance of Salmonella Typhimurium in egg increases due to repetitive irradiation with electron beam

    Energy Technology Data Exchange (ETDEWEB)

    Tesfai, Adiam T.; Beamer, Sarah K.; Matak, Kristen E. [West Virginia University, Division of Animal and Nutritional Sciences, PO Box 6108, Morgantown, WV 26508 (United States); Jaczynski, Jacek, E-mail: Jacek.Jaczynski@mail.wvu.ed [West Virginia University, Division of Animal and Nutritional Sciences, PO Box 6108, Morgantown, WV 26508 (United States)

    2011-04-15

    Ionizing radiation improves food safety. However, foodborne pathogens develop increased resistance in response to sub-lethal stresses such as heat, pH, antibiotics, etc. Therefore, it is hypothesized that foodborne pathogens may develop increased radio-resistance to electron beam (e-beam) radiation. The objective was to determine if D{sub 10}-value for Salmonella Typhimurium in de-shelled raw egg (egg white and yolk mixed together) increases due to repetitive processing with e-beam at sub-lethal doses. Survivors were enumerated on non-selective (TSA) and selective (XLD) media. Survivors from the highest dose were isolated and used in subsequent e-beam cycle. This process was repeated four times for a total of five e-beam cycles. D{sub 10}-values for S. Typhimurium enumerated on TSA and XLD following each e-beam cycle were calculated as inverse reciprocal of the slope of survivor curves. D{sub 10}-values for the ATCC strain were 0.59{+-}0.031 and 0.46{+-}0.022 kGy on TSA and XLD, respectively. However, following the fifth e-beam cycle, the respective D{sub 10}-values increased (P<0.05) to 0.69{+-}0.026 and 0.61{+-}0.029 kGy, respectively. S. Typhimurium showed a trend (P>0.05) to develop radio-resistance faster on selective media, likely due to facilitated selection of radio-resistant cells within microbial population following each e-beam cycle. For all five e-beam cycles, S. Typhimurium had higher (P<0.05) D{sub 10}-values on non-selective media, indicating that sub-lethal injury followed by cellular repair and recovery are important for radio-resistance and inactivation of this microorganism. This study demonstrated that e-beam efficiently inactivates S. Typhimurium in raw egg; however, similar to other inactivation techniques and factors affecting microbial growth, S. Typhimurium develops increased radio-resistance if repetitively processed with e-beam at sub-lethal doses.

  4. Microbial micropatches within microbial hotspots

    Science.gov (United States)

    Smith, Renee J.; Tobe, Shanan S.; Paterson, James S.; Seymour, Justin R.; Oliver, Rod L.; Mitchell, James G.

    2018-01-01

    The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur. PMID:29787564

  5. Validation of a Rapid Bacteria Endospore Enumeration System for Planetary Protection Application

    Science.gov (United States)

    Chen, Fei; Kern, Roger; Kazarians, Gayane; Venkateswaran, Kasthuri

    NASA monitors spacecraft surfaces to assure that the presence of bacterial endospores meets strict criteria at launch, to minimize the risk of inadvertent contamination of the surface of Mars. Currently, the only approved method for enumerating the spores is a culture based assay that requires three days to produce results. In order to meet the demanding schedules of spacecraft assembly, a more rapid spore detection assay is being considered as an alternate method to the NASA standard culture-based assay. The Millipore Rapid Microbiology Detection System (RMDS) has been used successfully for rapid bioburden enumeration in the pharmaceutical and food industries. The RMDS is rapid and simple, shows high sensitivity (to 1 colony forming unit [CFU]/sample), and correlates well with traditional culture-based methods. It combines membrane filtration, adenosine triphosphate (ATP) bioluminescence chemistry, and image analysis based on photon detection with a Charge Coupled Device (CCD) camera. In this study, we have optimized the assay conditions and evaluated the use of the RMDS as a rapid spore detection tool for NASA applications. In order to select for spores, the samples were subjected to a heat shock step before proceeding with the RMDS incubation protocol. Seven species of Bacillus (nine strains) that have been repeatedly isolated from clean room environments were assayed. All strains were detected by the RMDS in 5 hours and these assay times were repeatedly demonstrated along with low image background noise. Validation experiments to compare the Rapid Sore Assay (RSA) and NASA standard assay (NSA) were also performed. The evaluation criteria were modeled after the FDA Guideline of Process Validation, and Analytical Test Methods. This body of research demonstrates that the Rapid Spore Assay (RSA) is quick, and of equivalent sensitivity to the NASA standard assay, potentially reducing the assay time for bacterial endospores from over 72 hours to less than 8 hours

  6. Use of enrichment real-time PCR to enumerate salmonella on chicken parts.

    Science.gov (United States)

    Oscar, T P

    2014-07-01

    Salmonella bacteria that survive cooking or that cross-contaminate other food during meal preparation and serving represent primary routes of consumer exposure to this pathogen from chicken. In the present study, enrichment real-time PCR (qPCR) was used to enumerate Salmonella bacteria that contaminate raw chicken parts at retail or that cross-contaminate cooked chicken during simulated meal preparation and serving. Whole raw chickens obtained at retail were partitioned into wings, breasts, thighs, and drumsticks using a sterilized knife and cutting board, which were then used to partition a cooked chicken breast to assess cross-contamination. After enrichment in buffered peptone water (400 ml, 8 h, 40°C, 80 rpm), subsamples were used for qPCR and cultural isolation of Salmonella. In some experiments, chicken parts were spiked with 0 to 3.6 log of Salmonella Typhimurium var. 5- to generate a standard curve for enumeration by qPCR. Of 10 raw chickens examined, 7 (70%) had one or more parts contaminated with Salmonella. Of 80 raw parts examined, 15 (19%) were contaminated with Salmonella. Of 20 cooked chicken parts examined, 2 (10%) were cross-contaminated with Salmonella. Predominant serotypes identified were Typhimurium (71%) and its variants (var. 5-, monophasic, and nonmotile) and Kentucky (18%). The number of Salmonella bacteria on contaminated parts ranged from one to two per part. Results of this study indicated that retail chicken parts examined were contaminated with low levels of Salmonella, which resulted in low levels of cross-contamination during simulated meal preparation and serving. Thus, if consumers properly handle and prepare the chicken, it should pose no or very low risk of consumer exposure to Salmonella.

  7. The Application of Digital Pathology to Improve Accuracy in Glomerular Enumeration in Renal Biopsies.

    Directory of Open Access Journals (Sweden)

    Avi Z Rosenberg

    Full Text Available In renal biopsy reporting, quantitative measurements, such as glomerular number and percentage of globally sclerotic glomeruli, is central to diagnostic accuracy and prognosis. The aim of this study is to determine the number of glomeruli and percent globally sclerotic in renal biopsies by means of registration of serial tissue sections and manual enumeration, compared to the numbers in pathology reports from routine light microscopic assessment.We reviewed 277 biopsies from the Nephrotic Syndrome Study Network (NEPTUNE digital pathology repository, enumerating 9,379 glomeruli by means of whole slide imaging. Glomerular number and the percentage of globally sclerotic glomeruli are values routinely recorded in the official renal biopsy pathology report from the 25 participating centers. Two general trends in reporting were noted: total number per biopsy or average number per level/section. Both of these approaches were assessed for their accuracy in comparison to the analogous numbers of annotated glomeruli on WSI.The number of glomeruli annotated was consistently higher than those reported (p<0.001; this difference was proportional to the number of glomeruli. In contrast, percent globally sclerotic were similar when calculated on total glomeruli, but greater in FSGS when calculated on average number of glomeruli (p<0.01. The difference in percent globally sclerotic between annotated and those recorded in pathology reports was significant when global sclerosis is greater than 40%.Although glass slides were not available for direct comparison to whole slide image annotation, this study indicates that routine manual light microscopy assessment of number of glomeruli is inaccurate, and the magnitude of this error is proportional to the total number of glomeruli.

  8. A selective medium for the enumeration and differentiation of Lactobacillus delbrueckii ssp. bulgaricus.

    Science.gov (United States)

    Nwamaioha, Nwadiuto O; Ibrahim, Salam A

    2018-06-01

    Modified reinforced clostridial medium (mRCM) was developed and evaluated for the differential enumeration of Lactobacillus delbrueckii ssp. bulgaricus. Lactobacillus bulgaricus, an important species of lactic acid bacteria with health benefits, is used in the production of yogurt and other fermented foods. Our results showed that supplementing reinforced clostridial medium with 0.025% CaCl 2 , 0.01% uracil, and 0.2% Tween 80 (mRCM) significantly enhanced the growth rate of L. bulgaricus RR and ATCC 11842 strains as measured by the optical densities of these strains after 12 h of incubation at 42°C. The bacterial populations (plate count) of the RR and ATCC 11842 strains were 0.76 and 0.77 log cfu/g higher in mRCM than in de Man, Rogosa, and Sharpe and reinforced clostridial medium media, respectively. Conversely, the population counts for other bacterial species (Bifidobacterium, Lactobacillus rhamnosus, and Lactobacillus reuteri) were significantly inhibited in the mRCM medium. The addition of aniline blue dye to mRCM (mRCM-blue) improved the selectivity of L. bulgaricus in mixed lactic bacterial cultures compared with de Man, Rogosa, and Sharpe medium and lactic agar with regard to colony appearance and morphology. The mRCM-blue performed better than the conventional medium in culturing, enumerating, and differentiating L. bulgaricus. Therefore, mRCM-blue could be used as a selective medium to enhance the growth and differentiation of L. bulgaricus in order to meet the increasing demand for this beneficial species of bacteria. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  9. Assessing toxic levels of hydrocarbons on microbial degrader communities in vadose zone fill soils

    International Nuclear Information System (INIS)

    Schoenberg, T.H.; Long, S.C.

    1995-01-01

    Authentic fill samples were collected from the vadose zone at a highway travel plaza. The contamination at the site is a combination of gasoline, diesel, and waste oil resulting from leaking underground storage tanks. Microbial assessments including plate counts and specific-degrader enumerations were performed to establish the presence of degrader microbial communities, and thus bioremediation potential. Contaminant levels were estimated in samples by quantifying headspace VOCs in collection jars. Physical soil characteristics including soil grain size distribution and moisture content were measured to evaluate the potential ecological variables that would affect implementation of a bioremediation technology. Toxicity screening using the Microtox trademark acute toxicity assay was used to compare the level of toxicity present among samples. These analyses were used to assess the potential for using in situ bioventing remediation to clean-up the leaking underground storage tank spill study site. High contaminant levels appear to have exerted a toxic effect and resulted in smaller total microbial community sizes in highly contaminated areas (thousands of ppmv) of the site. Microtox trademark EC50 results generally corroborated with the trends of the enumeration experiments. Microbial characterization results indicate that in situ bioremediation would be possible at the study site. Soil heterogeneity appears to pose the greatest challenges to the design and implementation of bioremediation at this site

  10. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    Energy Technology Data Exchange (ETDEWEB)

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  11. Genome engineering for microbial natural product discovery.

    Science.gov (United States)

    Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

    2018-03-03

    The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Effect of storage time and temperature of equine feces on the subsequent enumeration of lactobacilli and cellulolytic bacteria

    Science.gov (United States)

    Cellulolytic bacteria and lactobacilli are beneficial microbes in the equine hindgut. There are several existing methodologies for the enumeration of these bacteria, which vary based on selective and differential media and sample handling procedures including storage time and temperature. The object...

  13. Enumeration of sugars and sugar alcohols hydroxyl groups by aqueous-based acetylation and MALDI-TOF mass spectrometry

    Science.gov (United States)

    A method is described for enumerating hydroxyl groups on analytes in aqueous media is described, and applied to some common polyalcohols (erythritol, mannitol, and xylitol) and selected carbohydrates. The analytes were derivatized in water with vinyl acetate in presence of sodium phosphate buffer. ...

  14. Accuracy and impact of spatial aids based upon satellite enumeration to improve indoor residual spraying spatial coverage.

    Science.gov (United States)

    Bridges, Daniel J; Pollard, Derek; Winters, Anna M; Winters, Benjamin; Sikaala, Chadwick; Renn, Silvia; Larsen, David A

    2018-02-23

    Indoor residual spraying (IRS) is a key tool in the fight to control, eliminate and ultimately eradicate malaria. IRS protection is based on a communal effect such that an individual's protection primarily relies on the community-level coverage of IRS with limited protection being provided by household-level coverage. To ensure a communal effect is achieved through IRS, achieving high and uniform community-level coverage should be the ultimate priority of an IRS campaign. Ensuring high community-level coverage of IRS in malaria-endemic areas is challenging given the lack of information available about both the location and number of households needing IRS in any given area. A process termed 'mSpray' has been developed and implemented and involves use of satellite imagery for enumeration for planning IRS and a mobile application to guide IRS implementation. This study assessed (1) the accuracy of the satellite enumeration and (2) how various degrees of spatial aid provided through the mSpray process affected community-level IRS coverage during the 2015 spray campaign in Zambia. A 2-stage sampling process was applied to assess accuracy of satellite enumeration to determine number and location of sprayable structures. Results indicated an overall sensitivity of 94% for satellite enumeration compared to finding structures on the ground. After adjusting for structure size, roof, and wall type, households in Nchelenge District where all types of satellite-based spatial aids (paper-based maps plus use of the mobile mSpray application) were used were more likely to have received IRS than Kasama district where maps used were not based on satellite enumeration. The probability of a household being sprayed in Nchelenge district where tablet-based maps were used, did not differ statistically from that of a household in Samfya District, where detailed paper-based spatial aids based on satellite enumeration were provided. IRS coverage from the 2015 spray season benefited from

  15. The Effect of Enumeration of Self-Relevant Words on Self-Focused Attention and Repetitive Negative Thoughts

    Science.gov (United States)

    Muranaka, Seiji; Sasaki, Jun

    2018-01-01

    Self-focused attention refers to awareness of self-referent, internally generated information. It can be categorized into dysfunctional (i.e., self-rumination) and functional (self-reflection) aspects. According to theory on cognitive resource limitations (e.g., Moreno, 2006), there is a difference in cognitive resource allocation between these two aspects of self-focused attention. We propose a new task, self-relevant word (SRW) enumeration, that can aid in behaviorally identifying individuals’ use of self-rumination and self-reflection. The present study has two purposes: to determine the association between self-focus and SRW enumeration, and to examine the effect of dysfunctional SRW enumeration on repetitive negative thinking. One hundred forty-six undergraduate students participated in this study. They completed a measure of state anxiety twice, before and after imagining a social failure situation. They also completed the SRW enumeration task, Repetitive Thinking Questionnaire, Short Fear of Negative Evaluation Scale, and Rumination-Reflection Questionnaire. A correlational analysis indicated a significant positive correlation between self-reflection and the number of SRWs. Furthermore, individuals high in self-reflection had a tendency to pay more attention to problems than did those high in self-rumination. A significant positive correlation was found between self-rumination and the strength of self-relevance of negative SRWs. Through a path analysis, we found a significant positive effect of the self-relevance of negative SRWs on repetitive negative thinking. Notably, however, the model that excluded self-rumination as an explanatory variable showed a better fit to the data than did the model that included it. In summary, SRW enumeration might enable selective and independent detection of the degree of self-reflection and self-rumination, and therefore should be examined in future research in order to design new behavioral procedures. PMID:29896140

  16. A shared, flexible neural map architecture reflects capacity limits in both visual short-term memory and enumeration.

    Science.gov (United States)

    Knops, André; Piazza, Manuela; Sengupta, Rakesh; Eger, Evelyn; Melcher, David

    2014-07-23

    Human cognition is characterized by severe capacity limits: we can accurately track, enumerate, or hold in mind only a small number of items at a time. It remains debated whether capacity limitations across tasks are determined by a common system. Here we measure brain activation of adult subjects performing either a visual short-term memory (vSTM) task consisting of holding in mind precise information about the orientation and position of a variable number of items, or an enumeration task consisting of assessing the number of items in those sets. We show that task-specific capacity limits (three to four items in enumeration and two to three in vSTM) are neurally reflected in the activity of the posterior parietal cortex (PPC): an identical set of voxels in this region, commonly activated during the two tasks, changed its overall response profile reflecting task-specific capacity limitations. These results, replicated in a second experiment, were further supported by multivariate pattern analysis in which we could decode the number of items presented over a larger range during enumeration than during vSTM. Finally, we simulated our results with a computational model of PPC using a saliency map architecture in which the level of mutual inhibition between nodes gives rise to capacity limitations and reflects the task-dependent precision with which objects need to be encoded (high precision for vSTM, lower precision for enumeration). Together, our work supports the existence of a common, flexible system underlying capacity limits across tasks in PPC that may take the form of a saliency map. Copyright © 2014 the authors 0270-6474/14/349857-10$15.00/0.

  17. The Effect of Enumeration of Self-Relevant Words on Self-Focused Attention and Repetitive Negative Thoughts

    Directory of Open Access Journals (Sweden)

    Seiji Muranaka

    2018-05-01

    Full Text Available Self-focused attention refers to awareness of self-referent, internally generated information. It can be categorized into dysfunctional (i.e., self-rumination and functional (self-reflection aspects. According to theory on cognitive resource limitations (e.g., Moreno, 2006, there is a difference in cognitive resource allocation between these two aspects of self-focused attention. We propose a new task, self-relevant word (SRW enumeration, that can aid in behaviorally identifying individuals’ use of self-rumination and self-reflection. The present study has two purposes: to determine the association between self-focus and SRW enumeration, and to examine the effect of dysfunctional SRW enumeration on repetitive negative thinking. One hundred forty-six undergraduate students participated in this study. They completed a measure of state anxiety twice, before and after imagining a social failure situation. They also completed the SRW enumeration task, Repetitive Thinking Questionnaire, Short Fear of Negative Evaluation Scale, and Rumination-Reflection Questionnaire. A correlational analysis indicated a significant positive correlation between self-reflection and the number of SRWs. Furthermore, individuals high in self-reflection had a tendency to pay more attention to problems than did those high in self-rumination. A significant positive correlation was found between self-rumination and the strength of self-relevance of negative SRWs. Through a path analysis, we found a significant positive effect of the self-relevance of negative SRWs on repetitive negative thinking. Notably, however, the model that excluded self-rumination as an explanatory variable showed a better fit to the data than did the model that included it. In summary, SRW enumeration might enable selective and independent detection of the degree of self-reflection and self-rumination, and therefore should be examined in future research in order to design new behavioral procedures.

  18. Advantages and disadvantages of the use of immunodetection techniques for the enumeration of micro-organisms and toxins in water

    CSIR Research Space (South Africa)

    Kfir, R

    1993-01-01

    Full Text Available and hepatitis A viruses; and the use of ELISA and immunofluorescence for the detection of bacteria (Legionella, faecal coliforms) and protozoan parasites (Giardia, Cryptosporidium). The production and use of monoclonal antibodies against algal toxins are also...

  19. Alternative microbial methods: An overview and selection criteria.

    Science.gov (United States)

    Jasson, Vicky; Jacxsens, Liesbeth; Luning, Pieternel; Rajkovic, Andreja; Uyttendaele, Mieke

    2010-09-01

    This study provides an overview and criteria for the selection of a method, other than the reference method, for microbial analysis of foods. In a first part an overview of the general characteristics of rapid methods available, both for enumeration and detection, is given with reference to relevant bibliography. Perspectives on future development and the potential of the rapid method for routine application in food diagnostics are discussed. As various alternative "rapid" methods in different formats are available on the market, it can be very difficult for a food business operator or for a control authority to select the most appropriate method which fits its purpose. Validation of a method by a third party, according to international accepted protocol based upon ISO 16140, may increase the confidence in the performance of a method. A list of at the moment validated methods for enumeration of both utility indicators (aerobic plate count) and hygiene indicators (Enterobacteriaceae, Escherichia coli, coagulase positive Staphylococcus) as well as for detection of the four major pathogens (Salmonella spp., Listeria monocytogenes, E. coli O157 and Campylobacter spp.) is included with reference to relevant websites to check for updates. In a second part of this study, selection criteria are introduced to underpin the choice of the appropriate method(s) for a defined application. The selection criteria link the definition of the context in which the user of the method functions - and thus the prospective use of the microbial test results - with the technical information on the method and its operational requirements and sustainability. The selection criteria can help the end user of the method to obtain a systematic insight into all relevant factors to be taken into account for selection of a method for microbial analysis. Copyright 2010 Elsevier Ltd. All rights reserved.

  20. 11 Soil Microbial Biomass

    African Journals Online (AJOL)

    186–198. Insam H. (1990). Are the soil microbial biomass and basal respiration governed by the climatic regime? Soil. Biol. Biochem. 22: 525–532. Insam H. D. and Domsch K. H. (1989). Influence of microclimate on soil microbial biomass. Soil Biol. Biochem. 21: 211–21. Jenkinson D. S. (1988). Determination of microbial.

  1. Molecular microbial ecology manual

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

    2004-01-01

    The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

  2. Microbial Rechargeable Battery

    NARCIS (Netherlands)

    Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

    2016-01-01

    Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

  3. Childhood microbial keratitis

    Directory of Open Access Journals (Sweden)

    Abdullah G Al Otaibi

    2012-01-01

    Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

  4. Quantitative microbiome profiling links gut community variation to microbial load.

    Science.gov (United States)

    Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

    2017-11-23

    Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

  5. Raman Spectroscopy of Microbial Pigments

    Science.gov (United States)

    Edwards, Howell G. M.; Oren, Aharon

    2014-01-01

    Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions. PMID:24682303

  6. Application of a good manufacturing practices checklist and enumeration of total coliform in swine feed mills

    Directory of Open Access Journals (Sweden)

    Debora da Cruz Payao Pellegrini

    2014-02-01

    Full Text Available A cross-sectional study in four swine feed mills aimed to evaluate the correlation between the score of the inspection checklist defined in the Normative Instruction 4 (IN 4/ Brazilian Ministry of Agriculture, Livestock and Food Supply, and the enumeration of total coliforms throughout the manufacturing process. The most of non-conformities was found in the physical structure of the feed mills. Feed mill B showed the lowest number of unconformities while units A and D had the largest number of nonconformities. In 38.53% (489/1269 of the samples the presence of total coliform was detected, however no significant difference in the bacterial counts was observed between sampling sites and feed mills. The logistic regression pointed higher odds ratio (OR for total coliforms isolation at dosing (OR = 9.51, 95% CI: 4.43 to 20.41, grinding (OR = 7.10, 95% CI = 3.27 to 15.40 and residues (OR = 6.21, 95% CI: 3.88 to 9.95 In spite of having the second score in the checklist inspection, feed mill C presented the highest odds for total coliforms isolation (OR= 2,43, IC 95%: 1,68-3,53. The data indicate no association between the score of checklist and the presence of hygienic indicators in feed mills.

  7. Development of quantitative real-time PCR for detection and enumeration of Enterobacteriaceae.

    Science.gov (United States)

    Takahashi, Hajime; Saito, Rumi; Miya, Satoko; Tanaka, Yuichiro; Miyamura, Natsumi; Kuda, Takashi; Kimura, Bon

    2017-04-04

    The family Enterobacteriaceae, members of which are widely distributed in the environment, includes many important human pathogens. In this study, a rapid real-time PCR method targeting rplP, coding for L16 protein, a component of the ribosome large subunit, was developed for enumerating Enterobacteriaceae strains, and its efficiency was evaluated using naturally contaminated food products. The rplP-targeted real-time PCR amplified Enterobacteriaceae species with Ct values of 14.0-22.8, whereas the Ct values for non-Enterobacteriaceae species were >30, indicating the specificity of this method for the Enterobacteriaceae. Using a calibration curve of Ct=-3.025 (log CFU/g)+37.35, which was calculated from individual plots of the cell numbers in different concentrations of 5 Enterobacteriaceae species, the rplP-targeted real-time PCR was applied to 51 food samples. A Enterobacteriaceae species in foods rapidly and accurately, and therefore, it can be used for the microbiological risk analysis of foods. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2015-01-01

    Background: The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. Methods: The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Results: Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Conclusions: Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy. PMID:26998346

  9. Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Starting with a system's relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy.

  10. Differential enumeration of subpopulations in concentrated frozen and lyophilized cultures of Lactobacillus delbrueckii ssp. bulgaricus.

    Science.gov (United States)

    Shao, Yuyu; Wang, Zhaoxia; Bao, Qiuhua; Zhang, Heping

    2017-11-01

    Differential enumeration of subpopulations in concentrated frozen and lyophilized cultures of Lactobacillus delbrueckii ssp. bulgaricus ND02 derived from 2 propagation procedures was determined. The subpopulations consisted of 3 categories (physiological states): viable cells capable of forming colonies on agar plates (VC+), viable cells incapable of forming colonies on agar plates (VC-), widely referred to as viable but nonculturable (VBNC) cells, and nonviable or dead cells (NVC). Counts of VC+ were recorded using a conventional plate count procedure. A fluorescent vital staining procedure that discriminates between viable (VC+ and VC-) and NVC cells was used to determine the number of viable and nonviable cells. Both propagation procedures had 2 variables: in procedure (P)1, the propagation medium was rich in yeast extract (4.0%) and the pH was maintained at 5.7; in P2, the medium was devoid of yeast extract and the pH was maintained at 5.1. The results showed that post-propagation operations-concentration of cells by centrifugation and subsequent freezing or lyophilization of cell concentrate-induced different degrees of transience from VC+ to VC- states in cells derived from P1 and P2. Compared with cells derived from P2, cells from P1 were more labile to stress associated with centrifugation, freezing, and lyophilization, as revealed by differential counting. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  11. The impact of dissolved inorganic nitrogen and phosphorous on responses of microbial plankton to the Texas City "Y" oil spill in Galveston Bay, Texas (USA).

    Science.gov (United States)

    Williams, Alicia K; Bacosa, Hernando P; Quigg, Antonietta

    2017-08-15

    Ongoing bioremediation research seeks to promote naturally occurring microbial polycyclic aromatic hydrocarbon (PAH) degradation during and after oil spill events. However, complex relationships among functionally different microbial groups, nutrients and PAHs remain unconstrained. We conducted a surface water survey and corresponding nutrient amendment bioassays following the Texas City "Y" oil spill in Galveston Bay, Texas. Resident microbial groups, defined as either heterotrophic or autotrophic were enumerated by flow cytometry. Heterotrophic abundance was increased by oil regardless of nutrient concentrations. Contrastingly, autotrophic abundance was inhibited by oil, but this reaction was less severe when nutrient concentrations were higher. Several PAH compounds were reduced in nutrient amended treatments relative to controls suggesting nutrient enhanced microbial PAH processing. These findings provide a first-look at nutrient limitation during microbial oil processing in Galveston Bay, an important step in understanding if nutrient additions would be a useful bioremediation strategy in this and other estuarine systems. Copyright © 2017. Published by Elsevier Ltd.

  12. Microbial Cell Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Doktycz, Mitchel John [ORNL; Sullivan, Claretta [Eastern Virginia Medical School; Mortensen, Ninell P [ORNL; Allison, David P [ORNL

    2011-01-01

    limitation on the maximum scan size (roughly 100 x 100 {mu}m) and the restricted movement of the cantilever in the Z (or height) direction. In most commercial AFMs, the Z range is restricted to roughly 10 {mu}m such that the height of cells to be imaged must be seriously considered. Nevertheless, AFM can provide structural-functional information at nanometer resolution and do so in physiologically relevant environments. Further, instrumentation for scanning probe microscopy continues to advance. Systems for high-speed imaging are becoming available, and techniques for looking inside the cells are being demonstrated. The ability to combine AFM with other imaging modalities is likely to have an even greater impact on microbiological studies. AFM studies of intact microbial cells started to appear in the literature in the 1990s. For example, AFM studies of Saccharomyces cerevisiae examined buddings cars after cell division and detailed changes related to cell growth processes. Also, the first AFM studies of bacterial biofilms appeared. In the late 1990s, AFM studies of intact fungal spores described clear changes in spore surfaces upon germination, and studies of individual bacterial cells were also described. These early bacterial imaging studies examined changes in bacterial morphology due to antimicrobial peptides exposure and bacterial adhesion properties. The majority of these early studies were carried out on dried samples and took advantage of the resolving power of AFM. The lack of cell mounting procedures presented an impediment for cell imaging studies. Subsequently, several approaches to mounting microbial cells have been developed, and these techniques are described later. Also highlighted are general considerations for microbial imaging and a description of some of the various applications of AFM to microbiology.

  13. Use of non-linear mixed-effects modelling and regression analysis to predict the number of somatic coliphages by plaque enumeration after 3 hours of incubation.

    Science.gov (United States)

    Mendez, Javier; Monleon-Getino, Antonio; Jofre, Juan; Lucena, Francisco

    2017-10-01

    The present study aimed to establish the kinetics of the appearance of coliphage plaques using the double agar layer titration technique to evaluate the feasibility of using traditional coliphage plaque forming unit (PFU) enumeration as a rapid quantification method. Repeated measurements of the appearance of plaques of coliphages titrated according to ISO 10705-2 at different times were analysed using non-linear mixed-effects regression to determine the most suitable model of their appearance kinetics. Although this model is adequate, to simplify its applicability two linear models were developed to predict the numbers of coliphages reliably, using the PFU counts as determined by the ISO after only 3 hours of incubation. One linear model, when the number of plaques detected was between 4 and 26 PFU after 3 hours, had a linear fit of: (1.48 × Counts 3 h + 1.97); and the other, values >26 PFU, had a fit of (1.18 × Counts 3 h + 2.95). If the number of plaques detected was PFU after 3 hours, we recommend incubation for (18 ± 3) hours. The study indicates that the traditional coliphage plating technique has a reasonable potential to provide results in a single working day without the need to invest in additional laboratory equipment.

