Science.gov

Sample records for adaptation bacteria sample

  1. Digital adaptive sampling.

    NASA Technical Reports Server (NTRS)

    Breazeale, G. J.; Jones, L. E.

    1971-01-01

    Discussion of digital adaptive sampling, which is consistently better than fixed sampling in noise-free cases. Adaptive sampling is shown to be feasible and, it is considered, should be studied further. It should be noted that adaptive sampling is a class of variable rate sampling in which the variability depends on system signals. Digital rather than analog laws should be studied, because cases can arise in which the analog signals are not even available. An extremely important problem is implementation.

  2. Adaptation, Bacteria and Maxwell's Demons

    NASA Astrophysics Data System (ADS)

    Galajda, Peter; Keymer, Juan E.; Austin, Robert H.

    2007-03-01

    We propose a method to study the adaptation of bacterial populations with an asymmetric wall of Maxwell Demon openings. A Maxwell Demon opening is a funnel which is easier to enter than to leave. The interaction of swimming cells with such a Maxwell Demon Wall results in a population density separation, in apparent (but not real) violation of the Second Law of Thermodynamics, as we will show. Bacteria can be exposed to spatial challenges in order to move to e. g. higher food levels. The question we address in these experiments is: do the bacteria adapt and overcome the Maxwell Demon Wall?

  3. Adaptive Sampling Proxy Application

    2012-10-22

    ASPA is an implementation of an adaptive sampling algorithm [1-3], which is used to reduce the computational expense of computer simulations that couple disparate physical scales. The purpose of ASPA is to encapsulate the algorithms required for adaptive sampling independently from any specific application, so that alternative algorithms and programming models for exascale computers can be investigated more easily.

  4. Adaptive Sampling Designs.

    ERIC Educational Resources Information Center

    Flournoy, Nancy

    Designs for sequential sampling procedures that adapt to cumulative information are discussed. A familiar illustration is the play-the-winner rule in which there are two treatments; after a random start, the same treatment is continued as long as each successive subject registers a success. When a failure occurs, the other treatment is used until…

  5. Sampling bacteria with a laser

    NASA Astrophysics Data System (ADS)

    Schwarzwälder, Kordula; Rutschmann, Peter

    2014-05-01

    Water quality is a topic of high interest and it's getting more and more important due to climate change and the implementation of European Water Framework Directive (WFD). One point of interest here is the inflow of bacteria into a river caused by combined sewer overflows which lead untreated wastewater including bacteria directly into a river. These bacteria remain in the river for a certain time, they settle down and can be remobilised again. In our study we want to investigate these processes of sedimentation and resuspension and use the results for the development of a software module coupled with the software Flow3D. Thereby we should be able to simulate and therefore predict the water quality influenced by combined sewer overflows. Hence we need to get information about the bacteria transport and fate. We need to know about the size of the bacteria or of the bacteria clumps and the size of the particles the bacteria are attached to. The agglomerates lead to different characteristics and velocities of settlement. The timespan during this bacteria can be detected in the bulk phase depends on many factors like the intensity of UV light, turbidity of the water, the temperature of the water, if there are grazers and a lot more. The size, density and composition of the agglomerates is just a part of all these influencing factors, but it is extremely difficult to differ between the other effects if we have no information about the simple sedimentation in default of these basic information. However we have a big problem getting the data. The chaining between bacteria or bacteria and particles is not too strong, so filtering the water to get a sieving curve may destroy these connections. We did some experiments similar to PIV (particle image velocimetry) measurements and evaluated the pictures with a macro written for the software ImageJ. Doing so we were able to get the concentration of bacteria in the water and collect information about the size of the bacteria. We

  6. Spectroscopic diagnostics for bacteria in biologic sample

    DOEpatents

    El-Sayed, Mostafa A.; El-Sayed, Ivan H.

    2002-01-01

    A method to analyze and diagnose specific bacteria in a biologic sample using spectroscopy is disclosed. The method includes obtaining the spectra of a biologic sample of a non-infected patient for use as a reference, subtracting the reference from the spectra of an infected sample, and comparing the fingerprint regions of the resulting differential spectrum with reference spectra of bacteria in saline. Using this diagnostic technique, specific bacteria can be identified sooner and without culturing, bacteria-specific antibiotics can be prescribed sooner, resulting in decreased likelihood of antibiotic resistance and an overall reduction of medical costs.

  7. Adaptive sampling for noisy problems

    SciTech Connect

    Cantu-Paz, E

    2004-03-26

    The usual approach to deal with noise present in many real-world optimization problems is to take an arbitrary number of samples of the objective function and use the sample average as an estimate of the true objective value. The number of samples is typically chosen arbitrarily and remains constant for the entire optimization process. This paper studies an adaptive sampling technique that varies the number of samples based on the uncertainty of deciding between two individuals. Experiments demonstrate the effect of adaptive sampling on the final solution quality reached by a genetic algorithm and the computational cost required to find the solution. The results suggest that the adaptive technique can effectively