  14. Coupling graph perturbation theory with scalable parallel algorithms for large-scale enumeration of maximal cliques in biological graphs

    International Nuclear Information System (INIS)

    Samatova, N F; Schmidt, M C; Hendrix, W; Breimyer, P; Thomas, K; Park, B-H

    2008-01-01

    Data-driven construction of predictive models for biological systems faces challenges from data intensity, uncertainty, and computational complexity. Data-driven model inference is often considered a combinatorial graph problem where an enumeration of all feasible models is sought. The data-intensive and the NP-hard nature of such problems, however, challenges existing methods to meet the required scale of data size and uncertainty, even on modern supercomputers. Maximal clique enumeration (MCE) in a graph derived from such biological data is often a rate-limiting step in detecting protein complexes in protein interaction data, finding clusters of co-expressed genes in microarray data, or identifying clusters of orthologous genes in protein sequence data. We report two key advances that address this challenge. We designed and implemented the first (to the best of our knowledge) parallel MCE algorithm that scales linearly on thousands of processors running MCE on real-world biological networks with thousands and hundreds of thousands of vertices. In addition, we proposed and developed the Graph Perturbation Theory (GPT) that establishes a foundation for efficiently solving the MCE problem in perturbed graphs, which model the uncertainty in the data. GPT formulates necessary and sufficient conditions for detecting the differences between the sets of maximal cliques in the original and perturbed graphs and reduces the enumeration time by more than 80% compared to complete recomputation

  15. Microbial electrosynthetic cells

    Energy Technology Data Exchange (ETDEWEB)

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

    2018-01-30

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

  16. Expansion and Compression of Time Correlate with Information Processing in an Enumeration Task.

    Directory of Open Access Journals (Sweden)

    Andreas Wutz

    Full Text Available Perception of temporal duration is subjective and is influenced by factors such as attention and context. For example, unexpected or emotional events are often experienced as if time subjectively expands, suggesting that the amount of information processed in a unit of time can be increased. Time dilation effects have been measured with an oddball paradigm in which an infrequent stimulus is perceived to last longer than standard stimuli in the rest of the sequence. Likewise, time compression for the oddball occurs when the duration of the standard items is relatively brief. Here, we investigated whether the amount of information processing changes when time is perceived as distorted. On each trial, an oddball stimulus of varying numerosity (1-14 items and duration was presented along with standard items that were either short (70 ms or long (1050 ms. Observers were instructed to count the number of dots within the oddball stimulus and to judge its relative duration with respect to the standards on that trial. Consistent with previous results, oddballs were reliably perceived as temporally distorted: expanded for longer standard stimuli blocks and compressed for shorter standards. The occurrence of these distortions of time perception correlated with perceptual processing; i.e. enumeration accuracy increased when time was perceived as expanded and decreased with temporal compression. These results suggest that subjective time distortions are not epiphenomenal, but reflect real changes in sensory processing. Such short-term plasticity in information processing rate could be evolutionarily advantageous in optimizing perception and action during critical moments.

  17. Yersinia enterocolitica in slaughter pig tonsils: enumeration and detection by enrichment versus direct plating culture.

    Science.gov (United States)

    Van Damme, Inge; Habib, Ihab; De Zutter, Lieven

    2010-02-01

    Tonsil samples from 139 slaughter pigs were examined for the presence of pathogenic Yersinia enterocolitica by enrichment procedures based on the standard method ISO 10273:2003. In addition, samples were tested by direct plating method to evaluate its efficiency compared to the enrichment culture methods and to quantify the level of contamination in porcine tonsils. In total, 52 samples (37.4%) were positive for pathogenic Y. enterocolitica, all belonging to bioserotype 4/O:3. Fifty out of the 52 positive samples (96.2%) were detected by direct plating. Enumeration showed an average concentration of 4.5 log(10) CFU g(-1) and 4.4 log(10) CFU g(-1) tonsil on Salmonella-Shigella-desoxycholate-calcium chloride (SSDC) and cefsulodin-irgasan-novobiocin (CIN) agar plates, respectively. The enrichment procedures recommended by the ISO 10273:2003 method were not optimal for the isolation of pathogenic Y. enterocolitica from pig tonsils: two days enrichment in irgasan-ticarcillin-potassium chlorate (ITC) broth resulted in an isolation rate of 84.6%, while 5 days enrichment in peptone-sorbitol-bile (PSB) broth recovered only 59.6% of positive samples. Reducing the enrichment time in PSB from 5 to 2 days resulted in a significantly higher recovery rate (94.2%) and might serve as an appropriate enrichment protocol for the isolation of pathogenic Y. enterocolitica from pig tonsils. Compared to enrichment culture methods, results based on direct plating can be obtained in a shorter time course and provide quantitative data that might be needed for further risk assessment studies.

  18. Comparison of New and Traditional Culture-Dependent Media for Enumerating Foodborne Yeasts and Molds.

    Science.gov (United States)

    Beuchat, Larry R; Mann, David A

    2016-01-01

    Fifty-six foods and food ingredients were analyzed for populations of naturally occurring yeasts and molds using Petrifilm rapid yeast and mold (RYM) count plates, Petrifilm yeast and mold (YM) count plates, dichloran rose bengal chloramphenicol (DRBC) agar plates, acidified potato dextrose agar (APDA) plates, and dichloran 18% glycerol (DG18) agar plates. Colonies were counted after incubating plates for 48, 72, and 120 h at 25°C. Of 56 foods in which either yeasts or molds were detected on at least one medium incubated for 120 h, neither yeasts nor molds were detected in 55.4, 73.2, 21.4, 19.6, and 71.4% of foods plated on the five respective media and incubated for 48 h; 10.7, 14.3, 3.6, 1.8, and 19.6% of foods were negative after 72 h, and 3.6, 1.8, 0, 0, and 0% of foods were negative after 120 h. Considering all enumeration media, correlation coefficients were 0.03 to 0.97 at 48 h of incubation; these values increased to 0.75 to 0.99 at 120 h. Coefficients of variation for total yeasts and molds were as high as 30.0, 30.8, and 27.2% at 48, 72, and 120 h, respectively. The general order of performance was DRBC = APDA > RYM Petrifilm > YM Petrifilm ≥ DG18 when plates were incubated for 48 h, DRBC > APDA > RYM Petrifilm > YM Petrifilm ≥ DG18 when plates were incubated for 72 h, and DRBC > APDA > RYM Petrifilm > YM Petrifilm > DG18 when plates were incubated for 120 h. Differences in performance among media are attributed to the diversity of yeasts and molds likely to be present in test foods and differences in nutrient, pH, and water activity requirements for resuscitation of stressed cells and colony development.

  19. An improved procedure for detection and enumeration of walrus signatures in airborne thermal imagery

    Science.gov (United States)

    Burn, Douglas M.; Udevitz, Mark S.; Speckman, Suzann G.; Benter, R. Bradley

    2009-01-01

    In recent years, application of remote sensing to marine mammal surveys has been a promising area of investigation for wildlife managers and researchers. In April 2006, the United States and Russia conducted an aerial survey of Pacific walrus (Odobenus rosmarus divergens) using thermal infrared sensors to detect groups of animals resting on pack ice in the Bering Sea. The goal of this survey was to estimate the size of the Pacific walrus population. An initial analysis of the U.S. data using previously-established methods resulted in lower detectability of walrus groups in the imagery and higher variability in calibration models than was expected based on pilot studies. This paper describes an improved procedure for detection and enumeration of walrus groups in airborne thermal imagery. Thermal images were first subdivided into smaller 200 x 200 pixel "tiles." We calculated three statistics to represent characteristics of walrus signatures from the temperature histogram for each the. Tiles that exhibited one or more of these characteristics were examined further to determine if walrus signatures were present. We used cluster analysis on tiles that contained walrus signatures to determine which pixels belonged to each group. We then calculated a thermal index value for each walrus group in the imagery and used generalized linear models to estimate detection functions (the probability of a group having a positive index value) and calibration functions (the size of a group as a function of its index value) based on counts from matched digital aerial photographs. The new method described here improved our ability to detect walrus groups at both 2 m and 4 m spatial resolution. In addition, the resulting calibration models have lower variance than the original method. We anticipate that the use of this new procedure will greatly improve the quality of the population estimate derived from these data. This procedure may also have broader applicability to thermal infrared

  20. Toxicity of vapor phase petroleum contaminants to microbial degrader communities

    International Nuclear Information System (INIS)

    Long, S.C.; Davey, C.A.

    1994-01-01

    Petroleum products constitute the largest quantity of synthetic organic chemical products produced in the US. They are comprised of mostly hydrocarbon constituents from many different chemical classes including alkenes, cycloalkanes, aromatic compounds, and polyaromatic hydrocarbons. Many petroleum constituents are classified as volatile organic compounds or VOCs. Petroleum products also constitute a major portion of environmental pollution. One emerging technology, with promise for applications to VOCs in subsurface soil environments, is bioventing coupled with soil vapor extraction. These technologies involve volatilization of contaminants into the soil gas phase by injection and withdrawal of air. This air movement causes enhancement of the aerobic microbial degradation of the mobilized vapors by the indigenous populations. This study investigated the effects of exposure of mixed, subsurface microbial communities to vapor phase petroleum constituents or vapors of petroleum mixtures. Soil slurries were prepared and plated onto mineral salts agar plates and exposed to vapor phase contaminants at equilibrium with pure product. Representative n-alkane, branched alkane, cycloalkane, and aromatic compounds were tested as well as petroleum product mixtures. Vapor exposure altered the numbers and morphologies of the colonies enumerated when compared to controls. However, even at high, equilibrium vapor concentrations, microbial degrader populations were not completely inhibited

  1. Microbial degradation of low-level radioactive waste

    International Nuclear Information System (INIS)

    Rogers, R.D.; Hamilton, M.A.; Veeh, R.H.; McConnell, J.W. Jr.

    1994-04-01

    The Nuclear Regulatory Commission stipulates that disposed low-level radioactive waste (LLW) be stabilized. Because of apparent ease of use and normal structural integrity, cement has been widely used as a binder to solidify LLW. However, the resulting waste forms are sometimes susceptible to failure due to the actions of waste constituents, stress, and environment. This report reviews laboratory efforts that are being developed to address the effects of microbiologically influenced chemical attack on cement-solidified LLW. Groups of microorganisms are being employed that are capable of metabolically converting organic and inorganic substrates into organic and mineral acids. Such acids aggressively react with cement and can ultimately lead to structural failure. Results on the application of mechanisms inherent in microbially influenced degradation of cement-based material are the focus of this report. Sufficient data-validated evidence of the potential for microbially influenced deterioration of cement-solidified LLW has been developed during the course of this study. These data support the continued development of appropriate tests necessary to determine the resistance of cement-solidified LLW to microbially induced degradation that could impact the stability of the waste form. They also justify the continued effort of enumeration of the conditions necessary to support the microbiological growth and population expansion

  2. Evaluation of microbially-influenced degradation of massive concrete structures

    International Nuclear Information System (INIS)

    Hamilton, M.A.; Rogers, R.D.; Zolynski, M.; Veeh, R.

    1996-01-01

    Many low level waste disposal vaults, both above and below ground, are constructed of concrete. One potential contributing agent to the destruction of concrete structures is microbially-influenced degradation (MID). Three groups of bacteria are known to create conditions that are conducive to destroying concrete integrity. They are sulfur oxidizing bacteria, nitrifying bacteria, and heterotrophic bacteria. Research is being conducted at the Idaho National Engineering Laboratory to assess the extent of naturally occurring microbially influenced degradation (MID) and its contribution to the deterioration of massive concrete structures. The preliminary steps to understanding the extent of MID, require assessing the microbial communities present on degrading concrete surfaces. Ultimately such information can be used to develop guidelines for preventive or corrective treatments for MID and aid in formulation of new materials to resist corrosion. An environmental study was conducted to determine the presence and activity of potential MID bacteria on degrading concrete surfaces of massive concrete structures. Scanning electron microscopy detected bacteria on the surfaces of concrete structures such as bridges and dams, where corrosion was evident. Enumeration of sulfur oxidizing thiobacilli and nitrogen oxidizing Nitrosomonas sp. and Nitrobacter sp. from surface samples was conducted. Bacterial community composition varied between sampling locations, and generally the presence of either sulfur oxidizers or nitrifiers dominated, although instances of both types of bacteria occurring together were encountered. No clear correlation between bacterial numbers and degree of degradation was exhibited

  3. Monitor and Protect Wigwam River Bull Trout for Koocanusa Reservoir : Summary of the Skookumchuck Creek Bull Trout Enumeration Project Final Report 2000-2002.

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, Jeremy; Baxter, James S.

    2002-12-01

    This report summarizes the third and final year of a bull trout (Salvelinus confluentus) enumeration project on Skookumchuck Creek in southeastern British Columbia. The fence and traps were operated from September 6th to October 11th 2002 in order to enumerate post-spawning bull trout. During the study period a total of 309 bull trout were captured at the fence. In total, 16 fish of undetermined sex, 114 males and 179 females were processed at the fence. Length and weight data, as well as recapture information, were collected for these fish. An additional 41 bull trout were enumerated upstream of the fence by snorkeling prior to fence removal. Coupled with the fence count, the total bull trout enumerated during the project was 350 individuals. Several fish that were tagged in the lower Bull River were recaptured in 2002, as were repeat and alternate year spawners previously enumerated in past years at the fence. A total of 149 bull trout redds were enumerated on the ground in 2002, of which 143 were in the 3.0 km index section (river km 27.5-30.5) that has been surveyed over the past six years. The results of the three year project are summarized, and population characteristics are discussed.

  4. Microbial accumulation of uranium

    International Nuclear Information System (INIS)

    Zhang Wei; Dong Faqin; Dai Qunwei

    2005-01-01

    The mechanism of microbial accumulation of uranium and the effects of some factors (including pH, initial uranium concentration, pretreatment of bacteria, and so on) on microbial accumulation of uranium are discussed briefly. The research direction and application prospect are presented. (authors)

  5. MICROBIAL FUEL CELL

    DEFF Research Database (Denmark)

    2008-01-01

    A novel microbial fuel cell construction for the generation of electrical energy. The microbial fuel cell comprises: (i) an anode electrode, (ii) a cathode chamber, said cathode chamber comprising an in let through which an influent enters the cathode chamber, an outlet through which an effluent...

  6. Microbial control of pollution

    Energy Technology Data Exchange (ETDEWEB)

    Fry, J C; Gadd, G M; Herbert, R A; Jones, C W; Watson-Craik, I A [eds.

    1992-01-01

    12 papers are presented on the microbial control of pollution. Topics covered include: bioremediation of oil spills; microbial control of heavy metal pollution; pollution control using microorganisms and magnetic separation; degradation of cyanide and nitriles; nitrogen removal from water and waste; and land reclamation and restoration.

  7. A combination of direct viable count and fluorescence in situ hybridization for specific enumeration of viable Lactobacillus delbrueckii subsp.bulgaricus and Streptococcus thermophilus.

    Science.gov (United States)

    García-Hernández, J; Moreno, Y; Amorocho, C M; Hernández, M

    2012-03-01

    We have developed a direct viable count (DVC)-FISH procedure for quickly and easily discriminating between viable and nonviable cells of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains, the traditional yogurt bacteria. direct viable count method has been modified and adapted for Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus analysis by testing different times of incubation and concentrations of DNA-gyrase inhibitors. DVC procedure has been combined with fluorescent in situ hybridization (FISH) for the specific detection of viable cells of both bacteria with specific rRNA oligonucleotide probes (DVC-FISH). Of the four antibiotics tested (novobiocin, nalidixic acid, pipemidic acid and ciprofloxacin), novobiocin was the most effective for DVC method and the optimum incubation time was 7 h for both bacteria. The number of viable cells was obtained by the enumeration of specific hybridized cells that were elongated at least twice their original length for Lactobacillus and twice their original size for Streptococcus. This technique was successfully applied to detect viable cells in inoculated faeces. Results showed that this DVC-FISH procedure is a quick and culture-independent useful method to specifically detect viable Lact. delbrueckii subsp. bulgaricus and Strep. thermophilus in different samples, being applied for the first time to lactic acid bacteria. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  8. Stable isotopes and biomarkers in microbial ecology

    NARCIS (Netherlands)

    Boschker, H.T.S.; Middelburg, J.J.

    2002-01-01

    The use of biomarkers in combination with stable isotope analysis is a new approach in microbial ecology and a number of papers on a variety of subjects have appeared. We will first discuss the techniques for analysing stable isotopes in biomarkers, primarily gas chromatography-combustion-isotope

  9. Microbial Metabolism and Inhibition Studies of Phenobarbital

    African Journals Online (AJOL)

    Erah

    techniques, high performance liquid chromatography (HPLC), mass spectrometry (MS) ... Keywords: Microbial metabolism, Phenobarbital, Inhibition studies, Rhizopus stolonifer, CYP 2C9, .... 24 h of incubation 0.5 ml of drug solution was ... mode, positive: spray voltage, 3.5 KV: ... Rhizopus stolonifer showed an extra peak at.

  10. Nitrogen transformations in stratified aquatic microbial ecosystems

    DEFF Research Database (Denmark)

    Revsbech, N. P.; Risgaard-Petersen, N.; Schramm, A.

    2006-01-01

    Abstract  New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about n...

  11. Modelling microbial interactions and food structure in predictive microbiology

    NARCIS (Netherlands)

    Malakar, P.K.

    2002-01-01

    Keywords: modelling, dynamic models, microbial interactions, diffusion, microgradients, colony growth, predictive microbiology.

    Growth response of microorganisms in foods is a complex process. Innovations in food production and preservation techniques have resulted in adoption of

  12. Microbial Fuel Cells for Organic-Contaminated Soil Remedial Applications

    NARCIS (Netherlands)

    Li, Xiaojing; Wang, Xin; Weng, Liping; Zhou, Qixing; Li, Yongtao

    2017-01-01

    Efficient noninvasive techniques are desired for repairing organic-contaminated soils. Bioelectrochemical technology, especially microbial fuel cells (MFCs), has been widely used to promote a polluted environmental remediation approach, and applications include wastewater, sludge, sediment, and

  13. Effects of the source of energy and minerals on microbial protein synthesis in rumen using 35S as indicator. Part of a coordinated programme on tracer techniques in studies on the use of non-protein nitrogen in ruminants

    International Nuclear Information System (INIS)

    Durant, M.

    1976-05-01

    Part I. The effect of the nature of carbohydrates and minerals on microbial growth in vitro was studied in vitro to intensify rumen microbial protein synthesis from non-protein nitrogen, using phosphorus incorporation (PR). The nature of starch greatly influences urea utilization. Among the tropical tubers studied, yam Cayenesis and canna Edulis give lower urea utilization than cassava and yam Dumetorum. However, this can be improved by processing. The effects are greatest when the proportion of urea to processed cereal is ca. 4-5%. S-addition as sulfate improves urea utilization with both natural and purified diets. Part II. Results from the Jouy and Ghent laboratories were analyzed statistically, to check the accuracy of the 32 P method for estimating microbial growth, using protein-free substrates. The linear relationship between PR and every other variable was studied. Two multivariate analyses, principal components and multiple regression, were applied. Net NH 3 utilization was predicted using the equations for substrates with proteins likely to be degraded. This method appears more accurate than using the N/P ratio in microflora. Equations should only be used under the specific experiments described

  14. Limitations of the A-1M method for fecal coliform enumeration in the Pacific oyster (Crassostrea gigas).

    Science.gov (United States)

    Kaysner, C A; Weagant, S D

    1987-01-01

    Use of the A-1M method, which was originally devised for testing water samples, has recently been extended for enumeration of fecal coliforms and Escherichia coli in shellfish and other food products. Results of our study indicate that while this method is reliable for analysis of growing waters, the use of the A-1M method for testing Pacific oysters may be less reliable because bacteria not belonging to the coliform group but which are sometimes present in these animals also give a positive reaction.

  15. Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

    Science.gov (United States)

    Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

    2007-09-01

    In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product.

  16. Variation in microbial population during composting of agro-industrial waste.

    Science.gov (United States)

    Coelho, Luísa; Reis, Mário; Dionísio, Lídia

    2013-05-01

    Two compost piles were prepared, using two ventilation systems: forced ventilation and ventilation through mechanical turning. The material to compost was a mixture of orange waste, olive pomace, and grass clippings (2:1:1 v/v). During the composting period (375 days), samples were periodically taken from both piles, and the enumeration of fungi, actinomycetes, and heterotrophic bacteria was carried out. All studied microorganisms were incubated at 25 and 55 °C after inoculation in appropriate growth media. Fungi were dominant in the early stages of both composting processes; heterotrophic bacteria proliferated mainly during the thermophilic stage, and actinomycetes were more abundant in the final stage of the composting process. Our results showed that the physical and chemical parameters: temperature, pH, moisture, and aeration influenced the variation of the microbial population along the composting process. This study demonstrated that composting of these types of wastes, despite the prolonged mesophilic stage, provided an expected microbial variation.

  17. Selective and differential enumerations of Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus casei and Bifidobacterium spp. in yoghurt--a review.

    Science.gov (United States)

    Ashraf, Rabia; Shah, Nagendra P

    2011-10-03

    Yoghurt is increasingly being used as a carrier of probiotic bacteria for their potential health benefits. To meet with a recommended level of ≥10(6) viable cells/g of a product, assessment of viability of probiotic bacteria in market preparations is crucial. This requires a working method for selective enumeration of these probiotic bacteria and lactic acid bacteria in yoghurt such as Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lb. acidophilus, Lb. casei and Bifidobacterium. This chapter presents an overview of media that could be used for differential and selective enumerations of yoghurt bacteria. De Man Rogosa Sharpe agar containing fructose (MRSF), MRS agar pH 5.2 (MRS 5.2), reinforced clostridial prussian blue agar at pH 5.0 (RCPB 5.0) or reinforced clostridial agar at pH 5.3 (RCA 5.3) are suitable for enumeration of Lb. delbrueckii subsp. bulgaricus when the incubation is carried out at 45°C for 72h. S. thermophilus (ST) agar and M17 are recommended for selective enumeration of S. thermophilus. Selective enumeration of Lb. acidophilus in mixed culture could be made in Rogosa agar added with 5-bromo-4-chloro-3-indolyl-β-d-glucopyranoside (X-Glu) or MRS containing maltose (MRSM) and incubation in a 20% CO2 atmosphere. Lb. casei could be selectively enumerated on specially formulated Lb. casei (LC) agar from products containing yoghurt starter bacteria (S. thermophilus and Lb. delbrueckii subsp. bulgaricus), Lb. acidophilus, Bifidobacterium spp. and Lb. casei. Bifidobacterium could be enumerated on MRS agar supplemented with nalidixic acid, paromomycin, neomycin sulphate and lithium chloride (MRS-NPNL) under anaerobic incubation at 37°C for 72h. Copyright © 2011. Published by Elsevier B.V.

  18. A great leap forward in microbial ecology.

    Science.gov (United States)

    Okabe, Satoshi; Oshiki, Mamoru; Kamagata, Yoichi; Yamaguchi, Nobuyasu; Toyofuku, Masanori; Yawata, Yutaka; Tashiro, Yosuke; Nomura, Nobuhiko; Ohta, Hiroyuki; Ohkuma, Moriya; Hiraishi, Akira; Minamisawa, Kiwamu

    2010-01-01

    Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

  19. Microbial Ecology: Where are we now?

    Science.gov (United States)

    Boughner, Lisa A; Singh, Pallavi

    2016-11-01

    Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages.

  20. Evolution of microbial pathogens

    National Research Council Canada - National Science Library

    DiRita, Victor J; Seifert, H. Steven

    2006-01-01

    ... A. Hogan vvi ■ CONTENTS 8. Evolution of Pathogens in Soil Rachel Muir and Man-Wah Tan / 131 9. Experimental Models of Symbiotic Host-Microbial Relationships: Understanding the Underpinnings of ...

  1. Methods in gut microbial ecology for ruminants

    International Nuclear Information System (INIS)

    Makkar, H.P.S.; McSweeney, C.S.

    2005-01-01

    This book presents a comprehensive up-to-date account of the methodologies and protocols for conventional and modern molecular techniques that are currently in use for studying the gut microbial ecology of ruminants. Each chapter has been contributed by experts in the field and methods have been presented in a recipe-like format designed for direct practical use in the laboratory and also to provide insight into the most appropriate techniques, their applications and the type of information that could be expected. The techniques and procedures described are also relevant and adaptable to other gastrointestinal ecosystems and the microbiology of anaerobic environments in general. This manual will 'demystify' the methods in molecular microbial ecology for readers who are novice in the field but are excited by the prospects of this technology. It would also be invaluable for the experienced workers striving for giving new dimension to their research - expanding the work in other fields and initiating cross-cutting activities

  2. Synthetic Electric Microbial Biosensors

    Science.gov (United States)

    2017-06-10

    domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited.   Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home   September, 2014

  3. A system for household enumeration and re-identification in densely populated slums to facilitate community research, education, and advocacy.

    Directory of Open Access Journals (Sweden)

    Dana R Thomson

    Full Text Available We devised and implemented an innovative Location-Based Household Coding System (LBHCS appropriate to a densely populated informal settlement in Mumbai, India.LBHCS codes were designed to double as unique household identifiers and as walking directions; when an entire community is enumerated, LBHCS codes can be used to identify the number of households located per road (or lane segment. LBHCS was used in community-wide biometric, mental health, diarrheal disease, and water poverty studies. It also facilitated targeted health interventions by a research team of youth from Mumbai, including intensive door-to-door education of residents, targeted follow-up meetings, and a full census. In addition, LBHCS permitted rapid and low-cost preparation of GIS mapping of all households in the slum, and spatial summation and spatial analysis of survey data.LBHCS was an effective, easy-to-use, affordable approach to household enumeration and re-identification in a densely populated informal settlement where alternative satellite imagery and GPS technologies could not be used.

  4. From Enumerating to Generating: A Linear Time Algorithm for Generating 2D Lattice Paths with a Given Number of Turns

    Directory of Open Access Journals (Sweden)

    Ting Kuo

    2015-05-01

    Full Text Available We propose a linear time algorithm, called G2DLP, for generating 2D lattice L(n1, n2 paths, equivalent to two-item  multiset permutations, with a given number of turns. The usage of turn has three meanings: in the context of multiset permutations, it means that two consecutive elements of a permutation belong to two different items; in lattice path enumerations, it means that the path changes its direction, either from eastward to northward or from northward to eastward; in open shop scheduling, it means that we transfer a job from one type of machine to another. The strategy of G2DLP is divide-and-combine; the division is based on the enumeration results of a previous study and is achieved by aid of an integer partition algorithm and a multiset permutation algorithm; the combination is accomplished by a concatenation algorithm that constructs the paths we require. The advantage of G2DLP is twofold. First, it is optimal in the sense that it directly generates all feasible paths without visiting an infeasible one. Second, it can generate all paths in any specified order of turns, for example, a decreasing order or an increasing order. In practice, two applications, scheduling and cryptography, are discussed.

  5. Microbial bioinformatics 2020.

    Science.gov (United States)

    Pallen, Mark J

    2016-09-01

    Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  6. Characterization of microbial communities in deep groundwater from granitic rock

    International Nuclear Information System (INIS)

    Jain, D.K.; Stroes-Gascoyne, S.; Providenti, M.; Tanner, C.; Cord, I.

    1997-01-01

    The microbial characteristics of deep granitic nutrient-poor groundwater from two boreholes at the Underground Research Laboratory of Atomic Energy of Canada Limited were studied. Scanning electron microscopy of the groundwater samples revealed significant numbers of bacteria of various sizes and shapes, including spherical, rod, and curved shaped. A few bacteria with appendages were also observed. Significant numbers of bacteria (∼l0 5 /mL) were enumerated using acridine orange (AO) staining. An active microbial population was detected with three direct methods and it ranged from 1 to 83% of the AO count, depending on the method used. Culturable aerobic and anaerobic (including facultative) heterotrophic bacteria ranged from 0.06 to 10.2% and 0.008 to 7.35%, respectively, of the AO count. Denitrifying. N 2 - fixing, sulphate-reducing, and iron-precipitating bacteria were present, but no iron-oxidizing bacteria or methanogens could be detected. Tentative identification of 160 isolates using the Biolog system showed a predominance of three Pseudomonas species, P. fluorescens, P. marginalis, and P. corrugata. Phospholipid fatty acid analysis showed that the bacteria in the groundwater samples faced starvation stress. However, laboratory studies showed that these bacteria can efficiently uptake and mineralize organic substrates when supplied. (author)

  7. Use of Readycult[tm] - LMX for enumeration of total coliforms and Escherichia coli in milk

    Directory of Open Access Journals (Sweden)

    Beloti Vanerli

    2002-01-01

    Full Text Available Readycult[tm] - LMX is a rapid method to test for the presence of total coliform bacteria and Escherichia coli in water, giving results in 24h. It is based on reactions of specific microbial enzymes or indicator nutrients of the medium. The goal of this paper was to study the use of Readycult[tm] - LMX to detect total coliform and E. coli in milk. One hundred twenty five samples of pasteurized and raw milk, collected in Londrina, PR, Brazil, were tested simultaneously by the most probable number (MPN method using Brilliant Green Bile Lactose Broth (2% (BRILA and Readycult[tm] - LMX. The Readycult[tm] - LMX test was evaluated for sensitivity, simplicity, and speed of results. There was a significant correlation between the results obtained by the two methods for total coliforms (r: 0.8224 and for E. coli (r: 0.8603. The two methods yielded similar results, but Readycult[tm] - LMX was easier to use. In addition, results were available as early as 24h.

  8. Advancing analytical algorithms and pipelines for billions of microbial sequences.

    Science.gov (United States)

    Gonzalez, Antonio; Knight, Rob

    2012-02-01

    The vast number of microbial sequences resulting from sequencing efforts using new technologies require us to re-assess currently available analysis methodologies and tools. Here we describe trends in the development and distribution of software for analyzing microbial sequence data. We then focus on one widely used set of methods, dimensionality reduction techniques, which allow users to summarize and compare these vast datasets. We conclude by emphasizing the utility of formal software engineering methods for the development of computational biology tools, and the need for new algorithms for comparing microbial communities. Such large-scale comparisons will allow us to fulfill the dream of rapid integration and comparison of microbial sequence data sets, in a replicable analytical environment, in order to describe the microbial world we inhabit. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Toxicity assessment using different bioassays and microbial biosensors.

    Science.gov (United States)

    Hassan, Sedky H A; Van Ginkel, Steven W; Hussein, Mohamed A M; Abskharon, Romany; Oh, Sang-Eun

    2016-01-01

    Toxicity assessment of water streams, wastewater, and contaminated sediments, is a very important part of environmental pollution monitoring. Evaluation of biological effects using a rapid, sensitive and cost effective method can indicate specific information on ecotoxicity assessment. Recently, different biological assays for toxicity assessment based on higher and lower organisms such as fish, invertebrates, plants and algal cells, and microbial bioassays have been used. This review focuses on microbial biosensors as an analytical device for environmental, food, and biomedical applications. Different techniques which are commonly used in microbial biosensing include amperometry, potentiometry, conductometry, voltammetry, microbial fuel cells, fluorescence, bioluminescence, and colorimetry. Examples of the use of different microbial biosensors in assessing a variety of environments are summarized. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    Science.gov (United States)

    Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.

  11. Deep subsurface microbial processes

    Science.gov (United States)

    Lovley, D.R.; Chapelle, F.H.

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  12. Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan.

    Science.gov (United States)

    Das, Suvendu; Liu, Chia-Chuan; Jean, Jiin-Shuh; Liu, Tsunglin

    2016-02-01

    Although dissimilatory arsenic reduction (DAsR) has been recognized as an important process for groundwater arsenic (As) enrichment, its characterization and association with in situ microbial activities and diversity in As-rich groundwater is barely studied. In this work, we collected As-rich groundwater at depths of 23, 300, and 313 m, respectively, from Yenshui-3, Budai-Shinwen, and Budai-4 of Chianan plain, southwestern Taiwan, and conducted incubation experiments using different electron donors, acceptors, and sulfate-reducing bacterial inhibitor (tungstate) to characterize DAsR. Moreover, bacterial diversity was evaluated using 454-pyrosequencing targeting bacterial 16S rRNAs. MPN technique was used to enumerate microorganisms with different in situ metabolic functions. The results revealed that DAsR in groundwater of Chianan plain was a biotic phenomenon (as DAsR was totally inhibited by filter sterilization), enhanced by the type of electron donor (in this case, lactate enhanced DAsR but acetate and succinate did not), and limited by the availability of arsenate. In addition to oxidative recycling of As(III), dissolution of As(V)-saturated manganese and iron minerals by indigenous dissimilatory Mn(IV)- and Fe(III)-reducing bacteria, and abiotic oxidation of As(III) with Mn(IV) regenerated As(V) in the groundwater. Sulfate-respiring bacteria contributed 7.4 and 28.2 % to the observed DAsR in groundwater of Yinshui-3 and Budai-Shinwen, respectively, whereas their contribution was negligible in groundwater of Budai-4. A noticeable variation in dominant genera Acinetobacter and Bacillus was observed within the groundwater. Firmicutes dominated in highly As-rich groundwater of Yenshui-3, whereas Proteobacteria dominated in comparatively less As-rich groundwater of Budai-Shinwen and Budai 4.

  13. Monitor and Protect Wigwam River Bull Trout for Koocanusa Reservoir : Summary of the Skookumchuck Creek Bull Trout Enumeration Project, Annual Report 2001.

    Energy Technology Data Exchange (ETDEWEB)

    Baxter, James S.; Baxter, Jeremy

    2002-03-01

    This report summarizes the second year of a bull trout (Salvelinus confluentus) enumeration project on Skookumchuck Creek in southeastern British Columbia. An enumeration fence and traps were installed on the creek from September 6th to October 12th 2001 to enable the capture of post-spawning bull trout emigrating out of the watershed. During the study period, a total of 273 bull trout were sampled through the enumeration fence. Length and weight were determined for all bull trout captured. In total, 39 fish of undetermined sex, 61 males and 173 females were processed through the fence. An additional 19 bull trout were observed on a snorkel survey prior to the fence being removed on October 12th. Coupled with the fence count, the total bull trout enumerated during this project was 292 fish. Several other species of fish were captured at the enumeration fence including westslope cutthroat trout (Oncorhynchus clarki lewisi), Rocky Mountain whitefish (Prosopium williamsoni), and kokanee (O. nerka). A total of 143 bull trout redds were enumerated on the ground in two different locations (river km 27.5-30.5, and km 24.0-25.5) on October 3rd. The majority of redds (n=132) were observed in the 3.0 km index section (river km 27.5-30.5) that has been surveyed over the past five years. The additional 11 redds were observed in a 1.5 km section (river km 24.0-25.5). Summary plots of water temperature for Bradford Creek, Sandown Creek, Buhl Creek, and Skookumchuck Creek at three locations suggested that water temperatures were within the temperature range preferred by bull trout for spawning, egg incubation, and rearing.

  14. Microbial conversion technologies

    Energy Technology Data Exchange (ETDEWEB)

    Lau, P. [National Research Council of Canada, Ottawa, ON (Canada). Bioconversion and Sustainable Development

    2006-07-01

    Microbes are a biomass and an valuable resource. This presentation discussed microbial conversion technologies along with background information on microbial cells, their characteristics and microbial diversity. Untapped opportunities for microbial conversion were identified. Metagenomic and genome mining approaches were also discussed, as they can provide access to uncultivated or unculturable microorganisms in communal populations and are an unlimited resource for biocatalysts, novel genes and metabolites. Genome mining was seen as an economical approach. The presentation also emphasized that the development of microbial biorefineries would require significant insights into the relevant microorganisms and that biocatalysts were the ultimate in sustainability. In addition, the presentation discussed the natural fibres initiative for biochemicals and biomaterials. Anticipated outputs were identified and work in progress of a new enzyme-retting cocktail to provide diversity and/or consistency in fibre characteristics for various applications were also presented. It was concluded that it is necessary to leverage understanding of biological processes to produce bioproducts in a clean and sustainable manner. tabs., figs.

  15. Validation of Microcapillary Flow Cytometry for Community-Based CD4+ T Lymphocyte Enumeration in Remote Burkina Faso

    Science.gov (United States)

    Renault, Cybèle A; Traore, Arouna; Machekano, Rhoderick N; Israelski, Dennis M

    2010-01-01

    Background: CD4+ T lymphocyte enumeration plays a critical role in the initiation and monitoring of HIV-infected patients on antiretroviral therapy. There is an urgent need for low-cost CD4+ enumeration technologies, particularly for use in dry, dusty climates characteristic of many small cities in Sub-Saharan Africa. Design: Cross-sectional study. Methods: Blood samples from 98 HIV-infected patients followed in a community HIV clinic in Ouahigouya, Burkina Faso were obtained for routine CD4+ T lymphocyte count monitoring. The blood samples were divided into two aliquots, on which parallel CD4+ measurements were performed using microcapillary (Guava EasyCD4) and dedicated (Becton Dickinson FACSCount) CD4+ enumeration systems. Spearman rank correlation coefficient was calculated, and the sensitivity, specificity and positive predictive value (PPV) for EasyCD4 <200 cells/µL were determined compared to the reference standard FACSCount CD4 <200 cells/µL. Results: Mean CD4 counts for the EasyCD4 and FACSCount were 313.75 cells/µL and 303.47 cells/µL, respectively. The Spearman rank correlation coefficient was 0.92 (p<0.001). Median values using EasyCD4 were higher than those with the FACSCount (p=0.004). For a CD4<350 cells/uL, sensitivity of the EasyCD4 was 93.9% (95%CI 85.2-98.3%), specificity was 90.6% (95% CI 75.0-98.0%), and PPV was 95.4% (95%CI 87.1-99.0%). Conclusion: Use of the EasyCD4 system was feasible and highly accurate in the harsh conditions of this remote city in Sub-Saharan Africa, demonstrating acceptable sensitivity and specificity compared to a standard operating system. Microcapillary flow cytometry offers a cost-effective alternative for community-based, point-of-care CD4+ testing and could play a substantial role in scaling up HIV care in remote, resource-limited settings. PMID:21253463

  16. Antimicrobial Materials for Advanced Microbial Control in Spacecraft Water Systems

    Science.gov (United States)

    Birmele, Michele; Caro, Janicce; Newsham, Gerard; Roberts, Michael; Morford, Megan; Wheeler, Ray

    2012-01-01

    Microbial detection, identification, and control are essential for the maintenance and preservation of spacecraft water systems. Requirements set by NASA put limitations on the energy, mass, materials, noise, cost, and crew time that can be devoted to microbial control. Efforts are being made to attain real-time detection and identification of microbial contamination in microgravity environments. Research for evaluating technologies for capability enhancement on-orbit is currently focused on the use of adenosine triphosphate (ATP) analysis for detection purposes and polymerase chain reaction (peR) for microbial identification. Additional research is being conducted on how to control for microbial contamination on a continual basis. Existing microbial control methods in spacecraft utilize iodine or ionic silver biocides, physical disinfection, and point-of-use sterilization filters. Although these methods are effective, they require re-dosing due to loss of efficacy, have low human toxicity thresholds, produce poor taste, and consume valuable mass and crew time. Thus, alternative methods for microbial control are needed. This project also explores ultraviolet light-emitting diodes (UV-LEDs), surface passivation methods for maintaining residual biocide levels, and several antimicrobial materials aimed at improving current microbial control techniques, as well as addressing other materials presently under analysis and future directions to be pursued.

  17. Evaluation of modified dichloran 18% glycerol (DG18) agar for enumerating fungi in wheat flour: a collaborative study.

    Science.gov (United States)

    Beuchat, L R; Hwang, C A

    1996-04-01

    Dichloran 18% glycerol agar base supplemented with 100 micrograms of chloramphenicol ml-1 (DG18 agar) was compared to DG18 agar supplemented with 100 micrograms of Triton X-301 ml-1 (DG18T) and DG18 agar supplemented with 1 microgram of iprodione [3-(3,5-dichlorophenyl)-N-(1-methyl-ethyl)-2,4-dioxo-1-imidazolidine- carboxamide] ml-1 (DG18I agar) for enumeration of fungi in ten brands of wheat flour. As the flours contained low fungal populations, all were inoculated with two to four strains of xerophilic fungi (Aspergillus candidus, A. penicillioides, Eurotium amstelodami, E. intermedium, E. repens, E. rubrum, E. tonophilum, E. umbrosum and Wallemia sebi), after which counts ranged from 3.87 to 6.37 log10 CFU g-1. Significantly higher populations (p repens or E. tonophilum had also been inoculated into at least one of the three flours showing significantly higher numbers of CFU on DG18T agar. Analysis of collapsed data from all samples showed that DG18T agar was significantly better than DG18 or DG18I agars at p < 0.10 but not at p < 0.05. Coefficients of variation for reproducibility (among-laboratory variation) were 8.4%, 7.5% and 8.6%, respectively, for DG18, DG18T and DG18I agars. DG18I agar restricted colony development most, especially for Eurotium species. Naturally occurring Penicillium species grew equally well on DG18 and DG18T agars, whereas W. sebi grew well on all three media. DG18T agar was judged to be superior to DG18 and DG18I agars for enumerating fungi in wheat flours.

  18. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.

    Science.gov (United States)

    Koch, Mathilde; Duigou, Thomas; Carbonell, Pablo; Faulon, Jean-Loup

    2017-12-19

    Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. Here, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on an E. coli model to complete E. coli metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of an E. coli cell lysate interfacing our workflow with OpenMS through the KNIME Analytics Platform. We provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.

  19. EVA Suit Microbial Leakage Investigation

    Data.gov (United States)

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

  20. The mind-body-microbial continuum

    OpenAIRE

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

    2011-01-01

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

  1. Nitrogen transformations in stratified aquatic microbial ecosystems

    DEFF Research Database (Denmark)

    Revsbech, Niels Peter; Risgaard-Petersen, N.; Schramm, Andreas

    2006-01-01

    Abstract  New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about n...... performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.......Abstract  New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about...... nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria...

  2. Molecular ecology of microbial mats

    NARCIS (Netherlands)

    Bolhuis, H.; Cretoiu, M.S.; Stal, L.J.

    2014-01-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep

  3. PCR Based Microbial Monitor for Analysis of Recycled Water Aboard the ISSA: Issues and Prospects

    Science.gov (United States)

    Cassell, Gail H.; Lefkowitz, Elliot J.; Glass, John I.

    1995-01-01

    The monitoring of spacecraft life support systems for the presence of health threatening microorganisms is paramount for crew well being and successful completion of missions. Development of technology to monitor spacecraft recycled water based on detection and identification of the genetic material of contaminating microorganisms and viruses would be a substantial improvement over current NASA plans to monitor recycled water samples that call for the use of conventional microbiology techniques which are slow, insensitive, and labor intensive. The union of the molecular biology techniques of DNA probe hybridization and polymerase chain reaction (PCR) offers a powerful method for the detection, identification, and quantification of microorganisms and viruses. This technology is theoretically capable of assaying samples in as little as two hours with specificity and sensitivity unmatched by any other method. A major advance in probe-hybridization/PCR has come about in a technology called TaqMan(TM), which was invented by Perkin Elmer. Instrumentation using TaqMan concepts is evolving towards devices that could meet NASA's needs of size, low power use, and simplicity of operation. The chemistry and molecular biology needed to utilize these probe-hybridization/PCR instruments must evolve in parallel with the hardware. The following issues of chemistry and biology must be addressed in developing a monitor: Early in the development of a PCR-based microbial monitor it will be necessary to decide how many and which organisms does the system need the capacity to detect. We propose a set of 17 different tests that would detect groups of bacteria and fungus, as well as specific eukaryotic parasites and viruses; In order to use the great sensitivity of PCR it will be necessary to concentrate water samples using filtration. If a lower limit of detection of 1 microorganism per 100 ml is required then the microbes in a 100 ml sample must be concentrated into a volume that can be

  4. Anaerobic microbial dehalogenation

    NARCIS (Netherlands)

    Smidt, H.; Vos, de W.M.

    2004-01-01

    The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the

  5. Diazotrophic microbial mats

    NARCIS (Netherlands)

    Severin, I.; Stal, L.J.; Seckbach, J.; Oren, A.

    2010-01-01

    Microbial mats have been the focus of scientific research for a few decades. These small-scale ecosystems are examples of versatile benthic communities of microorganisms, usually dominated by phototrophic bacteria (e.g., Krumbein et al., 1977; Jørgensen et al., 1983). They develop as vertically

  6. Microbial electrosynthesis of biochemicals

    NARCIS (Netherlands)

    Bajracharya, S.

    2016-01-01

    Microbial electrosynthesis (MES) is an electricity-driven production of chemicals from low-value waste using microorganisms as biocatalysts. MES from CO2 comprises conversion of CO2 to multi-carbon compounds employing microbes at the cathode which use electricity as an energy source. This thesis

  7. Microbial Enzymatic Degradation of Biodegradable Plastics.

    Science.gov (United States)

    Roohi; Bano, Kulsoom; Kuddus, Mohammed; Zaheer, Mohammed R; Zia, Qamar; Khan, Mohammed F; Ashraf, Ghulam Md; Gupta, Anamika; Aliev, Gjumrakch

    2017-01-01

    The renewable feedstock derived biodegradable plastics are important in various industries such as packaging, agricultural, paper coating, garbage bags and biomedical implants. The increasing water and waste pollution due to the available decomposition methods of plastic degradation have led to the emergence of biodegradable plastics and biological degradation with microbial (bacteria and fungi) extracellular enzymes. The microbes utilize biodegradable polymers as the substrate under starvation and in unavailability of microbial nutrients. Microbial enzymatic degradation is suitable from bioremediation point of view as no waste accumulation occurs. It is important to understand the microbial interaction and mechanism involved in the enzymatic degradation of biodegradable plastics under the influence of several environmental factors such as applied pH, thermo-stability, substrate molecular weight and/or complexity. To study the surface erosion of polymer film is another approach for hydrolytic degradation characteristion. The degradation of biopolymer is associated with the production of low molecular weight monomer and generation of carbon dioxide, methane and water molecule. This review reported the degradation study of various existing biodegradable plastics along with the potent degrading microbes (bacteria and fungi). Patents available on plastic biodegradation with biotechnological significance is also summarized in this paper. This paper assesses that new disposal technique should be adopted for the degradation of polymers and further research is required for the economical production of biodegradable plastics along with their enzymatic degradation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  8. Oocyte batch development and enumeration in the European anchovy (Engraulis encrasicolus

    Directory of Open Access Journals (Sweden)

    R. FERRERI

    2016-09-01

    Full Text Available An alternative method to the traditional hydrated oocyte (HO method has been evaluated for the Sicilian anchovy, Engraulis encrasicolus. The method is based on the processing of ovarian whole mount images and the identification of the spawning batch in oocyte size frequency distributions and shows the advantage that it can be applied to various oocyte stages rather than strictly to the HO stage. Despite the peculiar elliptical shape of anchovy oocytes, this image analysis technique was fully successful since the yolked stage appeared to perform equally to the HO stage for anchovy batch fecundity measurements.

  9. Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook

    Directory of Open Access Journals (Sweden)

    Kela P. Weber

    2016-11-01

    Full Text Available The field of treatment wetlands (TWs is rapidly expanding and, arguably, is tasked with studying and understanding one of the most complex water treatment systems available. Microbial communities are generally considered to be responsible for the majority of wastewater constituent degradation in TWs. However, they are also known to be spatially heterogeneous, temporally dynamic, as well as structurally and functionally diverse. Presented here is a meta-analysis of all peer reviewed TW journal articles which utilized a microbial community assessment methodology over the period of 1988 to July 2016. A total of 1101 papers were reviewed, 512 from 1988 to 2012, 215 of which included a microbial community assessment aspect and were subsequently classified as representing past research, and 589 from 2013 to July 2016, 196 of which were classified as representing current TW microbial community research. In general, TW microbial community research has increased over time, with a marked surge in the past four years. Microbial community structure is currently the most commonly used methodological type followed by activity, enumeration and function, respectively. Areas of research focus included nitrogen transformations (156, organic degradation (33, and emerging contaminants (32, with general characterization studies also accounting for a significant proportion (243. Microbial communities from a range of TW systems have been investigated over the last four years with meso-scale (10–1000 L being the most commonly studied system size followed by large-scale (>100,000 L, micro-scale (<10 L, and pilot-scale (1000–100,000 L. Free water surface flow (SF, horizontal subsurface flow (HF, and vertical flow (VF systems are being studied in approximately equal proportions with the majority of studies focused on gaining fixed media/biofilm samples for analysis (rather than from the rhizosphere or interstitial water. Looking at efforts from a regional perspective

  10. Detection and enumeration of periodontopathogenic bacteria in subgingival biofilm of pregnant women

    Directory of Open Access Journals (Sweden)

    Fernanda Campos Machado

    2012-10-01

    Full Text Available The aim of this study was to use the fluorescence in situ hybridization (FISH technique to test the hypothesis of qualitative and quantitative differences of 8 periodontopathogens between pregnant and non-pregnant women. This cross-sectional study included 20 pregnant women in their second trimester of pregnancy and 20 non-pregnant women. Probing depth, bleeding on probing, clinical attachment level, and presence of calculus were recorded. Subgingival plaque samples were collected and the FISH technique identified the presence and numbers of Aggregatibacter actinomycetemcomitans, Tannerella forsythia, Campylobacter rectus, Porphyromonas gingivalis, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia and Prevotella nigrescens. The Mann-Whitney U-test was applied to compare the data between the two groups. The mean age, ethnicity, marital status, education, and economic level in both groups were similar. The clinical parameters showed no significant differences between pregnant and non-pregnant women. The numbers of subgingival periodontopathogens were not found to be significantly different between groups, despite the higher mean counts of P. intermedia in pregnant women. Colonization patterns of the different bacteria most commonly associated with periodontal disease were not different in the subgingival plaque of pregnant and non-pregnant women.

  11. Airstream fractionation of vesicular-arbuscular mycorrhizal fungi: concentration and enumeration of propagules.

    Science.gov (United States)

    Tommerup, I C

    1982-09-01

    Spores and fragments of vesicular-arbuscular mycorrhizal fungi in dry soils were concentrated up to 100-fold when the soils were partitioned by fluidization and elutriation with a series of upward airstreams at progressively increasing velocities. The propagules were transported with the finer soil particles according to their equivalent spherical diameters. The system was used to predict the transport of propagules by wind. Concentrated propagules were rapidly separated from the soil particles in each soil fraction by an aqueous flotation method. The technique is proposed as a quantitative method for estimating the numbers of spores and fragments of mycorrhizae. The scheme includes a viability test that was used to differentiate between potentially infective propagules and those that were either dormant or incapable of regrowth.

  12. Competition between autotrophic and heterotrophic microbial plankton for inorganic nutrients induced by variability in estuarine biophysicochemical conditions

    Science.gov (United States)

    Williams, A.; Quigg, A.

    2016-02-01

    Competition for inorganic nutrients between autotrophic and heterotrophic fractions of microbial plankton (0.2-20μm) was investigated at two stations in a sub-tropical estuary, Galveston Bay, Texas. Competition potential between these groups is enhanced because individuals are similar in size, reducing variability among their nutrient uptake efficiencies. Further, in estuaries, allochthonous supplements to autochthonous carbon may satisfy heterotrophic requirements, allowing alternative factors to limit abundance. The relative abundance of autotrophs and heterotrophs stained with SYBR Green I and enumerated on a Beckman Coulter Gallios flow cytometer were evaluated monthly during a year-long study. Shifts in the relative in situ abundance were significantly related to temperature, dissolved inorganic nitrogen (DIN), phosphorous (Pi), and total organic carbon (TOC) concentrations revealing opposing gradients of limitation by different abiotic factors. In corresponding in vitro nutrient enrichment bioassays the relative contribution of autotrophic or heterotrophic microbial plankton to significant enrichment responses varied. Only during macro- (>20μm) phytoplankton blooms do autotrophic microbial plankton respond to nutrient enrichment. Contrastingly, the heterotrophic microbial plankton responded to nutrient enrichment primarily when temperature limitation was alleviated. Therefore, the potential for autotrophic and heterotrophic microbial plankton competition for limiting nutrients is highest when autotrophic microbial plankton are also competing with larger phytoplankton during bloom events. Based on this evidence, we hypothesize that the autotrophic microbial fraction has a competitive advantage over the heterotrophs for inorganic nutrients in Galveston Bay. The observed microbial competition during estuarine phytoplankton blooms may have important consequences on biogeochemical processes including carbon and nutrient cycling.

  13. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  14. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  15. Degradation of microbial polyesters.

    Science.gov (United States)

    Tokiwa, Yutaka; Calabia, Buenaventurada P

    2004-08-01

    Microbial polyhydroxyalkanoates (PHAs), one of the largest groups of thermoplastic polyesters are receiving much attention as biodegradable substitutes for non-degradable plastics. Poly(D-3-hydroxybutyrate) (PHB) is the most ubiquitous and most intensively studied PHA. Microorganisms degrading these polyesters are widely distributed in various environments. Although various PHB-degrading microorganisms and PHB depolymerases have been studied and characterized, there are still many groups of microorganisms and enzymes with varying properties awaiting various applications. Distributions of PHB-degrading microorganisms, factors affecting the biodegradability of PHB, and microbial and enzymatic degradation of PHB are discussed in this review. We also propose an application of a new isolated, thermophilic PHB-degrading microorganism, Streptomyces strain MG, for producing pure monomers of PHA and useful chemicals, including D-3-hydroxycarboxylic acids such as D-3-hydroxybutyric acid, by enzymatic degradation of PHB.

  16. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    ) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source...... of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global...... microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require...

  17. Enumeration and biomass estimation of planktonic bacteria and viruses by transmission electron microscopy

    International Nuclear Information System (INIS)

    Borsheim, K.Y.; Bratbak, G.; Heldal, M.

    1990-01-01

    Bacteria and virus particles were harvested from water samples by ultracentrifugation directly onto Formvar-coated electron microscopy grids and counted in a transmission electron microscope. With this technique, we have counted and sized bacteria and viruses in marine water samples and during laboratory incubations. By X-ray microanalysis, we could determine the elemental composition and dry-matter content of individual bacteria. The dry weight/volume ratio for the bacteria was 600 fg of dry weight microns-3. The potassium content of the bacteria was normal compared with previous estimates from other bacterial assemblages; thus, this harvesting procedure did not disrupt the bacterial cells. Virus particles were, by an order of magnitude, more abundant than bacteria in marine coastal waters. During the first 5 to 7 days of incubation, the total number of viruses increased exponentially at a rate of 0.4 day-1 and thereafter declined. The high proliferation rate suggests that viral parasitism may affect mortality of bacteria in aquatic environments

  18. Fluorescence detection, enumeration and characterization of single circulating cells in vivo: technology, applications and future prospects

    Science.gov (United States)

    Hartmann, Carolin; Patil, Roshani; Lin, Charles P.; Niedre, Mark

    2018-01-01

    There are many diseases and biological processes that involve circulating cells in the bloodstream, such as cancer metastasis, immunology, reproductive medicine, and stem cell therapies. This has driven significant interest in new technologies for the study of circulating cells in small animal research models and clinically. Most currently used methods require drawing and enriching blood samples from the body, but these suffer from a number of limitations. In contrast, ‘in vivo flow cytometry’ (IVFC) refers to set of technologies that allow study of cells directly in the bloodstream of the organism in vivo. In recent years the IVFC field has grown significantly and new techniques have been developed, including fluorescence microscopy, multi-photon, photo-acoustic, and diffuse fluorescence IVFC. In this paper we review recent technical advances in IVFC, with emphasis on instrumentation, contrast mechanisms, and detection sensitivity. We also describe key applications in biomedical research, including cancer research and immunology. Last, we discuss future directions for IVFC, as well as prospects for broader adoption by the biomedical research community and translation to humans clinically.

  19. Microbial decontamination of dried date by Gamma-irradiation

    International Nuclear Information System (INIS)

    Majd, F.; Motamedi, F.; Abhari, M.

    2000-01-01

    Dried date is one of the export item from Iran. It can be contaminated during the processing and storage using nuclear techniques such as irradiation of food can increase the shelf life of agricultural products and improve their quality. This technique can be used for food decontamination of dried fruits according the standard authorized limitation. In this research different doses of Gamma Irradiation were used for microbial decontamination.he rest indicates that the optimum dose to reduce microbial contamination and increase shelf life is 5 kGy

  20. Microbial and chemical markers: runoff transfer in animal manure-amended soils.

    Science.gov (United States)

    Jaffrezic, Anne; Jardé, Emilie; Pourcher, Anne-Marie; Gourmelon, Michèle; Caprais, Marie-Paule; Heddadj, Djilali; Cottinet, Patrice; Bilal, Muhamad; Derrien, Morgane; Marti, Romain; Mieszkin, Sophie

    2011-01-01

    Fecal contamination of water resources is evaluated by the enumeration of the fecal coliforms and Enterococci. However, the enumeration of these indicators does not allow us to differentiate between the sources of fecal contamination. Therefore, it is important to use alternative indicators of fecal contamination to identify livestock contamination in surface waters. The concentration of fecal indicators (, enteroccoci, and F-specific bacteriophages), microbiological markers (Rum-2-bac, Pig-2-bac, and ), and chemical fingerprints (sterols and stanols and other chemical compounds analyzed by 3D-fluorescence excitation-matrix spectroscopy) were determined in runoff waters generated by an artificial rainfall simulator. Three replicate plot experiments were conducted with swine slurry and cattle manure at agronomic nitrogen application rates. Low amounts of bacterial indicators (1.9-4.7%) are released in runoff water from swine-slurry-amended soils, whereas greater amounts (1.1-28.3%) of these indicators are released in runoff water from cattle-manure-amended soils. Microbial and chemical markers from animal manure were transferred to runoff water, allowing discrimination between swine and cattle fecal contamination in the environment via runoff after manure spreading. Host-specific bacterial and chemical markers were quantified for the first time in runoff waters samples after the experimental spreading of swine slurry or cattle manure. American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.

  1. Assessment of the microbial populations in field and test pit experiments at Elliot Lake, Ontario, Canada

    International Nuclear Information System (INIS)

    Silver, M.; Taylor, J.B.

    1981-01-01

    Enumeration of aerobic and anaerobic heterotrophic (organic carbon-using) bacteria shows the establishment of a microbial population on vegetated tailings. The development of a population of heterotrophic bacteria, 90% of which are obligate aerobes, in the top 5 cm of the tailings is indicative of normal soil formation. The cell concentration decrease is greater than that found in older, well-developed soils. Iron-oxidizing thiobacilli are rarely present in the revegetated tailings, and then only at depths below 40 cm and at cell concentrations less than 100 cells/g. On an adjacent unvegetated portion of the tailings, fewer heterotrophic bacteria are found in the top 5 cm of the tailings. Iron-oxidizing thiobacilli are present uniformly in the top 47 cm. Enumeration of iron-oxidizing bacteria in the effluents of four test pit experiments indicate blockage of the drainage tiles in two experiments. Chemical conditions of the effluents are suitable for the formation of basic ferric precipitates that could cause this blockage

  2. Microbial counts of food contact surfaces at schools depending on a feeding scheme

    Directory of Open Access Journals (Sweden)

    Nthabiseng Nhlapo

    2014-11-01

    Full Text Available The prominence of disease transmission between individuals in confined environments is a concern, particularly in the educational environment. With respect to school feeding schemes, food contact surfaces have been shown to be potential vehicles of foodborne pathogens. The aim of this study was to assess the cleanliness of the surfaces that come into contact with food that is provided to children through the National School Nutrition Programme in central South Africa. In each school under study, microbiological samples were collected from the preparation surface and the dominant hand and apron of the food handler. The samples were analysed for total viable counts, coliforms, Escherichia coli, Staphylococcus aureus and yeasts and moulds. The criteria specified in the British Columbia Guide for Environmental Health Officers were used to evaluate the results. Total viable counts were high for all surfaces, with the majority of colonies being too numerous to count (over 100 colonies per plate. Counts of organisms were relatively low, with 20% of the surfaces producing unsatisfactory enumeration of S. aureus and E. coli and 30% unsatisfactory for coliforms. Yeast and mould produced 50% and 60% unsatisfactory counts from preparation surfaces and aprons, respectively. Statistically significant differences could not be established amongst microbial counts of the surfaces, which suggests cross-contamination may have occurred. Contamination may be attributed to foodstuffs and animals in the vicinity of the preparation area rather than to the food handlers, because hands had the lowest counts of enumerated organisms amongst the analysed surfaces.

  3. Starting up microbial enhanced oil recovery.

    Science.gov (United States)

    Siegert, Michael; Sitte, Jana; Galushko, Alexander; Krüger, Martin

    2014-01-01

    This chapter gives the reader a practical introduction into microbial enhanced oil recovery (MEOR) including the microbial production of natural gas from oil. Decision makers who consider the use of one of these technologies are provided with the required scientific background as well as with practical advice for upgrading an existing laboratory in order to conduct microbiological experiments. We believe that the conversion of residual oil into natural gas (methane) and the in situ production of biosurfactants are the most promising approaches for MEOR and therefore focus on these topics. Moreover, we give an introduction to the microbiology of oilfields and demonstrate that in situ microorganisms as well as injected cultures can help displace unrecoverable oil in place (OIP). After an initial research phase, the enhanced oil recovery (EOR) manager must decide whether MEOR would be economical. MEOR generally improves oil production but the increment may not justify the investment. Therefore, we provide a brief economical assessment at the end of this chapter. We describe the necessary state-of-the-art scientific equipment to guide EOR managers towards an appropriate MEOR strategy. Because it is inevitable to characterize the microbial community of an oilfield that should be treated using MEOR techniques, we describe three complementary start-up approaches. These are: (i) culturing methods, (ii) the characterization of microbial communities and possible bio-geochemical pathways by using molecular biology methods, and (iii) interfacial tension measurements. In conclusion, we hope that this chapter will facilitate a decision on whether to launch MEOR activities. We also provide an update on relevant literature for experienced MEOR researchers and oilfield operators. Microbiologists will learn about basic principles of interface physics needed to study the impact of microorganisms living on oil droplets. Last but not least, students and technicians trying to understand

  4. Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

    Science.gov (United States)

    Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

    2016-11-01

    Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

  5. Numerical and experimental characterization of solid-state micropore-based cytometer for detection and enumeration of biological cells.

    Science.gov (United States)

    Guo, Jinhong; Chen, Liang; Ai, Ye; Cheng, Yuanbing; Li, Chang Ming; Kang, Yuejun; Wang, Zhiming

    2015-03-01

    Portable diagnostic devices have emerged as important tools in various biomedical applications since they can provide an effective solution for low-cost and rapid clinical diagnosis. In this paper, we present a micropore-based resistive cytometer for the detection and enumeration of biological cells. The proposed device was fabricated on a silicon wafer by a standard microelectromechanical system processing technology, which enables a mass production of the proposed chip. The working principle of this cytometer is based upon a bias potential modulated pulse, originating from the biological particle's physical blockage of the micropore. Polystyrene particles of different sizes (7, 10, and 16 μm) were used to test and calibrate the proposed device. A finite element simulation was developed to predict the bias potential modulated pulse (peak amplitude vs. pulse bandwidth), which can provide critical insight into the design of this microfluidic flow cytometer. Furthermore, HeLa cells (a type of tumor cell lines) spiked in a suspension of blood cells, including red blood cells and white blood cells, were used to assess the performance for detecting and counting tumor cells. The proposed microfluidic flow cytometer is able to provide a promising platform to address the current unmet need for point-of-care clinical diagnosis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Enumeration of CD4 and CD8 T-cells in HIV infection in Zimbabwe using a manual immunocytochemical method

    DEFF Research Database (Denmark)

    Gomo, E; Ndhlovu, P; Vennervald, B J

    2001-01-01

    OBJECTIVES: To enumerate CD4 and CD8 T-cells using the simple and cheap immuno-alkaline phosphatase (IA) method and to compare it with flow cytometry (FC); and to study the effects of duration of sample storage on the IA method results. DESIGN: Method comparison study. SETTING: Blair Research...... Laboratory, Harare, Zimbabwe. SUBJECTS: 41 HIV positive and 11 HIV negative men and women from Harare participating in HIV studies at Blair Research Laboratory, Zimbabwe. MAIN OUTCOME MEASURES: CD4 and CD8 T-cell counts by FC and the IA method. RESULTS: The IA method and FC were highly correlated for CD4...... counts (Spearman rs = 0.91), CD4 percentage (rs = 0.84), CD8 count (rs = 0.83), CD8 percentage (rs = 0.96) and CD4/CD8 ratio (rs = 0.89). However, CD4 cell counts and percentage measured by the IA method were (mean difference +/- SE) 133 +/- 24 cells/microL [corrected] and 6.7 +/- 1.1% higher than those...

  7. Enumeration and identification of gram negative bacteria present in soil underlying urban waste-sites in southwestern Nigeria.

    Science.gov (United States)

    Achudume, A C; Olawale, J T

    2010-09-01

    Samples of soils underlying wastes were collected from four sites representing four demographic regions of a medium sized town in southwestern Nigeria. Standard methods and reference strains of isolated bacteria were employed for identification. Evaluation of the enzymatic and biochemical reactions showed that all isolated and identified microbes were non-fermenting heterotrophic (HTB). For example, Klebsiella pnemuniae may be involved in wound infections, particularly following bowel surgery. Similarly Pseudomonas aeruginosa can produce serious nosocomial infections if it gains access to the body through wounds or intravenous lines. From the 15 culure plates, 88 colonies with various characteristics were enumerated. They differed in aspect of viscosity and color. The bacterial species were identified by percent positive reactions while oxidative and sugar fermentation tests revealed various characteristics among the isolated strains. All of the isolates were negative for citrate utilization, gelatin liquefaction, nitrate reduction, methyl red and Voges Proskaur, motility and hydrogen sulphate production. The quantity of HTB present in an area serves as an index of the general sanitary conditions of that area. The presence of a large number of HTB, in an ecological area may be considered a liability as it can enhance the spread of diseases and on a larger scale may enable epidemics to arise. Therefore, there is need for control of waste sites by recovery and regular germicidal sanitation.

  8. Subseafloor Microbial Life in Venting Fluids from the Mid Cayman Rise Hydrothermal System

    Science.gov (United States)

    Huber, J. A.; Reveillaud, J.; Reddington, E.; McDermott, J. M.; Sylva, S. P.; Breier, J. A.; German, C. R.; Seewald, J.

    2012-12-01

    In hard rock seafloor environments, fluids emanating from hydrothermal vents are one of the best windows into the subseafloor and its resident microbial community. The functional consequences of an extensive population of microbes living in the subseafloor remains unknown, as does our understanding of how these organisms interact with one another and influence the biogeochemistry of the oceans. Here we report the abundance, activity, and diversity of microbes in venting fluids collected from two newly discovered deep-sea hydrothermal vents along the ultra-slow spreading Mid-Cayman Rise (MCR). Fluids for geochemical and microbial analysis were collected from the Von Damm and Piccard vent fields, which are located within 20 km of one another, yet have extremely different thermal, geological, and depth regimes. Geochemical data indicates that both fields are highly enriched in volatiles, in particular hydrogen and methane, important energy sources for and by-products of microbial metabolism. At both sites, total microbial cell counts in the fluids ranged in concentration from 5 x 10 4 to 3 x 10 5 cells ml-1 , with background seawater concentrations of 1-2 x 10 4 cells ml-1 . In addition, distinct cell morphologies and clusters of cells not visible in background seawater were seen, including large filaments and mineral particles colonized by microbial cells. These results indicate local enrichments of microbial communities in the venting fluids, distinct from background populations, and are consistent with previous enumerations of microbial cells in venting fluids. Stable isotope tracing experiments were used to detect utilization of acetate, formate, and dissolve inorganic carbon and generation of methane at 70 °C under anaerobic conditions. At Von Damm, a putatively ultra-mafic hosted site located at ~2200 m with a maximum temperature of 226 °C, stable isotope tracing experiments indicate methanogenesis is occurring in most fluid samples. No activity was detected

  9. Improvement of phosphorus availability by microbial phytase in broilers and pigs

    NARCIS (Netherlands)

    Simons, P.C.M.; Versteegh, H.A.J.; Jongbloed, A.W.; Kemme, P.A.; Slump, P.; Bos, K.D.; Wolters, M.G.E.; Beudeker, R.F.; Verschoor, G.J.

    2005-01-01

    Techniques have been developed to produce microbial phytase for addition to diets for simple-stomached animals, with the aim to improve phosphorus availability from phytate-P in plant sources. The activityof the crude microbial phytase showed pH optima at pH 5-5 and 2·5. The enzyme was able to

  10. Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-Locked Lakes of Schirmacher Oasis and the Perennially Ice-Covered Lake Untersee in East Antarctica

    Science.gov (United States)

    Huang, Jonathan; Hoover, Richard B.; Swain, Ashit; Murdock, Chris; Bej, Asim K.

    2010-01-01

    Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

  11. Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

    Science.gov (United States)

    Robador, Alberto; LaRowe, Douglas E.; Finkel, Steven E.; Amend, Jan P.; Nealson, Kenneth H.

    2018-01-01

    Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems. PMID:29449836

  12. Microbial Cell Dynamics Lab (MCDL)

    Data.gov (United States)

    Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

  13. Microbial products II

    Energy Technology Data Exchange (ETDEWEB)

    Pape, H; Rehm, H J [eds.

    1986-01-01

    The present volume deals mainly with compounds which have been detected as natural microbial products. Part 1 of this volume introduces the general aspects of the overproduction of metabolites and the concepts and genetics of secondary metabolism. Compounds such as nucleosides, nucleotides, coenzymes, vitamins and lipids are dealt with in part 2. Part 3 then is devoted to products and antibiotics with uses im medicine, veterinary medicine, plant protection and metabolites with antitumor activity. Several secondary metabolites have found uses in human and animal health care. With 244 figs., 109 tabs.

  14. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Directory of Open Access Journals (Sweden)

    Peter Larsen

    Full Text Available In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm. from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  15. Microbial bebop: creating music from complex dynamics in microbial ecology.

    Science.gov (United States)

    Larsen, Peter; Gilbert, Jack

    2013-01-01

    In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

  16. Microbial processes associated with roots of bulbous rush coated with iron plaques

    Energy Technology Data Exchange (ETDEWEB)

    Kusel, K.; Chabbi, A.; Trinkwalter, T. [University of Bayreuth, Bayreuth (Germany). BITOEK

    2003-11-01

    The objectives of this work were to enumerate the microbes involved in the turnover of iron and organic root exudates in the rhizoplane, to investigate the effect of oxygen and pH on the utilization of these exudates by the rhizobacteria, and to study the ability of the root-colonizing microbiota to reduce sulfate. Enumeration studies done at pH 3 demonstrated that 10{sup 6} Fe(III) reducers and 10{sup 7} Fe(II) oxidizers g (fresh wt root){sup -1} were associated with Juncus roots. When roots were incubated in goethite-containing medium without and with supplemental glucose, Fe(II) was formed at rates approximating 1.1 mmol g (fresh wt root) {sup -1} d{sup -1} and 3.6 mmol g (fresh wt root){sup -1} d{sup -1} under anoxic conditions, respectively. These results suggest that a rapid microbially mediated cycling of iron occurs in the rhizosphere of Juncus roots under changing redox conditions. Most-probable-number estimates of aerobes and anaerobes capable of consuming root exudates at pH 3 were similar in the rhizosphere sediment and in Juncus roots, but numbers of aerobes were significantly higher than those of anaerobes. At pH 3, supplemental organic exudates were primarily subject to aerobic oxidation to CO{sub 2} and not subject to fermentation. However, at pH 4.5, root exudates were also rapidly utilized under anoxic conditions. Root-associated sulfate reduction was not observed at pH 3 to 4.5 but was observed at pH 4.9. The pH increased during all root-incubation studies both under oxic and anoxic conditions. Thus, as result of the microbial turnover of organic root exudates, pH and CO{sub 2} levels might be elevated at the root surface and favor Juncus plants to colonize acidic habitats.

  17. Enumeration and characterization of arsenic-tolerant diazotrophic bacteria in a long-term heavy-metal-contaminated soil

    OpenAIRE

    Oliveira, A.; Pampulha, M.E.; Neto, M.M.; Almeida, A.C.

    2009-01-01

    The abundance of arsenic-tolerant diazotrophic bacteria was compared in a long-term contaminated soil versus a non-contaminated one. In addition, the characterization of tolerant diazotrophic bacteria was carried out. Differences in the number of heterotrophic N2 fixers were found between soils. Contaminated soil showed a decrease in the microbial population size of about 80%, confirming the great sensitivity of this group of soil bacteria to metals. However, quantitat...

  18. Absolute Enumeration of Probiotic Strains Lactobacillus acidophilus NCFM® and Bifidobacterium animalis subsp. lactis Bl-04® via Chip-Based Digital PCR

    Directory of Open Access Journals (Sweden)

    Sarah J. Z. Hansen

    2018-04-01

    Full Text Available The current standard for enumeration of probiotics to obtain colony forming units by plate counts has several drawbacks: long time to results, high variability and the inability to discern between bacterial strains. Accurate probiotic cell counts are important to confirm the delivery of a clinically documented dose for its associated health benefits. A method is described using chip-based digital PCR (cdPCR to enumerate Bifidobacterium animalis subsp. lactis Bl-04 and Lactobacillus acidophilus NCFM both as single strains and in combination. Primers and probes were designed to differentiate the target strains against other strains of the same species using known single copy, genetic differences. The assay was optimized to include propidium monoazide pre-treatment to prevent amplification of DNA associated with dead probiotic cells as well as liberation of DNA from cells with intact membranes using bead beating. The resulting assay was able to successfully enumerate each strain whether alone or in multiplex. The cdPCR method had a 4 and 5% relative standard deviation (RSD for Bl-04 and NCFM, respectively, making it more precise than plate counts with an industry accepted RSD of 15%. cdPCR has the potential to replace traditional plate counts because of its precision, strain specificity and the ability to obtain results in a matter of hours.

  19. Comparative evaluation of direct plating and most probable number for enumeration of low levels of Listeria monocytogenes in naturally contaminated ice cream products.

    Science.gov (United States)

    Chen, Yi; Pouillot, Régis; S Burall, Laurel; Strain, Errol A; Van Doren, Jane M; De Jesus, Antonio J; Laasri, Anna; Wang, Hua; Ali, Laila; Tatavarthy, Aparna; Zhang, Guodong; Hu, Lijun; Day, James; Sheth, Ishani; Kang, Jihun; Sahu, Surasri; Srinivasan, Devayani; Brown, Eric W; Parish, Mickey; Zink, Donald L; Datta, Atin R; Hammack, Thomas S; Macarisin, Dumitru

    2017-01-16

    A precise and accurate method for enumeration of low level of Listeria monocytogenes in foods is critical to a variety of studies. In this study, paired comparison of most probable number (MPN) and direct plating enumeration of L. monocytogenes was conducted on a total of 1730 outbreak-associated ice cream samples that were naturally contaminated with low level of L. monocytogenes. MPN was performed on all 1730 samples. Direct plating was performed on all samples using the RAPID'L.mono (RLM) agar (1600 samples) and agar Listeria Ottaviani and Agosti (ALOA; 130 samples). Probabilistic analysis with Bayesian inference model was used to compare paired direct plating and MPN estimates of L. monocytogenes in ice cream samples because assumptions implicit in ordinary least squares (OLS) linear regression analyses were not met for such a comparison. The probabilistic analysis revealed good agreement between the MPN and direct plating estimates, and this agreement showed that the MPN schemes and direct plating schemes using ALOA or RLM evaluated in the present study were suitable for enumerating low levels of L. monocytogenes in these ice cream samples. The statistical analysis further revealed that OLS linear regression analyses of direct plating and MPN data did introduce bias that incorrectly characterized systematic differences between estimates from the two methods. Published by Elsevier B.V.

  20. Microbial additives in the composting process

    Directory of Open Access Journals (Sweden)

    Noelly de Queiroz Ribeiro

    Full Text Available ABSTRACT Composting is the process of natural degradation of organic matter carried out by environmental microorganisms whose metabolic activities cause the mineralization and partial humification of substances in the pile. This compost can be beneficially applied to the soil as organic fertilizer in horticulture and agriculture. The number of studies involving microbial inoculants has been growing, and they aim to improve processes such as composting. However, the behavior of these inoculants and other microorganisms during the composting process have not yet been described. In this context, this work aimed to investigate the effects of using a microbial inoculum that can improve the composting process and to follow the bacterial population dynamics throughout the process using the high-resolution melt (HRM technique. To do so, we analysed four compost piles inoculated with Bacillus cereus, Bacillus megaterium, B. cereus + B. megaterium and a control with no inoculum. The analyses were carried out using samples collected at different stages of the process (5th to 110th days. The results showed that the bacterial inocula influenced the process of composting, altering the breakdown of cellulose and hemicelluloses and causing alterations to the temperature and nitrogen levels throughout the composting process. The use of a universal primer (rDNA 16S allowed to follow the microbial succession during the process. However, the design of a specific primer is necessary to follow the inoculum throughout the composting process with more accuracy.

  1. Microbial transformation of uranium in wastes

    International Nuclear Information System (INIS)

    Francis, A.J.; Dodge, C.J.; Gillow, J.B.; Cline, J.E.

    1989-01-01

    Contamination of soils, water, and sediments by radionuclides and toxic metals from the disposal of uranium processing wastes is a major national concern. Although much is known about the physico- chemical aspects of U, we have little information on the effects of aerobic and anaerobic microbial activities on the mobilization or immobilization of U and other toxic metals in mixed wastes. In order to understand the mechanisms of microbial transformations of uranium, we examined a contaminated pond sediment and a sludge sample from the uranium processing facility at Y-12 Plant, Oak Ridge, TN. The uranium concentration in the sediment and sludge samples was 923 and 3080 ug/g dry wt, respectively. In addition to U, the sediment and sludge samples contained high levels of toxic metals such as Cd, Cr, Cu, Hg, Pb, Ni, and Zn. The association of uranium with the various mineral fractions of the sediment and sludge was determined by selective chemical extraction techniques. Uranium was associated to varying degrees with the exchangeable carbonate, iron oxide, organic, and inert fractions in both samples. Initial results in samples amended with carbon and nitrogen indicate immobilization of U due to enhanced indigenous microbial activity under anaerobic conditions. 23 refs., 4 figs., 5 tabs

  2. Electron microscopy study of microbial mat in the North Fiji basin hydrothermal vent

    Science.gov (United States)

    Park, H.; Kim, J. W.; Lee, J. W.

    2017-12-01

    Hydrothermal vent systems consisting of hydrothermal vent, hydrothermal sediment and microbial mat are widely spread around the ocean, particularly spreading axis, continental margin and back-arc basin. Scientists have perceived that the hydrothermal systems, which reflect the primeval earth environment, are one of the best places to reveal the origin of life and extensive biogeochemical process of microbe-mineral interaction. In the present study multiline of analytical methods (X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM)) were utilized to investigate the mineralogy/chemistry of microbe-mineral interaction in hydrothermal microbial mat. Microbial mat samples were recovered by Canadian scientific submersible ROPOS on South Pacific North Fiji basin KIOST hydrothermal vent expedition 1602. XRD analysis showed that red-colored microbial mat contains Fe-oxides and Fe-oxyhydroxides. Various morphologies of minerals in the red-colored microbial mat observed by SEM are mainly showed sheath shaped, resembled with Leptothrix microbial structure, stalks shaped, similar with Marioprofundus microbial structure and globule shaped microbial structures. They are also detected with DNA analysis. The cross sectional observation of microbial structures encrusted with Fe-oxide and Fe-oxyhydroxide at a nano scale by Transmission Electron Microscopy (TEM) and Focused Ion Beam (FIB) technique was developed to verify the structural/biogeochemical properties in the microbe-mineral interaction. Systematic nano-scale measurements on the biomineralization in the microbial mat leads the understandings of biogeochemical environments around the hydrothermal vent.

  3. Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium.

    Science.gov (United States)

    Teixeira, Catarina; Almeida, C Marisa R; Nunes da Silva, Marta; Bordalo, Adriano A; Mucha, Ana P

    2014-09-15

    Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Diversity and enumeration of halophilic and alkaliphilic bacteria in Spanish-style green table-olive fermentations.

    Science.gov (United States)

    Lucena-Padrós, Helena; Ruiz-Barba, José Luis

    2016-02-01

    The presence and enumeration of halophilic and alkaliphilic bacteria in Spanish-style table-olive fermentations was studied. Twenty 10-tonne fermenters at two large manufacturing companies in Spain, previously studied through both culture dependent and independent (PCR-DGGE) methodologies, were selected. Virtually all this microbiota was isolated during the initial fermentation stage. A total of 203 isolates were obtained and identified based on 16S rRNA gene sequences. They belonged to 13 bacterial species, included in 11 genera. It was noticeable the abundance of halophilic and alkaliphilic lactic acid bacteria (HALAB). These HALAB belonged to the three genera of this group: Alkalibacterium, Marinilactibacillus and Halolactibacillus. Ten bacterial species were isolated for the first time from table olive fermentations, including the genera Amphibacillus, Natronobacillus, Catenococcus and Streptohalobacillus. The isolates were genotyped through RAPD and clustered in a dendrogram where 65 distinct strains were identified. Biodiversity indexes found statistically significant differences between both patios regarding genotype richness, diversity and dominance. However, Jaccard similarity index suggested that the halophilic/alkaliphilic microbiota in both patios was more similar than the overall microbiota at the initial fermentation stage. Thus, up to 7 genotypes of 6 different species were shared, suggesting adaptation of some strains to this fermentation stage. Morisita-Horn similarity index indicated a high level of codominance of the same species in both patios. Halophilic and alkaliphilic bacteria, especially HALAB, appeared to be part of the characteristic microbiota at the initial stage of this table-olive fermentation, and they could contribute to the conditioning of the fermenting brines in readiness for growth of common lactic acid bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Algorithm for complete enumeration based on a stroke graph to solve the supply network configuration and operations scheduling problem

    Directory of Open Access Journals (Sweden)

    Julien Maheut

    2013-07-01

    Full Text Available Purpose: The purpose of this paper is to present an algorithm that solves the supply network configuration and operations scheduling problem in a mass customization company that faces alternative operations for one specific tool machine order in a multiplant context. Design/methodology/approach: To achieve this objective, the supply chain network configuration and operations scheduling problem is presented. A model based on stroke graphs allows the design of an algorithm that enumerates all the feasible solutions. The algorithm considers the arrival of a new customized order proposal which has to be inserted into a scheduled program. A selection function is then used to choose the solutions to be simulated in a specific simulation tool implemented in a Decision Support System. Findings and Originality/value: The algorithm itself proves efficient to find all feasible solutions when alternative operations must be considered. The stroke structure is successfully used to schedule operations when considering more than one manufacturing and supply option in each step. Research limitations/implications: This paper includes only the algorithm structure for a one-by-one, sequenced introduction of new products into the list of units to be manufactured. Therefore, the lotsizing process is done on a lot-per-lot basis. Moreover, the validation analysis is done through a case study and no generalization can be done without risk. Practical implications: The result of this research would help stakeholders to determine all the feasible and practical solutions for their problem. It would also allow to assessing the total costs and delivery times of each solution. Moreover, the Decision Support System proves useful to assess alternative solutions. Originality/value: This research offers a simple algorithm that helps solve the supply network configuration problem and, simultaneously, the scheduling problem by considering alternative operations. The proposed system

  6. The use of income information of census enumeration area as a proxy for the household income in a household survey.

    Science.gov (United States)

    Gomes, Fabio S; Vasconcellos, Mauricio Tl; Anjos, Luiz A

    2009-09-22

    Some of the Census Enumeration Areas' (CEA) information may help planning the sample of population studies but it can also be used for some analyses that require information that is more difficult to obtain at the individual or household level, such as income. This paper verifies if the income information of CEA can be used as a proxy for household income in a household survey. A population-based survey conducted from January to December 2003 obtained data from a probabilistic sample of 1,734 households of Niterói, Rio de Janeiro, Brazil. Uniform semi-association models were adjusted in order to obtain information about the agreement/disagreement structure of data. The distribution of nutritional status categories of the population of Niterói according to income quintiles was performed using both CEA- and household-level income measures and then compared using Wald statistics for homogeneity. Body mass index was calculated using body mass and stature data measured in the households and then used to define nutritional status categories according to the World Health Organization. All estimates and statistics were calculated accounting for the structural information of the sample design and a significance level lower than 5% was adopted. The classification of households in the quintiles of household income was associated with the classification of these households in the quintiles of CEA income. The distribution of the nutritional status categories in all income quintiles did not differ significantly according to the source of income information (household or CEA) used in the definition of quintiles. The structure of agreement/disagreement between quintiles of the household's monthly per capita income and quintiles of the head-of-household's mean nominal monthly income of the CEA, as well as the results produced by these measures when they were associated with the nutritional status of the population, showed that the CEA's income information can be used when income

  7. An improved automated procedure for informal and temporary dwellings detection and enumeration, using mathematical morphology operators on VHR satellite data

    Science.gov (United States)

    Jenerowicz, Małgorzata; Kemper, Thomas

    2016-10-01

    Every year thousands of people are displaced by conflicts or natural disasters and often gather in large camps. Knowing how many people have been gathered is crucial for an efficient relief operation. However, it is often difficult to collect exact information on the total number of the population. This paper presents the improved morphological methodology for the estimation of dwellings structures located in several Internally Displaced Persons (IDPs) Camps, based on Very High Resolution (VHR) multispectral satellite imagery with pixel sizes of 1 meter or less including GeoEye-1, WorldView-2, QuickBird-2, Ikonos-2, Pléiades-A and Pléiades-B. The main topic of this paper is the approach enhancement with selection of feature extraction algorithm, the improvement and automation of pre-processing and results verification. For the informal and temporary dwellings extraction purpose the high quality of data has to be ensured. The pre-processing has been extended by including the input data hierarchy level assignment and data fusion method selection and evaluation. The feature extraction algorithm follows the procedure presented in Jenerowicz, M., Kemper, T., 2011. Optical data are analysed in a cyclic approach comprising image segmentation, geometrical, textural and spectral class modeling aiming at camp area identification. The successive steps of morphological processing have been combined in a one stand-alone application for automatic dwellings detection and enumeration. Actively implemented, these approaches can provide a reliable and consistent results, independent of the imaging satellite type and different study sites location, providing decision support in emergency response for the humanitarian community like United Nations, European Union and Non-Governmental relief organizations.

  8. Microbial ecology of phototrophic biofilms

    NARCIS (Netherlands)

    Roeselers, G.

    2007-01-01

    Biofilms are layered structures of microbial cells and an extracellular matrix of polymeric substances, associated with surfaces and interfaces. Biofilms trap nutrients for growth of the enclosed microbial community and help prevent detachment of cells from surfaces in flowing systems. Phototrophic

  9. Microbial transformation of Isopimpinellin by Glomerella cingulata.

    Science.gov (United States)

    Marumoto, Shinsuke; Miyazawa, Mitsuo

    2011-01-01

    Microbial transformation studies conducted on isopimpinellin (1) by the fungus Glomerella cingulata have revealed that 1 was metabolized to give the corresponding reduced acid, 5,8-dimethoxy-6,7-furano-hydrocoumaric acid (2). The structure of metabolite 2 was elucidated by high-resolution mass spectrometry (HR-MS), extensive NMR techniques, including (1)H NMR, (13)C NMR, (1)H-(1)H correlation spectroscopy (COSY), heteronuclear multiple quantum coherence (HMQC) and heteonuclear multiple bond coherence (HMBC). The biotransformed product 2 showed weak a in vitro β-secretase (BACE1) inhibitory effect.

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

    African Journals Online (AJOL)

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

  11. Microbial causes of endodontic flare-ups.

    Science.gov (United States)

    Siqueira, Jose F

    2003-07-01

    Inter-appointment flare-up is characterized by the development of pain, swelling or both, following endodontic intervention. The causative factors of flare-ups encompass mechanical, chemical and/or microbial injury to the pulp or periradicular tissues. Of these factors, microorganisms are arguably the major causative agents of flare-ups. Even though the host is usually unable to eliminate the root canal infection, mobilization and further concentration of defence components at the periradicular tissues impede spreading of infection, and a balance between microbial aggression and host defences is commonly achieved. There are some situations during endodontic therapy in which such a balance may be disrupted in favour of microbial aggression, and an acute periradicular inflammation can ensue. Situations include apical extrusion of infected debris, changes in the root canal microbiota and/or in environmental conditions caused by incomplete chemo-mechanical preparation, secondary intraradicular infections and perhaps the increase in the oxidation-reduction potential within the root canal favouring the overgrowth of the facultative bacteria. Based on these situations, preventive measures against infective flare-ups are proposed, including selection of instrumentation techniques that extrude lesser amounts of debris apically; completion of the chemo-mechanical procedures in a single visit; use of an antimicrobial intracanal medicament between appointments in the treatment of infected cases; not leaving teeth open for drainage and maintenance of the aseptic chain throughout endodontic treatment. Knowledge about the microbial causes of flare-ups and adoption of appropriate preventive measures can significantly reduce the incidence of this highly distressing and undesirable clinical phenomenon.

  12. Hydrodynamics of microbial filter feeding

    DEFF Research Database (Denmark)

    Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia

    2017-01-01

    Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate......-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude......; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet...

  13. Microbial corrosion of metallic materials in a deep nuclear-waste repository

    Directory of Open Access Journals (Sweden)

    Stoulil J.

    2016-06-01

    Full Text Available The study summarises current knowledge on microbial corrosion in a deep nuclear-waste repository. The first part evaluates the general impact of microbial activity on corrosion mechanisms. Especially, the impact of microbial metabolism on the environment and the impact of biofilms on the surface of structure materials were evaluated. The next part focuses on microbial corrosion in a deep nuclear-waste repository. The study aims to suggest the development of the repository environment and in that respect the viability of bacteria, depending on the probable conditions of the environment, such as humidity of bentonite, pressure in compact bentonite, the impact of ionizing radiation, etc. The last part is aimed at possible techniques for microbial corrosion mechanism monitoring in the conditions of a deep repository. Namely, electrochemical and microscopic techniques were discussed.

  14. Enumeration Verification System (EVS)

    Data.gov (United States)

    Social Security Administration — EVS is a batch application that processes for federal, state, local and foreign government agencies, private companies and internal SSA customers and systems. Each...

  15. Oligarchies: Naming, Enumerating Counting

    Directory of Open Access Journals (Sweden)

    Jacques Derrida

    2010-01-01

    Full Text Available The following text is the first chapter of Jacques Derrida’s book Politiques de l’amitié [The Politics of Friendship], being the exemplary and standard case of deconstruction, in this particular case, of philosophical texts (Cicero, Plato and, notably, Aristotle. The starting point for the discussion is the performative contradiction inscribed in the wellknown fragment On friendship from Essays by Michel de Montaigne: “O mes amis, il n’y a nul amy” (O my friends, there is no friend. Apparently, everything here is well-known and obvious, even the very notion of friendship, but as we proceed in the argument provided by Derrida, the obvious becomes less obvious to us and takes on new shades and hues in meaning, acquires new values. What is objective mixes in this fascinating argument with what is subjective. What is friendship? What is friendship today? Is friendship limited to just private sphere of interpersonal relations? The answer to the latter question is, according to Derrida, clearly negative. In the course of his argument he states: “There is no democracy without a community of friends”. This argument provides clues to understand a particular archeology of the notion, revealing oblique senses and contexts of the word “friendship”, its istory shown from the antiquity to the present day.

  16. Microbial Activity and Silica Degradation in Rice Straw

    Science.gov (United States)

    Kim, Esther Jin-kyung

    Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity

  17. Polyphenol and Microbial Profile of On-farm Cocoa Beans Fermented with Selected Microbial Consortia

    Directory of Open Access Journals (Sweden)

    Tochukwu Vincent Balogu

    2017-09-01

    Full Text Available Background and Objective: Quality and preference of cocoa as raw material for various mcocoa products primarily depend on fermentation techniques that modulate the resultant flavour and the phytochemical properties. This study investigated the combined effect of selected microbial consortia and bioreactors on phytochemical profiles of fermented cocoa beans.Material and Methods: Three microbial consortia labeled as Treatments (T-1, T-2, T-3 were used as starter culture (≈105cells ml-1 for on-farm cocoa fermentation on three chambers (basket, woodbox, and plastic for 7 days. These novel consortia were T-1, Staphylococcus spp + Pseudomonas spp+ Bacillus spp, T-2, Staphylococcus spp + Pseudomonas spp +L. lactis, and T-3, Bacillus spp+ Lactobacillus spp + Saccharomyces spp+ Torulopsis spp.Results and Conclusion: The microbial profile were significantly (P≤0.05 altered by all treatments (T-1, T-2, T-3 and microbial frequency was enhanced by 5 -22.5%. T-3 and T-1 significantly altered phenolic content in basket chamber. Tannin was significantly (p≤0.05 varied by T-1(basket, plastic, wood box and T-2(plastic. Tannin: polyphenol conversion ratio adopted as fermented cocoa bean quality benchmark was significantly enhanced by T-1 (basket, woodbox and T-2 (plastic, but was significantly suppressed by T-3 (basket. This study evidently concluded that the appropriate synergy of microbial flora and fermenting chambers could achieve good cocoa quality with low polyphenol content (best for cocoa beverages or high polyphenol content (best for pharmaceutical, confectionery and nutraceutical industries. These findings would avail an economic alternative to the expensive polyphenol reconstitution of cocoa butter used for various industrial products, thereby maximizing economic benefits for both cocoa farmers and industrialists.Conflict of interest: The authors declare no conflict of interest.

  18. Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

    Science.gov (United States)

    Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

    2015-12-01

    Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

  19. New microbial growth factor

    Science.gov (United States)

    Bok, S. H.; Casida, L. E., Jr.

    1977-01-01

    A screening procedure was used to isolate from soil a Penicillium sp., two bacterial isolates, and a Streptomyces sp. that produced a previously unknown microbial growth factor. This factor was an absolute growth requirement for three soil bacteria. The Penicillium sp. and one of the bacteria requiring the factor, an Arthrobacter sp., were selected for more extensive study concerning the production and characteristics of the growth factor. It did not seem to be related to the siderochromes. It was not present in soil extract, rumen fluid, or any other medium component tested. It appears to be a glycoprotein of high molecular weight and has high specific activity. When added to the diets for a meadow-vole mammalian test system, it caused an increased consumption of diet without a concurrent increase in rate of weight gain.

  20. The maturing of microbial ecology.

    Science.gov (United States)

    Schmidt, Thomas M

    2006-09-01

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

  1. Global microbialization of coral reefs.

    Science.gov (United States)

    Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

    2016-04-25

    Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

  2. Microbial biosensors for environmental monitoring

    Directory of Open Access Journals (Sweden)

    David VOGRINC

    2015-12-01

    Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

  3. Microbial electrode sensor for alcohols

    Energy Technology Data Exchange (ETDEWEB)

    Hikuma, M [Ajinomoto Co., Inc., Kawasaki, Japan; Kubo, T; Yasuda, T; Karube, I; Suzuki, S

    1979-10-01

    A microbial electrode consisting of immobilized microorganisms, a gas permeable Teflon membrane, and an oxygen electrode was prepared for the continuous determination of methyl and ethyl alcohols. Immobilized Trichosporon brassicae was employed for a microbial electrode sensor for ethyl alcohol. When a sample solution containing ethyl alcohol was injected into a microbial electrode system, the current of the electrode decreased markedly with time until a steady state was reached. The response time was within 10 min by the steady state method and within 6 min by the pulse method. A linear relationship was observed between the current decrease and the concentration of ethyl alcohol below 22.5 mg/liter. The current was reproducible within +- 6% of the relative error when a sample solution containing 16.5 mg/liter ethyl alcohol. The standard deviation was 0.5 mg/liter in 40 experiments. The selectivity of the microbial electrode sensor for ethyl alcohol was satisfactory. The microbial electrode sensor was applied to a fermentation broth of yeasts and satisfactory comparative results were obtained (correlation coefficient 0.98). The current output of the microbial electrode sensor was almost constant for more than three weeks and 2100 assays. A microbial electrode sensor using immobilized bacteria for methyl alcohol was also described.

  4. Assessment of the application of an automated electronic milk analyzer for the enumeration of total bacteria in raw goat milk.

    Science.gov (United States)

    Ramsahoi, L; Gao, A; Fabri, M; Odumeru, J A

    2011-07-01

    Automated electronic milk analyzers for rapid enumeration of total bacteria counts (TBC) are widely used for raw milk testing by many analytical laboratories worldwide. In Ontario, Canada, Bactoscan flow cytometry (BsnFC; Foss Electric, Hillerød, Denmark) is the official anchor method for TBC in raw cow milk. Penalties are levied at the BsnFC equivalent level of 50,000 cfu/mL, the standard plate count (SPC) regulatory limit. This study was conducted to assess the BsnFC for TBC in raw goat milk, to determine the mathematical relationship between the SPC and BsnFC methods, and to identify probable reasons for the difference in the SPC:BsnFC equivalents for goat and cow milks. Test procedures were conducted according to International Dairy Federation Bulletin guidelines. Approximately 115 farm bulk tank milk samples per month were tested for inhibitor residues, SPC, BsnFC, psychrotrophic bacteria count, composition (fat, protein, lactose, lactose and other solids, and freezing point), and somatic cell count from March 2009 to February 2010. Data analysis of the results for the samples tested indicated that the BsnFC method would be a good alternative to the SPC method, providing accurate and more precise results with a faster turnaround time. Although a linear regression model showed good correlation and prediction, tests for linearity indicated that the relationship was linear only beyond log 4.1 SPC. The logistic growth curve best modeled the relationship between the SPC and BsnFC for the entire sample population. The BsnFC equivalent to the SPC 50,000 cfu/mL regulatory limit was estimated to be 321,000 individual bacteria count (ibc)/mL. This estimate differs considerably from the BsnFC equivalent for cow milk (121,000 ibc/mL). Because of the low frequency of bulk tank milk pickups at goat farms, 78.5% of the samples had their oldest milking in the tank to be 6.5 to 9.0 d old when tested, compared with the cow milk samples, which had their oldest milking at 4 d

  5. The use of income information of census enumeration area as a proxy for the household income in a household survey

    Directory of Open Access Journals (Sweden)

    Vasconcellos Mauricio TL

    2009-09-01

    Full Text Available Abstract Background Some of the Census Enumeration Areas' (CEA information may help planning the sample of population studies but it can also be used for some analyses that require information that is more difficult to obtain at the individual or household level, such as income. This paper verifies if the income information of CEA can be used as a proxy for household income in a household survey. Methods A population-based survey conducted from January to December 2003 obtained data from a probabilistic sample of 1,734 households of Niterói, Rio de Janeiro, Brazil. Uniform semi-association models were adjusted in order to obtain information about the agreement/disagreement structure of data. The distribution of nutritional status categories of the population of Niterói according to income quintiles was performed using both CEA- and household-level income measures and then compared using Wald statistics for homogeneity. Body mass index was calculated using body mass and stature data measured in the households and then used to define nutritional status categories according to the World Health Organization. All estimates and statistics were calculated accounting for the structural information of the sample design and a significance level lower than 5% was adopted. Results The classification of households in the quintiles of household income was associated with the classification of these households in the quintiles of CEA income. The distribution of the nutritional status categories in all income quintiles did not differ significantly according to the source of income information (household or CEA used in the definition of quintiles. Conclusion The structure of agreement/disagreement between quintiles of the household's monthly per capita income and quintiles of the head-of-household's mean nominal monthly income of the CEA, as well as the results produced by these measures when they were associated with the nutritional status of the population

  6. Deep Subsurface Microbial Communities Shaped by the Chicxulub Impactor

    Science.gov (United States)

    Cockell, C. S.; Coolen, M.; Schaefer, B.; Grice, K.; Gulick, S. P. S.; Morgan, J. V.; Kring, D. A.; Osinski, G.

    2017-12-01

    Fresh core material was obtained by drilling of the Chicxulub impact crater during IODP-ICDP Expedition 364 to assess the present-day biosphere in the crater structure. Cell enumerations through the core show that beneath the post-impact sedimentary rock there is a region of enhanced cell abundance that corresponds to the upper impact suevite layer (Units 1G/2A). We also observed a peak in cell numbers in samples at the bottom of suevite Unit 2C and between the suevitic and grainitoid interface (Unit 3/4). These patterns may reflect preferential movement of fluid and/or availability of nutrients and energy at interfaces. 16S rDNA analysis allows us to rule out contamination of the suevite material since no taxa associated with the drilling mud were observed. Two hundred and fifty microbial enrichments were established using diverse culture media for heterotrophs, autotrophs and chemolithotrophs at temperatures consistent with measured core temperatures. Six yielded growth in the breccia, lower breccia and upper granitoid layer and they affiliated with Acidiphilium, Thermoanaerobacteracea and Desulfohalbiaceae. The latter exhibited visible microbial sulfate-reduction. By contrast, the granitoid material exhibited low cell abundances, most samples were below direct cell detection. DNA extraction revealed pervasive low level contamination by drilling mud taxa, consistent with the highly fractured, high porosity of the impact-shocked granitoids. Few taxa can be attributed to an indigenous biota and no enrichments (at 60 and 70°C) yielded growth. These data show that even with a porosity approximately an order of magnitude greater than most unshocked granites, the uplifted granites have not experienced sufficient fluid flow to establish a significant deep biosphere. Paleosterilisation of the material during impact may have re-set colonisation and the material may have originally been below the depth at which temperatures exceeded the upper temperature limit for life

  7. Microbial quality of agricultural water in Central Florida

    Science.gov (United States)

    Topalcengiz, Zeynal; Strawn, Laura K.

    2017-01-01

    The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR) sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL) from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds). Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci) were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity) measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001). The invA gene (Salmonella) was detected in 26/540 (4.8%) samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%), fliC (51.8%), eaeA (17.4%), rfbE (17.4%), stx-I (32.6%), stx-II (9.4%). While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8%) or STEC (stx-I-32.6%, stx-II-9.4%) was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural surface

  8. Microbial quality of agricultural water in Central Florida.

    Directory of Open Access Journals (Sweden)

    Zeynal Topalcengiz

    Full Text Available The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds. Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001. The invA gene (Salmonella was detected in 26/540 (4.8% samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%, fliC (51.8%, eaeA (17.4%, rfbE (17.4%, stx-I (32.6%, stx-II (9.4%. While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8% or STEC (stx-I-32.6%, stx-II-9.4% was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural

  9. Microbial quality of agricultural water in Central Florida.

    Science.gov (United States)

    Topalcengiz, Zeynal; Strawn, Laura K; Danyluk, Michelle D

    2017-01-01

    The microbial quality of water that comes into the edible portion of produce is believed to directly relate to the safety of produce, and metrics describing indicator organisms are commonly used to ensure safety. The US FDA Produce Safety Rule (PSR) sets very specific microbiological water quality metrics for agricultural water that contacts the harvestable portion of produce. Validation of these metrics for agricultural water is essential for produce safety. Water samples (500 mL) from six agricultural ponds were collected during the 2012/2013 and 2013/2014 growing seasons (46 and 44 samples respectively, 540 from all ponds). Microbial indicator populations (total coliforms, generic Escherichia coli, and enterococci) were enumerated, environmental variables (temperature, pH, conductivity, redox potential, and turbidity) measured, and pathogen presence evaluated by PCR. Salmonella isolates were serotyped and analyzed by pulsed-field gel electrophoresis. Following rain events, coliforms increased up to 4.2 log MPN/100 mL. Populations of coliforms and enterococci ranged from 2 to 8 and 1 to 5 log MPN/100 mL, respectively. Microbial indicators did not correlate with environmental variables, except pH (P<0.0001). The invA gene (Salmonella) was detected in 26/540 (4.8%) samples, in all ponds and growing seasons, and 14 serotypes detected. Six STEC genes were detected in samples: hly (83.3%), fliC (51.8%), eaeA (17.4%), rfbE (17.4%), stx-I (32.6%), stx-II (9.4%). While all ponds met the PSR requirements, at least one virulence gene from Salmonella (invA-4.8%) or STEC (stx-I-32.6%, stx-II-9.4%) was detected in each pond. Water quality for tested agricultural ponds, below recommended standards, did not guarantee the absence of pathogens. Investigating the relationships among physicochemical attributes, environmental factors, indicator microorganisms, and pathogen presence allows researchers to have a greater understanding of contamination risks from agricultural surface

  10. Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

    Science.gov (United States)

    Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

    2013-04-01

    The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to

  11. Probabilistic quantitative microbial risk assessment model of norovirus from wastewater irrigated vegetables in Ghana using genome copies and fecal indicator ratio conversion for estimating exposure dose

    DEFF Research Database (Denmark)

    Owusu-Ansah, Emmanuel de-Graft Johnson; Sampson, Angelina; Amponsah, Samuel K.

    2017-01-01

    physical and environmental factors that might influence the reliability of using indicator organisms in microbial risk assessment. The challenges facing analytical studies on virus enumeration (genome copies or particles) have contributed to the already existing lack of data in QMRA modelling. This study......The need to replace the commonly applied fecal indicator conversions ratio (an assumption of 1:10− 5 virus to fecal indicator organism) in Quantitative Microbial Risk Assessment (QMRA) with models based on quantitative data on the virus of interest has gained prominence due to the different...... attempts to fit a QMRA model to genome copies of norovirus data. The model estimates the risk of norovirus infection from the intake of vegetables irrigated with wastewater from different sources. The results were compared to the results of a corresponding model using the fecal indicator conversion ratio...

  12. The microbial ecology of permafrost

    DEFF Research Database (Denmark)

    Jansson, Janet; Tas, Neslihan

    2014-01-01

    Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

  13. Defining Disturbance for Microbial Ecology.

    Science.gov (United States)

    Plante, Craig J

    2017-08-01

    Disturbance can profoundly modify the structure of natural communities. However, microbial ecologists' concept of "disturbance" has often deviated from conventional practice. Definitions (or implicit usage) have frequently included climate change and other forms of chronic environmental stress, which contradict the macrobiologist's notion of disturbance as a discrete event that removes biomass. Physical constraints and disparate biological characteristics were compared to ask whether disturbances fundamentally differ in microbial and macroorganismal communities. A definition of "disturbance" for microbial ecologists is proposed that distinguishes from "stress" and other competing terms, and that is in accord with definitions accepted by plant and animal ecologists.

  14. Experimental techniques; Techniques experimentales

    Energy Technology Data Exchange (ETDEWEB)

    Roussel-Chomaz, P. [GANIL CNRS/IN2P3, CEA/DSM, 14 - Caen (France)

    2007-07-01

    This lecture presents the experimental techniques, developed in the last 10 or 15 years, in order to perform a new class of experiments with exotic nuclei, where the reactions induced by these nuclei allow to get information on their structure. A brief review of the secondary beams production methods will be given, with some examples of facilities in operation or under project. The important developments performed recently on cryogenic targets will be presented. The different detection systems will be reviewed, both the beam detectors before the targets, and the many kind of detectors necessary to detect all outgoing particles after the reaction: magnetic spectrometer for the heavy fragment, detection systems for the target recoil nucleus, {gamma} detectors. Finally, several typical examples of experiments will be detailed, in order to illustrate the use of each detector either alone, or in coincidence with others. (author)

  15. Possibilities for the detection of microbial life on extrasolar planets.

    Science.gov (United States)

    Knacke, Roger F

    2003-01-01

    We consider possibilities for the remote detection of microbial life on extrasolar planets. The Darwin/Terrestrial Planet Finder (TPF) telescope concepts for observations of terrestrial planets focus on indirect searches for life through the detection of atmospheric gases related to life processes. Direct detection of extraterrestrial life may also be possible through well-designed searches for microbial life forms. Satellites in Earth orbit routinely monitor colonies of terrestrial algae in oceans and lakes by analysis of reflected ocean light in the visible region of the spectrum. These remote sensing techniques suggest strategies for extrasolar searches for signatures of chlorophylls and related photosynthetic compounds associated with life. However, identification of such life-related compounds on extrasolar planets would require observations through strong, interfering absorptions and scattering radiances from the remote atmospheres and landmasses. Techniques for removal of interfering radiances have been extensively developed for remote sensing from Earth orbit. Comparable techniques would have to be developed for extrasolar planet observations also, but doing so would be challenging for a remote planet. Darwin/TPF coronagraph concepts operating in the visible seem to be best suited for searches for extrasolar microbial life forms with instruments that can be projected for the 2010-2020 decades, although resolution and signal-to-noise ratio constraints severely limit detection possibilities on terrestrial-type planets. The generation of telescopes with large apertures and extremely high spatial resolutions that will follow Darwin/TPF could offer striking possibilities for the direct detection of extrasolar microbial life.

  16. Recent developments in nucleic acid based techniques for use in rumen manipulation

    Directory of Open Access Journals (Sweden)

    Christopher McSweeney

    2009-07-01

    Full Text Available Nucleic acid-based techniques which can be used to characterise complex microbial communities without incubation are now being employed regularly in ruminant nutrition studies. Conventional culture-based methods for enumerating rumen microorganisms (bacteria, archaea, protozoa, and fungi have been superseded and are now used mainly to obtain pure isolates of novel organisms and reference strains that are required for the development and validation of the nucleic acid approaches. These reference strains are also essential for physiological studies of the lifestyle of the organisms as well as sources of genomic DNA and RNA that can be analysed for functional gene activity. The foundation of the molecular ecology techniques is 16S/18S rDNA sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The use of this marker gene in assays involving the use of single nucleic acid probes or primer sets is rapidly evolving to high throughput approaches such as microarray analysis and new generation sequencing technologies. While these analyses are very informative for determining the composition of the microbial community and monitoring changes in population size, they can only infer function based on these observations. The focus of nucleic acid research is now shifting to the functional analysis of the ecosystem which involves the measurement of functional genes and their expression in the predominant or specific members of the rumen microbial community. Functional gene studies are less developed than 16S rDNA-based analysis of community structure. Also for gene expression studies there are inherent problems involved in extracting high quality RNA from digesta, and priming cDNA synthesis from bacterial mRNA. This paper reviews nucleic acid based molecular methods which have recently been developed for studying the structure and function of rumen microbial

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  18. Microbial Life of North Pacific Oceanic Crust

    Science.gov (United States)

    Schumann, G.; Koos, R.; Manz, W.; Reitner, J.

    2003-12-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed reactions that influence the geophysical properties of these environments. Drilling into 45-Ma oceanic basaltic crust in a deepwater environment during ODP Leg 200 provided a promising opportunity to explore the abundance, diversity and activity of micro-organisms. The combined use of culture-independent molecular phylogenetic analyses and enrichment culture techniques is an advantageous approach in investigating subsurface microbial ecosystems. Enrichment culture methods allow the evaluation of potential activities and functions. Microbiological investigations revealed few aerobic cultivable, in part hitherto unknown, micro-organisms in deep submarine sediments and basaltic lava flows. 16S rDNA sequencing of isolates from sediment revealed the next relatives to be members of the genera Halomonas, Pseudomonas, and Lactobacillus. Within the Pseudomonadaceae the closest relative is Acinetobacter sp., which was isolated from a deep subsurface environment. The next phylogenetical relatives within the Halomonadaceae are bacteria typically isolated from Soda lakes, which are considered as model of early life conditions. Interestingly, not only sediment bacteria could be obtained in pure culture. Aerobic strains could also be successfully isolated from the massive tholeiitic basalt layer at a depth of 76.16 mbsf (46 m below the sediment/basement contact). These particular isolates are gram-positive with low G+C content of DNA, phylogenetically affiliated to the phylum Firmicutes. The closest neighbors are e.g. a marine Bacillus isolated from the Gulf of Mexico and a low G+C gram-positive bacterium, which belongs to the microbial flora in the deepest sea mud of the Mariana Trench, isolated from a depth of 10,897 m. Based on the similarity values, the isolates represent hitherto undescribed species of the deep

  19. Application of Sequence-based Methods in Human MicrobialEcology

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-08-29

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  20. Recent advances of microbial breeding via heavy-ion mutagenesis at IMP.

    Science.gov (United States)

    Hu, W; Li, W; Chen, J

    2017-10-01

    Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future. © 2017 The Society for Applied Microbiology.

  1. Enumeration of Salmonids in the Okanogan Basin Using Underwater Video, Performance Period: October 2005 (Project Inception) - 31 December 2006.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Peter N.; Rayton, Michael D.; Nass, Bryan L.; Arterburn, John E.

    2007-06-01

    The Confederated Tribes of the Colville Reservation (Colville Tribes) identified the need for collecting baseline census data on the timing and abundance of adult salmonids in the Okanogan River Basin in order to determine basin and tributary-specific spawner distributions, evaluate the status and trends of natural salmonid production in the basin, document local fish populations, and augment existing fishery data. This report documents the design, installation, operation and evaluation of mainstem and tributary video systems in the Okanogan River Basin. The species-specific data collected by these fish enumeration systems are presented along with an evaluation of the operation of a facility that provides a count of fish using an automated method. Information collected by the Colville Tribes Fish & Wildlife Department, specifically the Okanogan Basin Monitoring and Evaluation Program (OBMEP), is intended to provide a relative abundance indicator for anadromous fish runs migrating past Zosel Dam and is not intended as an absolute census count. Okanogan Basin Monitoring and Evaluation Program collected fish passage data between October 2005 and December 2006. Video counting stations were deployed and data were collected at two locations in the basin: on the mainstem Okanogan River at Zosel Dam near Oroville, Washington, and on Bonaparte Creek, a tributary to the Okanogan River, in the town of Tonasket, Washington. Counts at Zosel Dam between 10 October 2005 and 28 February 2006 are considered partial, pilot year data as they were obtained from the operation of a single video array on the west bank fishway, and covered only a portion of the steelhead migration. A complete description of the apparatus and methodology can be found in 'Fish Enumeration Using Underwater Video Imagery - Operational Protocol' (Nass 2007). At Zosel Dam, totals of 57 and 481 adult Chinook salmon were observed with the video monitoring system in 2005 and 2006, respectively. Run

  2. An automated technique for most-probable-number (MPN) analysis of densities of phagotrophic protists with lux-AB labelled bacteria as growth medium

    DEFF Research Database (Denmark)

    Ekelund, Flemming; Christensen, Søren; Rønn, Regin

    1999-01-01

    An automated modification of the most-probable-number (MPN) technique has been developed for enumeration of phagotrophic protozoa. The method is based on detection of prey depletion in micro titre plates rather than on presence of protozoa. A transconjugant Pseudomonas fluorescens DR54 labelled w...

  3. MICROBIAL MATS - A JOINT VENTURE

    NARCIS (Netherlands)

    VANGEMERDEN, H

    Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and

  4. Microbial production of gaseous hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Hideo

    1987-10-20

    Microbial production of ethylene, isobutane and a saturated gaseous hydrocarbon mixture was described. Microbial ethylene production was studied with Penicillium digitatum IFO 9372 and a novel pathway of the ethylene biosynthesis through alpha-ketoglutarate was proposed. Rhodotorula minuta IFO 1102 was selected for the microbial production of isobutane and the interesting actions of L-leucine and L-phenylalanine for the isobutane production were found. It was finally presented about the microbial production of a saturated gaseous hydrocarbon mixture with Rhizopus japonicus IFO 4758 was described. A gas mixture was produced through a chemical reaction of SH compounds and some cellular component such as squalene under aerobic conditions. (4 figs, 7 tabs, 41 refs)

  5. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  6. Microbial safety of foods

    International Nuclear Information System (INIS)

    Bandekar, J.R.

    2013-01-01

    Despite advances in hygiene, consumer knowledge and food treatment and processing, food-borne diseases have become one of the most widespread public health problems in the world to-day. About two thirds of all outbreaks are traced to microbial contaminated food - one of the most hazardous being Clostridium botulinum, E. coli 0157: H7 and Salmonella. The pathogens can be introduced in the food products anywhere in the food chain and hence it is of prime important to have microbial vigilance in the entire food chain. WHO estimates that food-borne and water-borne diarrhoeal diseases taken together kill about 2.2 million people annually. The infants, children, elderly and immune-compromised people are particularly susceptible to food-borne diseases. Unsafe food causes many acute and life-long diseases, ranging from diarrhoeal diseases to various forms of cancer. A number of factors such as emergence of new food-borne pathogens, development of drug resistance in the pathogens, changing life style, global trade of food etc. are responsible for the continued persistence of food-borne diseases. Due to consumer demand, a number of Ready-To-Eat (RTE) minimally processed foods are increasingly marketed. However, there is increased risk of food-borne diseases with these products. The food-borne disease outbreaks due to E. coli O157:H7, Listeria monocytogenes, Salmonella and Campylobacter are responsible for recall of many foods resulting in heavy losses to food industry. The development of multi drug resistant pathogens due to indiscriminate use of antibiotics is also a major problem. Food Technology Division of Bhabha Atomic Research Centre has been working on food-borne bacterial pathogens particularly Salmonella, Campylobacter, Vibrio and Aeromonas species, their prevalence in export quality seafood as well in foods sold in retail market such as poultry, fish, sprouts and salads. These pathogens from Indian foods have been characterized for the presence of virulence genes

  7. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  8. Does availability of physical activity and food outlets differ by race and income? Findings from an enumeration study in a health disparate region.

    Science.gov (United States)

    Hill, Jennie L; Chau, Clarice; Luebbering, Candice R; Kolivras, Korine K; Zoellner, Jamie

    2012-09-06

    Low-income, ethnic/racial minorities and rural populations are at increased risk for obesity and related chronic health conditions when compared to white, urban and higher-socio-economic status (SES) peers. Recent systematic reviews highlight the influence of the built environment on obesity, yet very few of these studies consider rural areas or populations. Utilizing a CBPR process, this study advances community-driven causal models to address obesity by exploring the difference in resources for physical activity and food outlets by block group race and income in a small regional city that anchors a rural health disparate region. To guide this inquiry we hypothesized that lower income and racially diverse block groups would have fewer food outlets, including fewer grocery stores and fewer physical activity outlets. We further hypothesized that walkability, as defined by a computed walkability index, would be lower in the lower income block groups. Using census data and GIS, base maps of the region were created and block groups categorized by income and race. All food outlets and physical activity resources were enumerated and geocoded and a walkability index computed. Analyses included one-way MANOVA and spatial autocorrelation. In total, 49 stores, 160 restaurants and 79 physical activity outlets were enumerated. There were no differences in the number of outlets by block group income or race. Further, spatial analyses suggest that the distribution of outlets is dispersed across all block groups. Under the larger CPBR process, this enumeration study advances the causal models set forth by the community members to address obesity by providing an overview of the food and physical activity environment in this region. This data reflects the food and physical activity resources available to residents in the region and will aid many of the community-academic partners as they pursue intervention strategies targeting obesity.

  9. Does availability of physical activity and food outlets differ by race and income? Findings from an enumeration study in a health disparate region

    Directory of Open Access Journals (Sweden)

    Hill Jennie L

    2012-09-01

    Full Text Available Abstract Background Low-income, ethnic/racial minorities and rural populations are at increased risk for obesity and related chronic health conditions when compared to white, urban and higher-socio-economic status (SES peers. Recent systematic reviews highlight the influence of the built environment on obesity, yet very few of these studies consider rural areas or populations. Utilizing a CBPR process, this study advances community-driven causal models to address obesity by exploring the difference in resources for physical activity and food outlets by block group race and income in a small regional city that anchors a rural health disparate region. To guide this inquiry we hypothesized that lower income and racially diverse block groups would have fewer food outlets, including fewer grocery stores and fewer physical activity outlets. We further hypothesized that walkability, as defined by a computed walkability index, would be lower in the lower income block groups. Methods Using census data and GIS, base maps of the region were created and block groups categorized by income and race. All food outlets and physical activity resources were enumerated and geocoded and a walkability index computed. Analyses included one-way MANOVA and spatial autocorrelation. Results In total, 49 stores, 160 restaurants and 79 physical activity outlets were enumerated. There were no differences in the number of outlets by block group income or race. Further, spatial analyses suggest that the distribution of outlets is dispersed across all block groups. Conclusions Under the larger CPBR process, this enumeration study advances the causal models set forth by the community members to address obesity by providing an overview of the food and physical activity environment in this region. This data reflects the food and physical activity resources available to residents in the region and will aid many of the community-academic partners as they pursue intervention

  10. Microbial genomes: Blueprints for life

    Energy Technology Data Exchange (ETDEWEB)

    Relman, David A.; Strauss, Evelyn

    2000-12-31

    Complete microbial genome sequences hold the promise of profound new insights into microbial pathogenesis, evolution, diagnostics, and therapeutics. From these insights will come a new foundation for understanding the evolution of single-celled life, as well as the evolution of more complex life forms. This report is an in-depth analysis of scientific issues that provides recommendations and will be widely disseminated to the scientific community, federal agencies, industry and the public.

  11. Chronic alcoholism and microbial keratitis.

    OpenAIRE

    Ormerod, L. D.; Gomez, D. S.; Schanzlin, D. J.; Smith, R. E.

    1988-01-01

    In a series of 227 consecutive, non-referred patients with microbial keratitis an analysis of the accumulated hospital records showed that one-third were associated with chronic alcoholism. The diagnosis of alcoholism was usually unsuspected on admission to hospital. The microbial pathogenesis in these patients was distinctive; coagulase-negative staphylococci, alpha- and beta-streptococci, moraxellae, enteric Gram-negative bacilli, and polymicrobial infections were unusually prominent. Pseud...

  12. Development of a rapid approach for the enumeration of Escherichia coli in riverbed sediment: case study, the Apies River, South Africa

    CSIR Research Space (South Africa)

    Abia

    2015-12-01

    Full Text Available stream_source_info Abia_2015_ABSTRACT.pdf.txt stream_content_type text/plain stream_size 3292 Content-Encoding UTF-8 stream_name Abia_2015_ABSTRACT.pdf.txt Content-Type text/plain; charset=UTF-8 Journal of Soils... and Sediments Development of a rapid approach for the enumeration of Escherichia coli in riverbed sediment: case study, the Apies River, South Africa L. K. A. Abia: M. N. B. Momba Department of Environmental, Water and Earth Science, Tshwane University...

  13. A collaborative study on a Nordic standard protocol for detection and enumeration of thermotolerant Campylobacter in food (NMKL 119, 3. Ed., 2007)

    DEFF Research Database (Denmark)

    Rosenquist, Hanne; Bengtsson, Anja; Hansen, Tina Beck

    2007-01-01

    A Nordic standard protocol for detection and enumeration of thermotolerant Campylobacter in food has been elaborated (NMKL 119, 3. Ed., 2007). Performance and precision characteristics of this protocol were evaluated in a collaborative study with participation of 14 laboratories from seven European...... jejuni (SLV-542). Expected concentrations (95% C.I.) (cfu g(-1) or ml(-1)) of both strains in matrices were 0.6-1.4 and 23-60 for qualitative detection, and 0.6-1.4; 23-60; and 420-1200 for semi-quantitative detection. For quantitative determination, the expected concentrations of C. jejuni/C. coli were...

  14. Enumeration of Salmonellae in Table Eggs, Pasteurized Egg Products, and Egg-Containing Dishes by Using Quantitative Real-Time PCR

    DEFF Research Database (Denmark)

    Jakočiūnė, Džiuginta; Pasquali, Frédérique; da Silva, Cristiana Soares

    2014-01-01

    PCR) was employed for enumeration of salmonellae in different matrices: table eggs, pasteurized egg products, and egg-containing dishes. Salmonella enterica serovar Enteritidis and S. enterica serovar Tennessee were used to artificially contaminate these matrices. The results showed a linear regression between...... the numbers of salmonellae and the quantification cycle (Cq) values for all matrices used, with the exception of pasteurized egg white. Standard curves were constructed by using both stationary-phase cells and heat-stressed cells, with similar results. Finally, this method was used to evaluate the fate...

  15. In-Drift Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  16. In-Drift Microbial Communities

    International Nuclear Information System (INIS)

    Jolley, D.

    2000-01-01

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses

  17. Microbial production of biovanillin

    Directory of Open Access Journals (Sweden)

    A. Converti

    2010-10-01

    Full Text Available This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium.

  18. Microbial production of biovanillin.

    Science.gov (United States)

    Converti, A; Aliakbarian, B; Domínguez, J M; Bustos Vázquez, G; Perego, P

    2010-07-01

    This review aims at providing an overview on the microbial production of vanillin, a new alternative method for the production of this important flavor of the food industry, which has the potential to become economically competitive in the next future. After a brief description of the applications of vanillin in different industrial sectors and of its physicochemical properties, we described the traditional ways of providing vanillin, specifically extraction and chemical synthesis (mainly oxidation) and compared them with the new biotechnological options, i.e., biotransformations of caffeic acid, veratraldehyde and mainly ferulic acid. In the second part of the review, emphasis has been addressed to the factors most influencing the bioproduction of vanillin, specifically the age of inoculum, pH, temperature, type of co-substrate, as well as the inhibitory effects exerted either by excess substrate or product. The final part of the work summarized the downstream processes and the related unit operations involved in the recovery of vanillin from the bioconversion medium.

  19. Microbial Propionic Acid Production

    Directory of Open Access Journals (Sweden)

    R. Axayacatl Gonzalez-Garcia

    2017-05-01

    Full Text Available Propionic acid (propionate is a commercially valuable carboxylic acid produced through microbial fermentation. Propionic acid is mainly used in the food industry but has recently found applications in the cosmetic, plastics and pharmaceutical industries. Propionate can be produced via various metabolic pathways, which can be classified into three major groups: fermentative pathways, biosynthetic pathways, and amino acid catabolic pathways. The current review provides an in-depth description of the major metabolic routes for propionate production from an energy optimization perspective. Biological propionate production is limited by high downstream purification costs which can be addressed if the target yield, productivity and titre can be achieved. Genome shuffling combined with high throughput omics and metabolic engineering is providing new opportunities, and biological propionate production is likely to enter the market in the not so distant future. In order to realise the full potential of metabolic engineering and heterologous expression, however, a greater understanding of metabolic capabilities of the native producers, the fittest producers, is required.

  20. Handbook of software quality assurance techniques applicable to the nuclear industry

    Energy Technology Data Exchange (ETDEWEB)

    Bryant, J.L.; Wilburn, N.P.

    1987-08-01

    Pacific Northwest Laboratory is conducting a research project to recommend good engineering practices in the application of 10 CFR 50, Appendix B requirements to assure quality in the development and use of computer software for the design and operation of nuclear power plants for NRC and industry. This handbook defines the content of a software quality assurance program by enumerating the techniques applicable. Definitions, descriptions, and references where further information may be obtained are provided for each topic.

  1. Handbook of software quality assurance techniques applicable to the nuclear industry

    International Nuclear Information System (INIS)

    Bryant, J.L.; Wilburn, N.P.

    1987-08-01

    Pacific Northwest Laboratory is conducting a research project to recommend good engineering practices in the application of 10 CFR 50, Appendix B requirements to assure quality in the development and use of computer software for the design and operation of nuclear power plants for NRC and industry. This handbook defines the content of a software quality assurance program by enumerating the techniques applicable. Definitions, descriptions, and references where further information may be obtained are provided for each topic

  2. Brine treatment, smoking and storage techniques: their effects on the ...

    African Journals Online (AJOL)

    Journal of Food Technology in Africa ... Brine treatment, smoking and storage techniques: their effects on the microbial quality of smoked mackerel. ... off odour development, softening of the fish and positively affected personal preference.

  3. Characteristics and fates of soluble microbial products in ceramic membrane bioreactor at various sludge retention times.

    Science.gov (United States)

    Shin, Hang-Sik; Kang, Seok-Tae

    2003-01-01

    The formation and fate of soluble microbial products (SMP) in membrane bioreactor (MBR) was investigated at various sludge retention times (SRT) for 170 days. The SMP concentration was estimated by feeding glucose, which could be completely degraded, and by measuring the dissolved organic carbon (DOC) of the effluent from MBR. Under the conditions of SRT of 20 days, influent DOC of 112 mg/l and HRT of 6 h, the produced SMP was 4.7 mg DOC/l of which 57% was removed or retained by the membrane. DOC of MBR supernatant increased during 100 days and then gradually decreased. Specific UV absorbance showed that the accumulated compounds had a portion of larger, more aromatic, more hydrophobic and double-bond-rich organics, which originated from the decayed biomass. Molecular weight distributions of SMP in MBR supernatant showed that the acclimated microorganisms in a long SRT could decompose high molecular weight organics, it caused the shift of molecular weight distributions of SMP to a lower range. During the operation period, enumeration of active cells in the MBR showed that microbial inhibitions by accumulated SMP was not observed.

  4. Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

    Science.gov (United States)

    Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

    2017-02-01

    Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Biostimulation of Iron Reduction and Uranium Immobilization: Microbial and Mineralogical Controls

    International Nuclear Information System (INIS)

    Joel E. Kostka

    2008-01-01

    This project represented a joint effort between Florida State University (FSU), Rutgers University (RU), and the University of Illinois (U of I). FSU served as the lead institution and Dr. J.E. Kostka was responsible for project coordination, integration, and deliverables. This project was designed to elucidate the microbial ecology and geochemistry of metal reduction in subsurface environments at the U.S. DOE-NABIR Field Research Center at Oak Ridge, Tennessee (ORFRC). Our objectives were to: (1) characterize the dominant iron minerals and related geochemical parameters likely to limit U(VI) speciation, (2) directly quantify reaction rates and pathways of microbial respiration (terminal-electron-accepting) processes which control subsurface sediment chemistry, and (3) identify and enumerate the organisms mediating U(VI) transformation. A total of 31 publications and 47 seminars or meeting presentations were completed under this project. One M.S. thesis (by Nadia North) and a Ph.D. dissertation (by Lainie Petrie-Edwards) were completed at FSU during fall of 2003 and spring of 2005, respectively. Ph.D. students, Denise Akob and Thomas Gihring have continued the student involvement in this research since fall of 2004. All of the above FSU graduate students were heavily involved in the research, as evidenced by their regular attendance at PI meetings and ORFRC workshops

  6. [Characterization and microbial community shifts of rice strawdegrading microbial consortia].

    Science.gov (United States)

    Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

    2016-12-04

    To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

  7. Microbial analysis of meatballs cooled with vacuum and conventional cooling.

    Science.gov (United States)

    Ozturk, Hande Mutlu; Ozturk, Harun Kemal; Koçar, Gunnur

    2017-08-01

    Vacuum cooling is a rapid evaporative cooling technique and can be used for pre-cooling of leafy vegetables, mushroom, bakery, fishery, sauces, cooked food, meat and particulate foods. The aim of this study was to apply the vacuum cooling and the conventional cooling techniques for the cooling of the meatball and to show the vacuum pressure effect on the cooling time, the temperature decrease and microbial growth rate. The results of the vacuum cooling and the conventional cooling (cooling in the refrigerator) were compared with each other for different temperatures. The study shows that the conventional cooling was much slower than the vacuum cooling. Moreover, the microbial growth rate of the vacuum cooling was extremely low compared with the conventional cooling. Thus, the lowest microbial growth occurred at 0.7 kPa and the highest microbial growth was observed at 1.5 kPa for the vacuum cooling. The mass loss ratio for the conventional cooling and vacuum cooling was about 5 and 9% respectively.

  8. Biotechnological Aspects of Microbial Extracellular Electron Transfer

    Science.gov (United States)

    Kato, Souichiro

    2015-01-01

    Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

  9. Hydrodynamics of microbial filter feeding.

    Science.gov (United States)

    Nielsen, Lasse Tor; Asadzadeh, Seyed Saeed; Dölger, Julia; Walther, Jens H; Kiørboe, Thomas; Andersen, Anders

    2017-08-29

    Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis , and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

  10. Studies on potential effects of fumaric acid on rumen microbial fermentation, methane production and microbial community.

    Science.gov (United States)

    Riede, Susanne; Boguhn, Jeannette; Breves, Gerhard

    2013-01-01

    The greenhouse gas methane (CH4) contributes substantially to global climate change. As a potential approach to decrease ruminal methanogenesis, the effects of different dosages of fumaric acid (FA) on ruminal microbial metabolism and on the microbial community (archaea, bacteria) were studied using a rumen simulation technique (RUSITEC). FA acts as alternative hydrogen acceptor diverting 2H from methanogenesis of archaea towards propionate formation of bacteria. Three identical trials were conducted with 12 fermentation vessels over a period of 14 days. In each trial, four fermentation vessels were assigned to one of the three treatment groups differing in FA dosage: low fumaric acid (LFA), high fumaric acid (HFA) and without FA (control). FA was continuously infused with the buffer. Grass silage and concentrate served as substrate. FA led to decreases in pH and to higher production rates of total short chain fatty acids (SCFA) mediated by increases in propionate for LFA of 1.69 mmol d(-1) and in propionate and acetate production for HFA of 4.49 and 1.10 mmol d(-1), respectively. Concentrations of NH3-N, microbial crude protein synthesis, their efficiency, degradation of crude nutrients and detergent fibre fraction were unchanged. Total gas and CH4 production were not affected by FA. Effects of FA on structure of microbial community by means of single strand conformation polymorphism (SSCP) analyses could not be detected. Given the observed increase in propionate production and the unaffected CH4 production it can be supposed that the availability of reduction equivalents like 2H was not limited by the addition of FA in this study. It has to be concluded from the present study that the application of FA is not an appropriate approach to decrease the ruminal CH4 production.

  11. Effects of co-composting of lincomycin mycelia dregs with furfural slag on lincomycin degradation, maturity and microbial communities.

    Science.gov (United States)

    Ren, Shengtao; Guo, Xiali; Lu, Aqian; Guo, Xiaoying; Wang, Yan; Sun, Guoping; Guo, Weiwei; Ren, Chaobin; Wang, Lianzhong

    2018-05-26

    This paper investigated the effect of co-composting of lincomycin mycelia dregs (LMDs) with furfural slag on the degradation of lincomycin, maturity and microbial communities. Results showed that after 66 days composting, the concentration of lincomycin was removed above 99%. The final pH, C/N and germination index (GI) all met the national standards in maturity. Enumeration of total cultivable microbes showed the composting process was not inhibited by the addition of LMDs. Microbial diversity suggested that co-composting was beneficial to increase the abundance and diversity of bacterial communities for LMDs' treatment. Canonical correlation analysis (CCA) indicated the bacteria communities were strongly affected by residual lincomycin, with lincomycin reduced greatly, microbial communities of T and CK became similar at the end of composting. The potential bacteria to degrade lincomycin were Anaerococcus, Peptostreptococcus, and Lactobacillus. Based on these results, this research indicated that the co-composting was a feasible treatment for LMDs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Solving binary-state multi-objective reliability redundancy allocation series-parallel problem using efficient epsilon-constraint, multi-start partial bound enumeration algorithm, and DEA

    International Nuclear Information System (INIS)

    Khalili-Damghani, Kaveh; Amiri, Maghsoud

    2012-01-01

    In this paper, a procedure based on efficient epsilon-constraint method and data envelopment analysis (DEA) is proposed for solving binary-state multi-objective reliability redundancy allocation series-parallel problem (MORAP). In first module, a set of qualified non-dominated solutions on Pareto front of binary-state MORAP is generated using an efficient epsilon-constraint method. In order to test the quality of generated non-dominated solutions in this module, a multi-start partial bound enumeration algorithm is also proposed for MORAP. The performance of both procedures is compared using different metrics on well-known benchmark instance. The statistical analysis represents that not only the proposed efficient epsilon-constraint method outperform the multi-start partial bound enumeration algorithm but also it improves the founded upper bound of benchmark instance. Then, in second module, a DEA model is supplied to prune the generated non-dominated solutions of efficient epsilon-constraint method. This helps reduction of non-dominated solutions in a systematic manner and eases the decision making process for practical implementations. - Highlights: ► A procedure based on efficient epsilon-constraint method and DEA was proposed for solving MORAP. ► The performance of proposed procedure was compared with a multi-start PBEA. ► Methods were statistically compared using multi-objective metrics.

  13. Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

    International Nuclear Information System (INIS)

    Teixeira, Catarina; Almeida, C. Marisa R.; Nunes da Silva, Marta; Bordalo, Adriano A.; Mucha, Ana P.

    2014-01-01

    Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed

  14. Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Teixeira, Catarina [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Almeida, C. Marisa R.; Nunes da Silva, Marta [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Bordalo, Adriano A. [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Mucha, Ana P., E-mail: amucha@ciimar.up.pt [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal)

    2014-09-15

    Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed.

  15. Do swimming goggles limit microbial contamination of contact lenses?

    Science.gov (United States)

    Wu, Yvonne T; Tran, Jess; Truong, Michelle; Harmis, Najat; Zhu, Hua; Stapleton, Fiona

    2011-04-01

    Wearing goggles over contact lenses while swimming is often recommended by eye care professionals. Limited data are available to assess this recommendation. The purpose of this study was to examine whether wearing goggles while swimming limits bacterial colonization on contact lenses and whether the type of lens worn affects contamination rates. Twenty-three subjects underwent two swimming sessions at an ocean (salt water) pool (Maroubra beach Rock Pool, Sydney, Australia). Silicone hydrogel (Ciba Focus Night and Day) or hydrogel lenses (Ciba Focus Daily) were inserted into subjects' eyes before 30 min of swimming sessions, and subjects used modified goggles to mimic goggled and non-goggled conditions. At the end of each session, lenses were collected for microbial investigation. Viable bacterial colonies were classified as gram positive and gram negative and enumerated. The level of bacterial colonization on contact lenses between goggled and non-goggled conditions and between the two lens materials were compared. The range of colony forming units recovered from goggled lenses were 0 to 930 compared with 0 to 1210 on non-goggled lenses. The majority of subjects (16/23) had more microorganisms in the non-goggled condition than when wearing goggles (p = 0.03). Gram negative organisms were found in three non-goggled lenses. No significant difference was shown in the number of bacteria isolated from silicone hydrogel and hydrogel lenses (p > 0.6) irrespective of wearing goggles. Water samples had consistently higher numbers of bacterial counts than those adhered to the lenses; however, no association was found between the number of bacteria in the water sample and those found on the contact lenses. Consistently, fewer bacterial colonies were found on the goggled contact lens, thus suggesting goggles offer some protection against bacterial colonization of contact lenses while swimming. These data would support the recommendation encouraging lens wearers to use goggles

  16. MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

    Directory of Open Access Journals (Sweden)

    T. P. Pirog

    2015-08-01

    Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

  17. Microbial species delineation using whole genome sequences.

    Science.gov (United States)

    Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

    2015-08-18

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Exogenous lactobacilli mitigate microbial changes associated with grain fermentation (corn, oats, and wheat) by equine fecal microflora ex vivo.

    Science.gov (United States)

    Harlow, Brittany E; Lawrence, Laurie M; Harris, Patricia A; Aiken, Glen E; Flythe, Michael D

    2017-01-01

    Cereal grains are often included in equine diets. When starch intake exceeds foregut digestion starch will reach the hindgut, impacting microbial ecology. Probiotics (e.g., lactobacilli) are reported to mitigate GI dysbioses in other species. This study was conducted to determine the effect of exogenous lactobacilli on pH and the growth of amylolytic and lactate-utilizing bacteria. Feces were collected from 3 mature geldings fed grass hay with access to pasture. Fecal microbes were harvested by differential centrifugation, washed, and re-suspended in anaerobic media containing ground corn, wheat, or oats at 1.6% (w/v) starch and one of five treatments: Control (substrate only), L. acidophilus, L. buchneri, L. reuteri, or an equal mixture of all three (107 cells/mL, final concentration). After 24 h of incubation (37°C, 160 rpm), samples were collected for pH and enumerations of total amylolytics, Group D Gram-positive cocci (GPC; Enterococci, Streptococci), lactobacilli, and lactate-utilizing bacteria. Enumeration data were log transformed prior to ANOVA (SAS, v. 9.3). Lactobacilli inhibited pH decline in corn and wheat fermentations (P Exogenous lactobacilli decreased amylolytics, while increasing lactate-utilizers in corn and wheat fermentations (P Exogenous lactobacilli decreased the initial (first 8 h) rate of starch catalysis when wheat was the substrate, but did not decrease total (24 h) starch utilization in any case. These results indicate that exogenous lactobacilli can impact the microbial community and pH of cereal grain fermentations by equine fecal microflora ex vivo. Additionally, dead (autoclaved) exogenous lactobacilli had similar effects as live lactobacilli on fermentation. This latter result indicates that the mechanism by which lactobacilli impact other amylolytic bacteria is not simple resource competition.

  19. Microbial O2 consumption in the Aespoe tunnel

    International Nuclear Information System (INIS)

    Kotelnikova, S.; Pedersen, Karsten

    1998-04-01

    The report presents data on microbial O 2 reduction activities by microorganisms obtained with different techniques: Winkler method, gas chromatography, most probable numbering, enrichment technique, inhibitor analysis and radiotracer measurements. The samples were collected from boreholes and open funnel ponds at Aespoe in 1996-1998. The evaluation of the microbial activities in open ponds predicts the future microbial activities after the O 2 intrusion around the future repository. The metabolic potential of the microbial population inhabiting groundwater was evaluated on the basis of electron donors available and microbial 16S rRNA gene diversity. The contribution of different microbial groups to the O 2 reduction was elucidated using specific inhibitors selectively affecting different microbial groups. Our experiments show that microbial O 2 reduction occurs in deep groundwater. Carbon dioxide was produced concurrently with O 2 reduction confirming the biogenic nature of the reduction. The populations developed O 2 reduction rates and capacity depending on the initial concentration of dissolved O 2 reduction. Rates of O 2 reduction ranged from 0.32 to 4.5 μM/day. Depending on temperature and the type of groundwater the approximate time needed for consumption of 500 μM of dissolved O 2 ranged from 0.31 to 3.99 years. After approximately a 2 weeks period the microbial population in vitro was able to consume O 2 both at 30 deg C and 60 deg C. At 16 deg C no delay in O 2 consumption was observed. Our results demonstrated that methanotrophs survive in deep groundwater and that they were induced by O 2 . Some bacteria use Hg or CH 4 as electron donor instead of organic matter, which means that microbial O 2 reduction will occur also in deep groundwaters where the availability of organic carbon is limited. Specific CH 4 oxidation rates ranged between 3.00 and 220 nM CH 4 per litre per day. Comparison of the total O 2 reducing activities by gas chromatography and

  20. Microbial O{sub 2} consumption in the Aespoe tunnel

    Energy Technology Data Exchange (ETDEWEB)

    Kotelnikova, S.; Pedersen, Karsten [Goeteborg Univ. (Sweden). Dept. of Cell and Molecular Biology, Microbiology

    1998-04-01

    The report presents data on microbial O{sub 2} reduction activities by microorganisms obtained with different techniques: Winkler method, gas chromatography, most probable numbering, enrichment technique, inhibitor analysis and radiotracer measurements. The samples were collected from boreholes and open funnel ponds at Aespoe in 1996-1998. The evaluation of the microbial activities in open ponds predicts the future microbial activities after the O{sub 2} intrusion around the future repository. The metabolic potential of the microbial population inhabiting groundwater was evaluated on the basis of electron donors available and microbial 16S rRNA gene diversity. The contribution of different microbial groups to the O{sub 2} reduction was elucidated using specific inhibitors selectively affecting different microbial groups. Our experiments show that microbial O{sub 2} reduction occurs in deep groundwater. Carbon dioxide was produced concurrently with O{sub 2} reduction confirming the biogenic nature of the reduction. The populations developed O{sub 2} reduction rates and capacity depending on the initial concentration of dissolved O{sub 2} reduction. Rates of O{sub 2} reduction ranged from 0.32 to 4.5 {mu}M/day. Depending on temperature and the type of groundwater the approximate time needed for consumption of 500 {mu}M of dissolved O{sub 2} ranged from 0.31 to 3.99 years. After approximately a 2 weeks period the microbial population in vitro was able to consume O{sub 2} both at 30 deg C and 60 deg C. At 16 deg C no delay in O{sub 2} consumption was observed. Our results demonstrated that methanotrophs survive in deep groundwater and that they were induced by O{sub 2}. Some bacteria use Hg or CH{sub 4} as electron donor instead of organic matter, which means that microbial O{sub 2} reduction will occur also in deep groundwaters where the availability of organic carbon is limited. Specific CH{sub 4} oxidation rates ranged between 3.00 and 220 nM CH{sub 4} per litre per

  1. Rumen microbial changes in cattle fed diets with or without salinomycin.

    Science.gov (United States)

    Olumeyan, D B; Nagaraja, T G; Miller, G W; Frey, R A; Boyer, J E

    1986-02-01

    Four rumen-fistulated steers, randomly assigned to two groups (control and salinomycin fed) were used to monitor the changes in rumen microbial populations and volatile fatty acids (VFA) concentrations associated with feeding salinomycin (0.22 mg X kg-1 X day-1). Steers were adapted to an alfalfa hay and grain (80:20) diet before supplementing the diet with salinomycin, and then the diet was changed to 50:50 and 20:80 ratios of alfalfa hay to grain at 2-week intervals. Rumen samples for total and selective enumeration of anaerobic bacteria. VFA analysis, and enumeration of protozoa were collected during the 80:20 alfalfa hay-to-grain diet before salinomycin feeding, and during the 80:20, 50:50, and 20:80 hay-to-grain diets with salinomycin. At each sampling period, rumen samples were collected at 3 h after feeding on three consecutive days. Salinomycin feeding had no effect on rumen pH and total VFA concentration. The acetate-to-propionate ratio was significantly lower in salinomycin-fed steers than in the control. The molar proportion of butyrate increased in both control and salinomycin-fed steers. Total anaerobic bacterial counts were lower in salinomycin-fed steers than in the control steers after 8 weeks of salinomycin feeding. Salinomycin-resistant bacteria increased from 7.6 to 15.6% in salinomycin-fed steers but remained unchanged in control steers. Salinomycin had no effect on cellulolytic and lactate-utilizing bacteria, but the proportion of amylolytic bacteria was higher in salinomycin-fed steers than in control steers. The total number of protozoa decreased initially in salinomycin-fed steers. The initial reduction was due to reduced numbers of Entodinium species. Holotrichs were unaffected by salinomycin feeding.

  2. Microbial biomass carbon and enzyme activities of urban soils in Beijing.

    Science.gov (United States)

    Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

    2011-07-01

    To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.

  3. Impact of electrokinetic remediation on microbial communities within PCP contaminated soil

    International Nuclear Information System (INIS)

    Lear, G.; Harbottle, M.J.; Sills, G.; Knowles, C.J.; Semple, K.T.; Thompson, I.P.

    2007-01-01

    Electrokinetic techniques have been used to stimulate the removal of organic pollutants within soil, by directing contaminant migration to where remediation may be more easily achieved. The effect of this and other physical remediation techniques on the health of soil microbial communities has been poorly studied and indeed, largely ignored. This study reports the impact on soil microbial communities during the application of an electric field within ex situ laboratory soil microcosms contaminated with pentachlorophenol (PCP; 100 mg kg -1 oven dry soil). Electrokinetics reduced counts of culturable bacteria and fungi, soil microbial respiration and carbon substrate utilisation, especially close to the acidic anode where PCP accumulated (36 d), perhaps exacerbated by the greater toxicity of PCP at lower soil pH. There is little doubt that a better awareness of the interactions between soil electrokinetic processes and microbial communities is key to improving the efficacy and sustainability of this remediation strategy. - Electrokinetics negatively impacted soil

  4. What is microbial community ecology?

    Science.gov (United States)

    Konopka, Allan

    2009-11-01

    The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

  5. Microbial processes in coastal pollution

    International Nuclear Information System (INIS)

    Capone, D.G.; Bauer, J.E.

    1992-01-01

    In this chapter, the authors describe the nature and range of some of the interactions that can occur between the microbiota and environmental contaminants in coastal areas. The implications of such interactions are also discussed. Pollutant types include inorganic nutrients, heavy metals, bulk organics, organic contaminants, pathogenic microorganisms and microbial pollutants. Both the effects of pollutants such as petroleum hydrocarbons on natural microbial populations and the mitigation of contaminant effects by complexation and biodegradation are considered. Finally, several areas of emerging concerns are presented that involve a confluence of biogeochemistry, microbial ecology and applied and public health microbiology. These concerns range in relevance from local/regional to oceanic/global scales. 308 ref

  6. Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

    Science.gov (United States)

    De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

    2009-02-01

    Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to

  7. Strength and stability of microbial plugs in porous media

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, A.K. [NIPER/BDM-Oklahoma, Inc., Bartlesville, OK (United States); Sharma, M.M.; Georgiou, G. [Univ. of Texas, Austin, TX (United States)

    1995-12-31

    Mobility reduction induced by the growth and metabolism of bacteria in high-permeability layers of heterogeneous reservoirs is an economically attractive technique to improve sweep efficiency. This paper describes an experimental study conducted in sandpacks using an injected bacterium to investigate the strength and stability of microbial plugs in porous media. Successful convective transport of bacteria is important for achieving sufficient initial bacteria distribution. The chemotactic and diffusive fluxes are probably not significant even under static conditions. Mobility reduction depends upon the initial cell concentrations and increase in cell mass. For single or multiple static or dynamic growth techniques, permeability reduction was approximately 70% of the original permeability. The stability of these microbial plugs to increases in pressure gradient and changes in cell physiology in a nutrient-depleted environment needs to be improved.

  8. Soil microbial activities and its relationship with soil chemical ...

    African Journals Online (AJOL)

    The fields assessed are organically managed Soils (OMS), Inorganically Managed Soils (IMS) and an Uncultivated Land having grass coverage (ULS). Soil Microbial Respiration (SMR), Microbial Biomass Carbon (MBC), Microbial Biomass Nitrogen (MBN) and Microbial Biomass Phosphorus (MBP) were analyzed.

  9. Advanced Microscopy of Microbial Cells

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

    2011-01-01

    Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...... microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

  10. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  11. Microbial activity in the terrestrial subsurface

    International Nuclear Information System (INIS)

    Kaiser, J.P.; Bollag, J.M.

    1990-01-01

    Little is known about the layers under the earth's crust. Only in recent years have techniques for sampling the deeper subsurface been developed to permit investigation of the subsurface environment. Prevailing conditions in the subsurface habitat such as nutrient availability, soil composition, redox potential, permeability and a variety of other factors can influence the microflora that flourish in a given environment. Microbial diversity varies between geological formations, but in general sandy soils support growth better than soils rich in clay. Bacteria predominate in subsurface sediments, while eukaryotes constitute only 1-2% of the microorganisms. Recent investigations revealed that most uncontaminated subsurface soils support the growth of aerobic heteroorganotrophic bacteria, but obviously anaerobic microorganisms also exist in the deeper subsurface habitat. The microorganisms residing below the surface of the earth are capable of degrading both natural and xenobiotic contaminants and can thereby adapt to growth under polluted conditions. (author) 4 tabs, 77 refs

  12. Solving Microbial Spoilage Problems in Processed Foods

    Science.gov (United States)

    Clavero, Rocelle

    This chapter surveys common microbial food spoilage processes. The chapter is organized by food products and includes sections addressing spoilage in meat, poultry, fish; dairy products (milk, butter, cheese); beverage products; bakery products; canned foods; fruit and confectionery products; and emulsions. It addresses the isolation and identification of spoilage organisms and provides several case studies as examples. It introduces various organisms responsible for spoilage including Gram-positive lactic acid bacteria, Gram-negative aerobic bacteria, yeasts, molds, and fungal contaminants. Throughout the chapter, attention is given to when, where, and how spoilage organisms enter the food processing chain. Troubleshooting techniques are suggested. The effect (or lack of effect) of heating, dehydration, pH change, cooling, and sealing on various organisms is explained throughout. The chapter contains four tables that connect specific organisms to various spoilage manifestations in a variety of food products.

  13. Microbial Heat Recovery Cell (MHRC) System Concept

    Energy Technology Data Exchange (ETDEWEB)

    None

    2017-09-01

    This factsheet describes a project that aimed to develop a microbial heat recovery cell (MHRC) system that combines a microbial reverse electrodialysis technology with waste heat recovery to convert industrial effluents into electricity and hydrogen.

  14. Microbial quality of a marine tidal pool

    CSIR Research Space (South Africa)

    Genthe, Bettina

    1995-01-01

    Full Text Available In this study the source of microbial pollution to a tidal pool was investigated. Both adjacent seawater which could contribute to possible faecal pollution and potential direct bather pollution were studied. The microbial quality of the marine...

  15. Marine Microbial Systems Ecology: Microbial Networks in the Sea

    NARCIS (Netherlands)

    Muijzer, G.; Stal, L.J.; Cretoiu, M.S.

    2016-01-01

    Next-generation sequencing of DNA has revolutionized microbial ecology. Using this technology, it became for the first time possible to analyze hundreds of samples simultaneously and in great detail. 16S rRNA amplicon sequencing, metagenomics and metatranscriptomics became available to determine the

  16. Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

    Science.gov (United States)

    Hyde, A.; Joye, S. B.; Teske, A.

    2017-12-01

    Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

  17. Microbial populations in an agronomically managed mollisol treated with simulated acid rain

    International Nuclear Information System (INIS)

    Miller, K.W.; Cole, M.A.; Banwart, W.L.

    1991-01-01

    A fertile well-buffered mollisol (Flanagan silt loam, fine montmorillonitic mesic Aquic Arguidoll) under cultivation with corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] was subjected to simulated rain of pH 5.6, 4.2, and 3.0, while moisture-activated rain exclusion shelters provided protection from ambient rain. Soil was sampled to a depth of 3 cm on four dates throughout the 1985 growing season. The following microorganisms were enumerated by plate counts or most probable number: general heterotrophic bacteria, general soil fungi, free-living N-fixing bacteria, fluorescent pseudomonads, autotrophic ammonium-oxidizing, nitrite-oxidizing, and thio-sulfate-oxidizing bacteria. The ANOVA was used to determine the combined and individual effects of rain treatments, crop field, and sampling date. Crop field and sampling date affected microbial numbers more than rain treatments. Overall, rain treatment effects were limited to nitrite-oxidizing bacteria; lower numbers occurred in the corn field in subplots treated with rain of pH 4.2 and 3.0, and in the soybean field treated with rain of pH 3.0. The trend was strongest in June and July. In the corn field in subplots treated with rain of pH 3.0, numbers of thiosulfate-oxidizing bacteria were higher an numbers of general heterotrophic bacteria were lower; however, these trends were comparatively weak. Rain treatments caused essentially no decrease in soil pH, suggesting that acid rain constituents affect certain microbial populations without causing overt changes in pH. Because they appear to be unusually sensitive, nitrite-oxidizing bacteria could be used as experimental indicators of changes in soil microbial communities subjected to acid rain

  18. Microbial contamination of contact lenses, lens care solutions, and their accessories: a literature review.

    Science.gov (United States)

    Szczotka-Flynn, Loretta B; Pearlman, Eric; Ghannoum, Mahmoud

    2010-03-01

    A contact lens (CL) can act as a vector for microorganisms to adhere to and transfer to the ocular surface. Commensal microorganisms that uneventfully cohabitate on lid margins and conjunctivae and potential pathogens that are found transiently on the ocular surface can inoculate CLs in vivo. In the presence of reduced tissue resistance, these resident microorganisms or transient pathogens can invade and colonize the cornea or conjunctiva to produce inflammation or infection. The literature was reviewed and used to summarize the findings over the last 30 years on the identification, enumeration, and classification of microorganisms adherent to CLs and their accessories during the course of normal wear and to hypothesize the role that these microorganisms play in CL infection and inflammation. Lens handling greatly increases the incidence of lens contamination, and the ocular surface has a tremendous ability to destroy organisms. However, even when removed aseptically from the eye, more than half of lenses are found to harbor microorganisms, almost exclusively bacteria. Coagulase-negative Staphylococci are most commonly cultured from worn lenses; however, approximately 10% of lenses harbor Gram-negative and highly pathogenic species, even in asymptomatic subjects. In storage cases, the incidence of positive microbial bioburden is also typically greater than 50%. All types of care solutions can become contaminated, including up to 30% of preserved products. The process of CL-related microbial keratitis and inflammation is thought to be preceded by the presence or transfer or both of microorganisms from the lens to the ocular surface. Thus, this detailed understanding of lens-related bioburden is important in the understanding of factors associated with infectious and inflammatory complications. Promising mechanisms to prevent bacterial colonization on lenses and lens cases are forthcoming, which may decrease the incidence of microbially driven CL complications.

  19. Effect of different salt adaptation strategies on the microbial diversity, activity, and settling of nitrifying sludge in sequencing batch reactors

    NARCIS (Netherlands)

    Bassin, J.P.; Kleerebezem, R.; Muyzer, G.; Rosado, A.S.; Van Loosdrecht, M.C.M.; Dezotti, M.

    2011-01-01

    The effect of salinity on the activity of nitrifying bacteria, floc characteristics, and microbial community structure accessed by fluorescent in situ hybridization and polymerase chain reaction–denaturing gradient gel electrophoresis techniques was investigated. Two sequencing batch reactors (SRB1

  20. Phenotypic properties and microbial diversity of methanogenic granules from a full-scale UASB reactor treating brewery wastewater

    NARCIS (Netherlands)

    Diaz, E.E.; Stams, A.J.M.; Amils, R.; Sanz, J.L.

    2006-01-01

    Methanogenic granules from an anaerobic bioreactor that treated wastewater of a beer brewery consisted of different morphological types of granules. In this study, the microbial compositions of the different granules were analyzed by molecular microbiological techniques: cloning, denaturing gradient

  1. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    NARCIS (Netherlands)

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

  2. Dismantling techniques

    International Nuclear Information System (INIS)

    Wiese, E.

    1998-01-01

    Most of the dismantling techniques used in a Decontamination and Dismantlement (D and D) project are taken from conventional demolition practices. Some modifications to the techniques are made to limit exposure to the workers or to lessen the spread of contamination to the work area. When working on a D and D project, it is best to keep the dismantling techniques and tools as simple as possible. The workers will be more efficient and safer using techniques that are familiar to them. Prior experience with the technique or use of mock-ups is the best way to keep workers safe and to keep the project on schedule

  3. Dismantling techniques

    Energy Technology Data Exchange (ETDEWEB)

    Wiese, E.

    1998-03-13

    Most of the dismantling techniques used in a Decontamination and Dismantlement (D and D) project are taken from conventional demolition practices. Some modifications to the techniques are made to limit exposure to the workers or to lessen the spread of contamination to the work area. When working on a D and D project, it is best to keep the dismantling techniques and tools as simple as possible. The workers will be more efficient and safer using techniques that are familiar to them. Prior experience with the technique or use of mock-ups is the best way to keep workers safe and to keep the project on schedule.

  4. Comparison of the quantitative dry culture methods with both conventional media and most probable number method for the enumeration of coliforms and Escherichia coli/coliforms in food.

    Science.gov (United States)

    Teramura, H; Sota, K; Iwasaki, M; Ogihara, H

    2017-07-01

    Sanita-kun™ CC (coliform count) and EC (Escherichia coli/coliform count), sheet quantitative culture systems which can avoid chromogenic interference by lactase in food, were evaluated in comparison with conventional methods for these bacteria. Based on the results of inclusivity and exclusivity studies using 77 micro-organisms, sensitivity and specificity of both Sanita-kun™ met the criteria for ISO 16140. Both media were compared with deoxycholate agar, violet red bile agar, Merck Chromocult™ coliform agar (CCA), 3M Petrifilm™ CC and EC (PEC) and 3-tube MPN, as reference methods, in 100 naturally contaminated food samples. The correlation coefficients of both Sanita-kun™ for coliform detection were more than 0·95 for all comparisons. For E. coli detection, Sanita-kun™ EC was compared with CCA, PEC and MPN in 100 artificially contaminated food samples. The correlation coefficients for E. coli detection of Sanita-kun™ EC were more than 0·95 for all comparisons. There were no significant differences in all comparisons when conducting a one-way analysis of variance (anova). Both Sanita-kun™ significantly inhibited colour interference by lactase when inhibition of enzymatic staining was assessed using 40 natural cheese samples spiked with coliform. Our results demonstrated Sanita-kun™ CC and EC are suitable alternatives for the enumeration of coliforms and E. coli/coliforms, respectively, in a variety of foods, and specifically in fermented foods. Current chromogenic media for coliforms and Escherichia coli/coliforms have enzymatic coloration due to breaking down of chromogenic substrates by food lactase. The novel sheet culture media which have film layer to avoid coloration by food lactase have been developed for enumeration of coliforms and E. coli/coliforms respectively. In this study, we demonstrated these media had comparable performance with reference methods and less interference by food lactase. These media have a possibility not only

  5. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

    Science.gov (United States)

    Rashid, Mamoon; Stingl, Ulrich

    2015-12-01

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

    KAUST Repository

    Rashid, Mamoon; Stingl, Ulrich

    2015-01-01

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70–80% of microbial diversity – recently called the “microbial dark matter” – remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

  7. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

    KAUST Repository

    Rashid, Mamoon

    2015-09-25

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70–80% of microbial diversity – recently called the “microbial dark matter” – remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

  8. Microbial incorporation of nitrogen in stream detritus

    Science.gov (United States)

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

    2001-01-01

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

  9. Results on Parity-Check Matrices With Optimal Stopping And/Or Dead-End Set Enumerators

    NARCIS (Netherlands)

    Weber, J.H.; Abdel-Ghaffar, K.A.S.

    2008-01-01

    The performance of iterative decoding techniques for linear block codes correcting erasures depends very much on the sizes of the stopping sets associated with the underlying Tanner graph, or, equivalently, the parity-check matrix representing the code. In this correspondence, we introduce the

  10. Comparison of multivariate microbial datasets with the Shannon index: An example using enzyme activity from diverse marine environments

    DEFF Research Database (Denmark)

    Steen, Andrew; Ziervogel, K.; Arnosti, C.

    2010-01-01

    Heterotrophic microbial communities contain substantial functional diversity, so studies of community function often generate multivariate data sets. Techniques for data reduction and analysis can help elucidate qualitative differences among sites from multivariate data sets that may be difficult...... of four cases, surface water communities accessed substrates at a more even rate than in deeper waters. The technique could usefully be applied to other types of data obtained in studies of microbial activity and the geochemical effects....

  11. Microbial communities in blueberry soils

    Science.gov (United States)

    Microbial communities thrive in the soil of the plant root zone and it is clear that these communities play a role in plant health. Although blueberry fields can be productive for decades, yields are sometimes below expectations and fields that are replanted sometimes underperform and/or take too lo...

  12. Advanced Microscopy of Microbial Cells

    DEFF Research Database (Denmark)

    Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

    2011-01-01

    microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

  13. Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

    Science.gov (United States)

    Grace, Joseph M.; Verseux, Cyprien; Gentry, Diana; Moffet, Amy; Thayabaran, Ramanen; Wong, Nathan; Rothschild, Lynn

    2013-01-01

    The adaptation of micro-organisms to their environments is a complex process of interaction between the pressures of the environment and of competition. Reducing this multifactorial process to environmental exposure in the laboratory is a common tool for elucidating individual mechanisms of evolution, such as mutation rates. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques. Current methods for controlled study of microbial adaptation limit the length of time, the depth of collected data, and the breadth of applied environmental conditions. Small idiosyncrasies in manual techniques can have large effects on outcomes; for example, there are significant variations in induced radiation resistances following similar repeated exposure protocols. We describe here a project under development to allow rapid cycling of multiple types of microbial environmental exposure. The system allows continuous autonomous monitoring and data collection of both single species and sampled communities, independently and concurrently providing multiple types of controlled environmental pressure (temperature, radiation, chemical presence or absence, and so on) to a microbial community in dynamic response to the ecosystem's current status. When combined with DNA sequencing and extraction, such a controlled environment can cast light on microbial functional development, population dynamics, inter- and intra-species competition, and microbe-environment interaction. The project's goal is to allow rapid, repeatable iteration of studies of both natural and artificial microbial adaptation. As an example, the same system can be used both to increase the pH of a wet soil aliquot over time while periodically sampling it for genetic activity analysis, or to repeatedly expose a culture of bacteria to the presence of a toxic metal, automatically adjusting the level of toxicity based on the

  14. Microbial profiling of dental plaque from mechanically ventilated patients.

    Science.gov (United States)

    Sands, Kirsty M; Twigg, Joshua A; Lewis, Michael A O; Wise, Matt P; Marchesi, Julian R; Smith, Ann; Wilson, Melanie J; Williams, David W

    2016-02-01

    Micro-organisms isolated from the oral cavity may translocate to the lower airways during mechanical ventilation (MV) leading to ventilator-associated pneumonia (VAP). Changes within the dental plaque microbiome during MV have been documented previously, primarily using culture-based techniques. The aim of this study was to use community profiling by high throughput sequencing to comprehensively analyse suggested microbial changes within dental plaque during MV. Bacterial 16S rDNA gene sequences were obtained from 38 samples of dental plaque sampled from 13 mechanically ventilated patients and sequenced using the Illumina platform. Sequences were processed using Mothur, applying a 97% gene similarity cut-off for bacterial species level identifications. A significant 'microbial shift' occurred in the microbial community of dental plaque during MV for nine out of 13 patients. Following extubation, or removal of the endotracheal tube that facilitates ventilation, sampling revealed a decrease in the relative abundance of potential respiratory pathogens and a compositional change towards a more predominantly (in terms of abundance) oral microbiota including Prevotella spp., and streptococci. The results highlight the need to better understand microbial shifts in the oral microbiome in the development of strategies to reduce VAP, and may have implications for the development of other forms of pneumonia such as community-acquired infection.

  15. Effects of microbial inhibitors on anaerobic degradation of DDT

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Y.S.; Chiu, T.C.; Yen, J.H. [National Taiwan Univ., Taipei (Taiwan)

    2004-09-15

    Chlorinated insecticide DDT [1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane] was extensively used for controlling pests in the agricultural field and human-being living environments in the past several decades. Due to the chemical stability, DDT was extremely persistent and recalcitrant in soils and sediments and it was banned by nations. Microorganisms usually play important roles in reducing organochlorine compounds in the environments. Under low-oxygen conditions, microbial dechlorination is thought as the onset of highly chlorinated compounds. Methanogenic and sulfate-reducing bacteria participate in microbial dechlorination under anaerobic condition has been reported. In this study, a mixed anaerobic culture enabling to dechlorinate DDT was obtained from river sediment in Taiwan. In order to understand the effect of these microorganisms on DDT dechlorination, microbial inhibitors BESA (2-bromoethanesulfonate) and molybdate, for inhibiting methanogenic and sulfate-reducing bacteria, respectively, were chosen to investigate the interaction between specific microbial communities and their degradation activities. Besides, a molecular technique, denaturing gradient gel electrophoresis (DGGE), based on analyzing the 16S rDNA of bacteria, was used for monitoring the bacterial community structure in this study.

  16. Enumeration, identification and decontamination of microorganisms on empty fruit bunches (EFB) and palm press fibre (PPF) from selected palm oil mills in the Peninsular Malaysia

    International Nuclear Information System (INIS)

    Foziah Ali; Muhammad Lebai Juri; Mat Rasol Awang

    1998-01-01

    The PPF and EFB temporarily disposed into the environment at the mill are heavily contaminated with micro-organisms, therefore require decontamination prior to utilisation. The current methods for decontaminating PPF and EFB has been briefly reviewed (Mat Rasol et. al.,1987). They suggested that these by-products can be effectively decontaminated by gamma-irradiation and the resulting sterilised by-products could subsequently be used for conversion into animals feeds by fermentation with fungi or chemical stock. The primary objectives of the investigation are: a) to enumerate contaminating microorganisms on PPF and EFB collected from various oil palm mills in the Peninsular Malaysia, and b) to establish the inactivation curves of the PPF and EFB from the selected palm oil mills

  17. Development and application of a new method for specific and sensitive enumeration of spores of nonproteolytic Clostridium botulinum types B, E, and F in foods and food materials.

    Science.gov (United States)

    Peck, Michael W; Plowman, June; Aldus, Clare F; Wyatt, Gary M; Izurieta, Walter Penaloza; Stringer, Sandra C; Barker, Gary C

    2010-10-01

    The highly potent botulinum neurotoxins are responsible for botulism, a severe neuroparalytic disease. Strains of nonproteolytic Clostridium botulinum form neurotoxins of types B, E, and F and are the main hazard associated with minimally heated refrigerated foods. Recent developments in quantitative microbiological risk assessment (QMRA) and food safety objectives (FSO) have made food safety more quantitative and include, as inputs, probability distributions for the contamination of food materials and foods. A new method that combines a selective enrichment culture with multiplex PCR has been developed and validated to enumerate specifically the spores of nonproteolytic C. botulinum. Key features of this new method include the following: (i) it is specific for nonproteolytic C. botulinum (and does not detect proteolytic C. botulinum), (ii) the detection limit has been determined for each food tested (using carefully structured control samples), and (iii) a low detection limit has been achieved by the use of selective enrichment and large test samples. The method has been used to enumerate spores of nonproteolytic C. botulinum in 637 samples of 19 food materials included in pasta-based minimally heated refrigerated foods and in 7 complete foods. A total of 32 samples (5 egg pastas and 27 scallops) contained spores of nonproteolytic C. botulinum type B or F. The majority of samples contained <100 spores/kg, but one sample of scallops contained 444 spores/kg. Nonproteolytic C. botulinum type E was not detected. Importantly, for QMRA and FSO, the construction of probability distributions will enable the frequency of packs containing particular levels of contamination to be determined.

  18. Enumeration of antigen-specific CD8+ T lymphocytes by single-platform, HLA tetramer-based flow cytometry: a European multicenter evaluation.

    Science.gov (United States)

    Heijnen, Ingmar A F M; Barnett, David; Arroz, Maria J; Barry, Simon M; Bonneville, Marc; Brando, Bruno; D'hautcourt, Jean-Luc; Kern, Florian; Tötterman, Thomas H; Marijt, Erik W A; Bossy, David; Preijers, Frank W M B; Rothe, Gregor; Gratama, Jan W

    2004-11-01

    HLA class I peptide tetramers represent powerful diagnostic tools for detection and monitoring of antigen-specific CD8(+) T cells. The impetus for the current multicenter study is the critical need to standardize tetramer flow cytometry if it is to be implemented as a routine diagnostic assay. Hence, the European Working Group on Clinical Cell Analysis set out to develop and evaluate a single-platform tetramer-based method that used cytomegalovirus (CMV) as the antigenic model. Absolute numbers of CMV-specific CD8(+) T cells were obtained by combining the percentage of tetramer-binding cells with the absolute CD8(+) T-cell count. Six send-outs of stabilized blood from healthy individuals or CMV-carrying donors with CMV-specific CD8(+) T-cell counts of 3 to 10 cells/microl were distributed to 7 to 16 clinical sites. These sites were requested to enumerate CD8(+) T cells and, in the case of CMV-positive donors, CMV-specific subsets on three separate occasions using the standard method. Between-site coefficients of variation of less than 10% (absolute CD8(+) T-cell counts) and approximately 30% (percentage and absolute numbers of CMV-specific CD8(+) T cells) were achieved. Within-site coefficients of variation were approximately 5% (absolute CD8(+) T-cell counts), approximately 9% (percentage CMV-specific CD8(+) T cells), and approximately 17% (absolute CMV-specific CD8(+) T-cell counts). The degree of variation tended to correlate inversely with the proportion of CMV-specific CD8(+) T-cell subsets. The single-platform MHC tetramer-based method for antigen-specific CD8(+) T-cell counting has been evaluated by a European group of laboratories and can be considered a reproducible assay for routine enumeration of antigen-specific CD8(+) T cells. (c) 2004 Wiley-Liss, Inc.

  19. Microbial Fe(III) Oxide Reduction in Chocolate Pots Hot Springs, Yellowstone National Park

    Science.gov (United States)

    Fortney, N. W.; Roden, E. E.; Boyd, E. S.; Converse, B. J.

    2014-12-01

    Previous work on dissimilatory iron reduction (DIR) in Yellowstone National Park (YNP) has focused on high temperature, low pH environments where soluble Fe(III) is utilized as an electron acceptor for respiration. Much less attention has been paid to DIR in lower temperature, circumneutral pH environments, where solid phase Fe(III) oxides are the dominant forms of Fe(III). This study explored the potential for DIR in the warm (ca. 40-50°C), circumneutral pH Chocolate Pots hot springs (CP) in YNP. Most probable number (MPN) enumerations and enrichment culture studies confirmed the presence of endogenous microbial communities that reduced native CP Fe(III) oxides. Enrichment cultures demonstrated sustained DIR coupled to acetate and lactate oxidation through repeated transfers over ca. 450 days. Pyrosequencing of 16S rRNA genes indicated that the dominant organisms in the enrichments were closely affiliated with the well known Fe(III) reducer Geobacter metallireducens. Additional taxa included relatives of sulfate reducing bacterial genera Desulfohalobium and Thermodesulfovibrio; however, amendment of enrichments with molybdate, an inhibitor of sulfate reduction, suggested that sulfate reduction was not a primary metabolic pathway involved in DIR in the cultures. A metagenomic analysis of enrichment cultures is underway in anticipation of identifying genes involved in DIR in the less well-characterized dominant organisms. Current studies are aimed at interrogating the in situ microbial community at CP. Core samples were collected along the flow path (Fig. 1) and subdivided into 1 cm depth intervals for geochemical and microbiological analysis. The presence of significant quantities of Fe(II) in the solids indicated that DIR is active in situ. A parallel study investigated in vitro microbial DIR in sediments collected from three of the coring sites. DNA was extracted from samples from both studies for 16S rRNA gene and metagenomic sequencing in order to obtain a

  20. The microbial ferrous wheel in a neutral pH groundwater seep

    Directory of Open Access Journals (Sweden)

    Eric eRoden

    2012-05-01

    Full Text Available Evidence for microbial Fe redox cycling was documented in a circumneutral pH groundwater seep near Bloomington, Indiana. Geochemical and microbiological analyses were conducted at two sites, a semi-consolidated microbial mat and a floating puffball structure. In situ voltammetric microelectrode measurements revealed steep opposing gradients of O2 and Fe(II at both sites, similar to other groundwater seep and sedimentary environments known to support microbial Fe redox cycling. The puffball structure showed an abrupt increase in dissolved Fe(II just at its surface (~ 5 cm depth, suggesting an internal Fe(II source coupled to active Fe(III reduction. MPN enumerations detected microaerophilic Fe(II-oxidizing bacteria (FeOB and dissimilatory Fe(III-reducing bacteria (FeRB at densities of 102-105 cells mL-1 in samples from both sites. In vitro Fe(III reduction experiments revealed the potential for immediate reduction (no lag period of native Fe(III oxides. Conventional full-length 16S rRNA gene clone libraries were compared withhigh throughput barcode sequencing of the V1, V4 or V6 variable regions of 16S rRNA genes in order to evaluate the extent to which new sequencing approaches could provide enhanced insight into the composition of Fe redox cycling microbial community structure. The composition of the clone libraries suggested a lithotroph-dominated microbial community centered around taxa related to known FeOB (e.g. Gallionella, Sideroxydans, Aquabacterium. Sequences related to recognized FeRB (e.g. Rhodoferax, Aeromonas, Geobacter, Desulfovibrio were also well represented. Overall, sequences related to known FeOB and FeRB accounted for 88 and 59% of total clone sequences in the mat and puffball libraries, respectively. Taxa identified in the barcode libraries showed partial overlap with the clone libraries, but were not always consistent across different variable regions and sequencing platforms. However, the barcode libraries provided

  1. Translation Techniques

    OpenAIRE

    Marcia Pinheiro

    2015-01-01

    In this paper, we discuss three translation techniques: literal, cultural, and artistic. Literal translation is a well-known technique, which means that it is quite easy to find sources on the topic. Cultural and artistic translation may be new terms. Whilst cultural translation focuses on matching contexts, artistic translation focuses on matching reactions. Because literal translation matches only words, it is not hard to find situations in which we should not use this technique.  Because a...

  2. Comparison of certain microbial counting methods which are ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-12-15

    Dec 15, 2009 ... tinuous food analyses. For example, the ... plate method for the enumeration of E. coli in foods. How- ... Although its preservation for 48 h is recommended in certain ..... Innovative Fungicide For Leather Industry: Essential Oil of.

  3. Comparison between McMaster and Mini-FLOTAC methods for the enumeration of Eimeria maxima oocysts in poultry excreta.

    Science.gov (United States)

    Bortoluzzi, C; Paras, K L; Applegate, T J; Verocai, G G

    2018-04-30

    Monitoring Eimeria shedding has become more important due to the recent restrictions to the use of antibiotics within the poultry industry. Therefore, there is a need for the implementation of more precise and accurate quantitative diagnostic techniques. The objective of this study was to compare the precision and accuracy between the Mini-FLOTAC and the McMaster techniques for quantitative diagnosis of Eimeria maxima oocyst in poultry. Twelve pools of excreta samples of broiler chickens experimentally infected with E. maxima were analyzed for the comparison between Mini-FLOTAC and McMaster technique using, the detection limits (dl) of 23 and 25, respectively. Additionally, six excreta samples were used to compare the precision of different dl (5, 10, 23, and 46) using the Mini-FLOTAC technique. For precision comparisons, five technical replicates of each sample (five replicate slides on one excreta slurry) were read for calculating the mean oocyst per gram of excreta (OPG) count, standard deviation (SD), coefficient of variation (CV), and precision of both aforementioned comparisons. To compare accuracy between the methods (McMaster, and Mini-FLOTAC dl 5 and 23), excreta from uninfected chickens was spiked with 100, 500, 1,000, 5,000, or 10,000 OPG; additional samples remained unspiked (negative control). For each spiking level, three samples were read in triplicate, totaling nine reads per spiking level per technique. Data were transformed using log10 to obtain normality and homogeneity of variances. A significant correlation (R = 0.74; p = 0.006) was observed between the mean OPG of the McMaster dl 25 and the Mini-FLOTAC dl 23. Mean OPG, CV, SD, and precision were not statistically different between the McMaster dl 25 and Mini-FLOTAC dl 23. Despite the absence of statistical difference (p > 0.05), Mini-FLOTAC dl 5 showed a numerically lower SD and CV than Mini-FLOTAC dl 23. The Pearson correlation coefficient revealed significant and positive

  4. Applications of neutron activation analysis technique

    International Nuclear Information System (INIS)

    Jonah, S. A.

    2000-07-01

    The technique was developed as far back as 1936 by G. Hevesy and H. Levy for the analysis of Dy using an isotopic source. Approximately 40 elements can be analyzed by instrumental neutron activation analysis (INNA) technique with neutrons from a nuclear reactor. By applying radiochemical separation, the number of elements that can be analysed may be increased to almost 70. Compared with other analytical methods used in environmental and industrial research, NAA has some unique features. These are multi-element capability, rapidity, reproducibility of results, complementarity to other methods, freedom from analytical blank and independency of chemical state of elements. There are several types of neutron sources namely: nuclear reactors, accelerator-based and radioisotope-based sources, but nuclear reactors with high fluxes of neutrons from the fission of 235 U give the most intense irradiation, and hence the highest available sensitivities for NAA. In this paper, the applications of NAA of socio-economic importance are discussed. The benefits of using NAA and related nuclear techniques for on-line applications in industrial process control are highlighted. A brief description of the NAA set-ups at CERT is enumerated. Finally, NAA is compared with other leading analytical techniques

  5. Chernozems microbial community under anthropogenic impact (Russia)

    Science.gov (United States)

    Ivashchenko, Kristina; Ananyeva, Nadezhda; Sushko, Sofia; Vasenev, Viacheslav

    2017-04-01

    Chernozems is important natural resource, which in the last decade under intense influence as a result of plowing and urbanization. The parameters of soil microbial community functioning might be identify some soil deterioration under the impacts. Our research was focused on assessment of microbial community status in different soil layers of virgin steppe, bare fallow and urban ecosystems (Kursk region). In each ecosystem, we chose randomly 3-5 spatially distributed sites, where soil samples were collected by auguring up to 0.5 m depth (each layer 10 cm thickness) and up to 1.5 m depth (0-10, 10-50, 50-100, 100-150 cm layers), totally 127 samples. The bulk density was measured for these soil layers. In all soil samples the microbial biomass carbon content (Cmic) was analyzed by substrate-induced respiration (SIR) method and basal respiration (BR) was assessed by CO2 rate production. The fungi-to-bacteria ratio (selective inhibition technique with antibiotics) was determined and portion of Cmic in soil organic carbon (Corg) content was calculated in topsoil (0-10 cm). The Corg (dichromate oxidation) and pHw (potentiometry) values were measured. The Cmic and BR profile pools were calculated using bulk density and thickness of studied layers. The Cmic (0-10 cm) was varied from 84 to 1954 µg C g-1 soil, in steppe it was on average 3-4 times higher than those in bare fallow and urban. The BR rate was amounted from 0.20 to 1.57 µg CO2-C g-1 soil h-1, however no significant difference between studied ecosystems was found. It was shown the relationship between Cmic, BR and Corg (the linear regression, R2=0.92 and 0.75, respectively, pecosystems row: virgin steppe>bare fallow>urban, and it was on average 6.0, 5.2 and 1.8, respectively. The Cmic profile pool (0.5 m) of steppe was reached up on average 206 g C m-2, and it was 2.0 and 2.5 times higher those bare fallow and urban, respectively. The BR profile pool (0.5 m) in steppe and bare fallow was reached up 5.9 and 5

  6. Toward Understanding, Managing, and Protecting Microbial Ecosystems

    Science.gov (United States)

    Bodelier, Paul L. E.

    2011-01-01

    Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

  7. Towards understanding, managing and protecting microbial ecosystems

    Directory of Open Access Journals (Sweden)

    Paul eBodelier

    2011-04-01

    Full Text Available Microbial communities are at the very basis of life on earth, catalysing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper indentifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

  8. Toward understanding, managing, and protecting microbial ecosystems.

    Science.gov (United States)

    Bodelier, Paul L E

    2011-01-01

    Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.

  9. Microbial Metabolism in Serpentinite Fluids

    Science.gov (United States)

    Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

    2013-12-01

    Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

  10. Key Concepts in Microbial Oceanography

    Science.gov (United States)

    Bruno, B. C.; Achilles, K.; Walker, G.; Weersing, K.; Team, A

    2008-12-01

    The Center for Microbial Oceanography: Research and Education (C-MORE) is a multi-institution Science and Technology Center, established by the National Science Foundation in 2006. C-MORE's research mission is to facilitate a more comprehensive understanding of the diverse assemblages of microorganisms in the sea, ranging from the genetic basis of marine microbial biogeochemistry including the metabolic regulation and environmental controls of gene expression, to the processes that underpin the fluxes of carbon, related bioelements, and energy in the marine environment. The C-MORE education and outreach program is focused on increasing scientific literacy in microbial oceanography among students, educators, and the general public. A first step toward this goal is defining the key concepts that constitute microbial oceanography. After lengthy discussions with scientists and educators, both within and outside C-MORE, we have arrived at six key concepts: 1) Marine microbes are very small and have been around for a long time; 2) Life on Earth could not exist without microbes; 3) Most marine microbes are beneficial; 4) Microbes are everywhere: they are extremely abundant and diverse; 5) Microbes significantly impact our global climate; and 6) There are new discoveries every day in the field of microbial oceanography. A C-MORE-produced brochure on these six key concepts will be distributed at the meeting. Advanced copies may be requested by email or downloaded from the C-MORE web site(http://cmore.soest.hawaii.edu/downloads/MO_key_concepts_hi-res.pdf). This brochure also includes information on career pathways in microbial oceanography, with the aim of broadening participation in the field. C-MORE is eager to work in partnership to incorporate these key concepts into other science literacy publications, particularly those involving ocean and climate literacy. We thank the following contributors and reviewers: P Chisholm, A Dolberry, and A Thompson (MIT); N Lawrence

  11. Microbial biomass in faeces of dairy cows affected by a nitrogen deficient diet.

    Science.gov (United States)

    Jost, Daphne Isabel; Aschemann, Martina; Lebzien, Peter; Joergensen, Rainer Georg; Sundrum, Albert

    2013-04-01

    Since more than half of the faecal nitrogen (N) originates from microbial N, the objective of the study was to develop a method for quantitatively detecting microbial biomass and portion of living microorganisms in dairy cattle faeces, including bacteria, fungi and archaea. Three techniques were tested: (1) the chloroform fumigation extraction (CFE) method, (2) detection of the fungal cell-membrane component ergosterol and (3) analysis of the cell wall components fungal glucosamine and bacterial muramic acid. In a second step, an N deficient (ND) and an N balanced (NB) diets were compared with respect to the impacts on faecal C and N fractions, microbial indices and digestibility. The mean values of microbial biomass C and N concentrations averaged around 37 and 4.9 mg g(-1) DM, respectively. Ergosterol, together with fungal glucosamine and bacterial muramic acid, revealed a 25% fungal C in relation to the total microbial C content in dairy cattle faeces. Changes in ruminal N supply showed significant effects on faecal composition. Faecal concentrations of NDF, hemicelluloses and undigested dietary N and the total C/N ratio were significantly higher in ND treatment compared to the NB treatment. N deficiency was reflected also by a higher microbial biomass C/N ratio. It was concluded that the assessment of microbial indices provides valuable information with respect to diet effects on faecal composition and the successive decomposition. Further studies should be conducted to explore the potentials for minimising nutrient losses from faeces.

  12. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

    Science.gov (United States)

    Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-04-26

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

  13. Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

    Science.gov (United States)

    Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

    2011-01-01

    Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.

  14. Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

    Science.gov (United States)

    Yu, Ping; Chen, Xingge; Li, Peng

    2017-09-01

    Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  15. Sequence-based Methods in Human Microbial Ecology: A The 2nd HumanGenome Comes of Age

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-06-01

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  16. Chromogenic media for the detection and/or enumeration of Listeria monocytogenes - results of trials performed by a working group of the International Organization for Standardization - ISO/TC 34/SC 9

    NARCIS (Netherlands)

    Beumer, R.R.; Hazeleger, W.C.

    2007-01-01

    The solid selective media PALCAM and Oxford agar originally described in the ISO (International Organization for Standardization) Standard 11290 part 1 and part 2 "Microbiology of food and animal feeding stuffs - Horizontal method for the detection and enumeration of Listeria monocytogenes", suffer

  17. Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

    2012-08-15

    Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes. (orig.)

  18. Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

    Science.gov (United States)

    Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

    2012-08-01

    Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

  19. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

    Science.gov (United States)

    Binga, Erik K; Lasken, Roger S; Neufeld, Josh D

    2008-03-01

    Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

  20. Protection of Antarctic microbial communities – ‘out of sight, out of mind’

    Science.gov (United States)

    Hughes, Kevin A.; Cowan, Don A.; Wilmotte, Annick

    2015-01-01

    Recent advances in molecular biology techniques have shown the presence of diverse microbial communities and endemic species in Antarctica. Endemic microbes may be a potential source of novel biotechnologically important compounds, including, for example, new antibiotics. Thus, the scientific and biotechnological value of Antarctic terrestrial microbial habitats can be compromised by human visitation to a greater extent than previously realized. The ever-increasing human footprint in Antarctica makes consideration of this topic more pressing, as the number of locations known to be pristine habitats, where increasingly sophisticated cutting-edge research techniques may be used to their full potential, declines. Examination of the Protected Areas system of the Antarctic Treaty shows that microbial habitats are generally poorly protected. No other continent on Earth is dominated to the same degree by microbial species, and real opportunities exist to develop new ways of conceptualizing and implementing conservation of microbial biogeography on a continental scale. Here we highlight potential threats both to the conservation of terrestrial microbial ecosystems, and to future scientific research requiring their study. PMID:25762992

  1. Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization.

    Science.gov (United States)

    Buysschaert, Benjamin; Kerckhof, Frederiek-Maarten; Vandamme, Peter; De Baets, Bernard; Boon, Nico

    2018-02-01

    The analysis of microbial populations is fundamental, not only for developing a deeper understanding of microbial communities but also for their engineering in biotechnological applications. Many methods have been developed to study their characteristics and over the last few decades, molecular analysis tools, such as DNA sequencing, have been used with considerable success to identify the composition of microbial populations. Recently, flow cytometric fingerprinting is emerging as a promising and powerful method to analyze bacterial populations. So far, these methods have primarily been used to observe shifts in the composition of microbial communities of natural samples. In this article, we apply a flow cytometric fingerprinting method to discriminate among 29 Lactobacillus strains. Our results indicate that it is possible to discriminate among 27 Lactobacillus strains by staining with SYBR green I and that the discriminatory power can be increased by combined SYBR green I and propidium iodide staining. Furthermore, we illustrate the impact of physiological changes on the fingerprinting method by demonstrating how flow cytometric fingerprinting is able to discriminate the different growth phases of a microbial culture. The sensitivity of the method is assessed by its ability to detect changes in the relative abundance of a mix of polystyrene beads down to 1.2%. When a mix of bacteria was used, the sensitivity was as between 1.2% and 5%. The presented data demonstrate that flow cytometric fingerprinting is a sensitive and reproducible technique with the potential to be applied as a method for the dereplication of bacterial isolates. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

  2. Microbial kinetic for In-Storage-Psychrophilic Anaerobic Digestion (ISPAD).

    Science.gov (United States)

    Madani-Hosseini, Mahsa; Mulligan, Catherine N; Barrington, Suzelle

    2014-12-15

    In-Storage-Psychrophilic-Anaerobic-Digestion (ISPAD) is a wastewater storage tank converted into an anaerobic digestion (AD) system by means of an airtight floating geo-membrane. For process optimization, ISPAD requires modelling with well-established microbial kinetics coefficients. The present objectives were to: obtain kinetics coefficients for the modelling of ISPAD; compare the prediction of the conventional and decomposition fitting approach, an innovative fitting technique used in other fields of science, and; obtain equations to predict the maximum growth rate (μmax) of microbial communities as a function of temperature. The method consisted in conducting specific Substrate Activity Tests (SAT) using ISPAD inoculum to monitor the rate of degradation of specific substrates at 8, 18 and 35 °C. Microbial kinetics coefficients were obtained by fitting the Monod equations to SAT. The statistical procedure of Least Square Error analysis was used to minimize the Sum of Squared Errors (SSE) between the measured ISPAD experimental data and the Monod equation values. Comparing both fitting methods, the decomposition approach gave higher correlation coefficient (R) for most kinetics values, as compared to the conventional approach. Tested to predict μmax with temperature, the Square Root equation better predicted temperature dependency of both acidogens and propionate degrading acetogens, while the Arrhenius equation better predicted that of methanogens and butyrate degrading acetogens. Increasing temperature from 18 to 35 °C did not affect butyrate degrading acetogens, likely because of their dominance, as demonstrated by microbial population estimation. The estimated ISPAD kinetics coefficients suggest a robust psychrophilic and mesophilic coexisting microbial community demonstrating acclimation to ambient temperature. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Microbial Inactivation by Ultrasound Assisted Supercritical Fluids

    Science.gov (United States)

    Benedito, Jose; Ortuño, Carmen; Castillo-Zamudio, Rosa Isela; Mulet, Antonio

    A method combining supercritical carbon dioxide (SC-CO2) and high power ultrasound (HPU) has been developed and tested for microbial/enzyme inactivation purposes, at different process conditions for both liquid and solid matrices. In culture media, using only SC-CO2, the inactivation rate of E. coli and S. cerevisiae increased with pressure and temperature; and the total inactivation (7-8 log-cycles) was attained after 25 and 140 min of SC-CO2 (350 bar, 36 °C) treatment, respectively. Using SC-CO2+HPU, the time for the total inactivation of both microorganisms was reduced to only 1-2 min, at any condition selected. The SC-CO2+HPU inactivation of both microorganisms was slower in juices (avg. 4.9 min) than in culture media (avg. 1.5 min). In solid samples (chicken, turkey ham and dry-cured pork cured ham) treated with SC-CO2 and SC-CO2+HPU, the inactivation rate of E. coli increased with temperature. The application of HPU to the SC-CO2 treatments accelerated the inactivation rate of E. coli and that effect was more pronounced in treatments with isotonic solution surrounding the solid food samples. The application of HPU enhanced the SC-CO2 inactivation mechanisms of microorganisms, generating a vigorous agitation that facilitated the CO2 solubilization and the mass transfer process. The cavitation generated by HPU could damage the cell walls accelerating the extraction of vital constituents and the microbial death. Thus, using the combined technique, reasonable industrial processing times and mild process conditions could be used which could result into a cost reduction and lead to the minimization in the food nutritional and organoleptic changes.

  4. Microbial Flocculant for Nature Soda

    Energy Technology Data Exchange (ETDEWEB)

    Qin, Peiyong; Zhang, Tong; Chen, Cuixian

    2004-03-31

    Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculant was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.

  5. Subsurface microbial habitats on Mars

    Science.gov (United States)

    Boston, P. J.; Mckay, C. P.

    1991-01-01

    We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.

  6. Microbial activity at Yucca Mountain

    International Nuclear Information System (INIS)

    Horn, J.M.; Meike, A.

    1995-01-01

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified

  7. Microbial activity at Yucca Mountain

    Energy Technology Data Exchange (ETDEWEB)

    Horn, J.M.; Meike, A.

    1995-09-25

    The U.S. Department of Energy is engaged in a suitability study for a potential geological repository at Yucca Mountain, Nevada, for the containment and storage of commercially generated spent fuel and defense high-level nuclear waste. There is growing recognition of the role that biotic factors could play in this repository, either directly through microbially induced corrosion (MIC), or indirectly by altering the chemical environment or contributing to the transport of radionuclides. As a first step toward describing and predicting these processes, a workshop was held on April 10-12, 1995, in Lafayette, California. The immediate aims of the workshop were: (1) To identify microbially related processes relevant to the design of a radioactive waste repository under conditions similar to those at Yucca Mountain. (2) To determine parameters that are critical to the evaluation of a disturbed subterranean environment. (3) To define the most effective means of investigating the factors thus identified.

  8. Laser engineering of microbial systems

    Science.gov (United States)

    Yusupov, V. I.; Gorlenko, M. V.; Cheptsov, V. S.; Minaev, N. V.; Churbanova, E. S.; Zhigarkov, V. S.; Chutko, E. A.; Evlashin, S. A.; Chichkov, B. N.; Bagratashvili, V. N.

    2018-06-01

    A technology of laser engineering of microbial systems (LEMS) based on the method of laser-induced transfer of heterogeneous mixtures containing microorganisms (laser bioprinting) is described. This technology involves laser printing of soil microparticles by focusing near-infrared laser pulses on a specially prepared gel/soil mixture spread onto a gold-coated glass plate. The optimal range of laser energies from the point of view of the formation of stable jets and droplets with minimal negative impact on living systems of giant accelerations, laser pulse irradiation, and Au nanoparticles was found. Microsamples of soil were printed on glucose-peptone-yeast agar plates to estimate the LEMS process influence on structural and morphological microbial diversity. The obtained results were compared with traditionally treated soil samples. It was shown that LEMS technology allows significantly increasing the biodiversity of printed organisms and is effective for isolating rare or unculturable microorganisms.

  9. Microbial Corrosion and Cracking in Steel

    DEFF Research Database (Denmark)

    Hilbert, Lisbeth Rischel

    1998-01-01

    The aim of the report is to give a fundamental understanding of the response of different electrochemical techniques on carbon steel in a sulphide environment as well as in a biologically active sulphate-reducing environment (SRB). This will form the basis for further studies and for recommendati......The aim of the report is to give a fundamental understanding of the response of different electrochemical techniques on carbon steel in a sulphide environment as well as in a biologically active sulphate-reducing environment (SRB). This will form the basis for further studies...... will be based on results from the entire 3 year period, but only selected experimental data primarily from the latest experiments will be presented in detail here.Microbial corrosion of carbon steel under influence of sulphate-reducing bacteria (SRB) is characterised by the formation of both biofilm...... and corrosion products (ferrous sulphides) on the metal surface. Experiments have been conducted on carbon steel exposed in near neutral (pH 6 to 8.5) saline hydrogen sulphide environment (0 to 100 mg/l total dissolved sulphide) for a period of 14 days. Furthermore coupons have been exposed in a bioreactor...

  10. Problems with the microbial production of butanol.

    Science.gov (United States)

    Zheng, Yan-Ning; Li, Liang-Zhi; Xian, Mo; Ma, Yu-Jiu; Yang, Jian-Ming; Xu, Xin; He, Dong-Zhi

    2009-09-01

    With the incessant fluctuations in oil prices and increasing stress from environmental pollution, renewed attention is being paid to the microbial production of biofuels from renewable sources. As a gasoline substitute, butanol has advantages over traditional fuel ethanol in terms of energy density and hygroscopicity. A variety of cheap substrates have been successfully applied in the production of biobutanol, highlighting the commercial potential of biobutanol development. In this review, in order to better understand the process of acetone-butanol-ethanol production, traditional clostridia fermentation is discussed. Sporulation is probably induced by solvent formation, and the molecular mechanism leading to the initiation of sporulation and solventogenesis is also investigated. Different strategies are employed in the metabolic engineering of clostridia that aim to enhancing solvent production, improve selectivity for butanol production, and increase the tolerance of clostridia to solvents. However, it will be hard to make breakthroughs in the metabolic engineering of clostridia for butanol production without gaining a deeper understanding of the genetic background of clostridia and developing more efficient genetic tools for clostridia. Therefore, increasing attention has been paid to the metabolic engineering of E. coli for butanol production. The importation and expression of a non-clostridial butanol-producing pathway in E. coli is probably the most promising strategy for butanol biosynthesis. Due to the lower butanol titers in the fermentation broth, simultaneous fermentation and product removal techniques have been developed to reduce the cost of butanol recovery. Gas stripping is the best technique for butanol recovery found so far.

  11. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

    Science.gov (United States)

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

    2014-06-17

    Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. Copyright © 2014 John Wiley & Sons, Inc.

  12. Theory of microbial genome evolution

    Science.gov (United States)

    Koonin, Eugene

    Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

  13. Nuclear techniques in animal agriculture

    International Nuclear Information System (INIS)

    Young, B.A.

    1981-01-01

    Nuclear technology plays an integral part in research to improve the health and productivity of animals. The use of radioisotopes and ionizing radiations in animal agriculture is briefly reviewed. The radioimmunoassay techniques give the opportunity of measuring and following precisely hormonal patterns in animals over the reproductive cycle. Simply by analysing a sample of blood, milk, or other body fluid, minute hormone concentrations can be assayed and the reproductive status of the animal assessed. The radioimmunoassay procedure uses antigens which are isotopically labelled, usually with 125 I, and antibodies specifically developed for each hormone. The onset of sexual maturity, of oestrus, or the influence of environmental, nutritional or other factors on the reproductive state of an animal can be studied. An example of the use of the radioimmunoassay technique is illustrated in the coordinated research program of the IAEA which focuses on improving domestic buffalo production. Nuclear techniques, particularly the use of stable and radioactive tracers are providing important insights into the functioning of the digestive system of ruminants, its qualitative dynamics and metabolism. For assessing the products of the rumen, particularly volatile fatty acids which become an energy source, and microbial proteins which become a protein source for the animal, materials labelled with 14 C, 3 H, 35 S, 15 N and 32 P are used. As an illustrative example, the results of one study of nitrogen metabolism, microbial protein and rumen bypass protein synthesis in cattle are shown

  14. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    Science.gov (United States)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the

  15. Fourteenth-Sixteenth Microbial Genomics Conference-2006-2008

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Jeffrey H

    2011-04-18

    The concept of an annual meeting on the E. coli genome was formulated at the Banbury Center Conference on the Genome of E. coli in October, 1991. The first meeting was held on September 10-14, 1992 at the University of Wisconsin, and this was followed by a yearly series of meetings, and by an expansion to include The fourteenth meeting took place September 24-28, 2006 at Lake Arrowhead, CA, the fifteenth September 16-20, 2007 at the University of Maryland, College Park, MD, and the sixteenth September 14-18, 2008 at Lake Arrowhead. The full program for the 16th meeting is attached. There have been rapid and exciting advances in microbial genomics that now make possible comparing large data sets of sequences from a wide variety of microbial genomes, and from whole microbial communities. Examining the “microbiomes”, the living microbial communities in different host organisms opens up many possibilities for understanding the landscape presented to pathogenic microorganisms. For quite some time there has been a shifting emphasis from pure sequence data to trying to understand how to use that information to solve biological problems. Towards this end new technologies are being developed and improved. Using genetics, functional genomics, and proteomics has been the recent focus of many different laboratories. A key element is the integration of different aspects of microbiology, sequencing technology, analysis techniques, and bioinformatics. The goal of these conference is to provide a regular forum for these interactions to occur. While there have been a number of genome conferences, what distinguishes the Microbial Genomics Conference is its emphasis on bringing together biology and genetics with sequencing and bioinformatics. Also, this conference is the longest continuing meeting, now established as a major regular annual meeting. In addition to its coverage of microbial genomes and biodiversity, the meetings also highlight microbial communities and the use of

  16. Microbial terroir for wine grapes

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, J. A.; van der Lelie, D.; Zarraonaindia, I.

    2013-12-05

    The viticulture industry has been selectively growing vine cultivars with different traits (grape size, shape, color, flavor, yield of fruit, and so forth) for millennia, and small variations in soil composition, water management, climate, and the aspect of vineyards have long been associated with shifts in these traits. As such, many different clonal varieties of vines exist, even within given grape varieties, such as merlot, pinot noir, and chardonnay. The commensal microbial flora that coexists with the plant may be one of the key factors that influence these traits. To date, the role of microbes has been largely ignored, outside of microbial pathogens, mainly because the technologies did not exist to allow us to look in any real depth or breadth at the community structure of the multitudes of bacterial and fungal species associated with each plant. In PNAS, Bokulich et al. (1) used next-generation sequencing of 16S rRNA and internal transcribed spacer ribosomal sequence to determine the relative abundances of bacteria and fungi, respectively, from grape must (freshly pressed grape juice, containing the skins and seeds) from plants in eight vineyards representing four of the major wine growing regions in California. The authors show that the microbiomes (bacterial and fungal taxonomic structure) associated with this early fermentation stage show defined biogeography, illustrating that different wine-growing regions maintain different microbial communities, with some influences from the grape variety and the year of production.

  17. Diagnostic techniques

    International Nuclear Information System (INIS)

    Berquist, T.H.; Bender, C.E.; James, E.M.; Brown, M.L.; McLeod, R.A.; Broderick, D.F.; Welch, T.J.

    1989-01-01

    Proper application of imaging procedures is essential to obtain needed information for diagnosis and therapy planning in patients with suspected foot and/or ankle pathology. This paper provides basic background data for the numerous imaging techniques

  18. Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

    Science.gov (United States)

    Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

    2018-01-01

    This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of

  19. The application of different techniques to determine activated sludge ...

    African Journals Online (AJOL)

    The application of different techniques to determine activated sludge kinetic parameters in a food industry wastewater. ... method) and a respirometric technique based on oxygen consumption measurements, were used to compare microbial parameters using a wastewater model system of a potato processing plant.

  20. Frequency Of Isolation Of Salmonella From Commercial Poultry Feeds And Their Anti-Microbial Resistance Profiles, Imo State, Nigeria

    Directory of Open Access Journals (Sweden)

    Okoli IC

    2006-09-01

    Full Text Available This study was conducted to determine the frequency of isolation of salmonella and their microbial resistance profiles across different commercial poultry feeds sold in Imo State, Nigeria. Thirty-six bulk feed samples were colleted from 154 bag across different feed types and brands which included Guinea (GF, Top (TF, Vital (VF, Extra (EF, Animal care (AF and livestock (LF feeds. The salmonella isolated were tested against 14 anti-microbial drugs using the disc diffusion method. Bacterial load enumeration of the samples indicated a range of <30 colony forming unit (CFU to overgrowth at 104 serial dilutions. Eight feed samples (22.2% which cuts across the entire feed brands expect EF were positive for salmonella. The highest prevalence of 28.8% and 25.0% were recorded for LF and TF respectively, while VF, GF and AF had 11.1 and 10.0% respectively. Salmonella isolates showed high rates of resistance (51-100% against nitrofurantoin, ampicillin, tetracycline and ceftriazole, while moderate rates (31-50% were recorded for chloramphenicol, oxfloxacin and cotrimoxazole. Low resistance rates (1-30% were on the other hand recorded against ciprofloxacin and amoxycillin clavulanate (Augumentine, whereas zero resistance was demonstrated against pefloxacin, gentamycin, streptomycin and nalidixic. Commercial feeds form important channels for the dissemination of multi-drug resistant salmonella in Imo State, Nigeria.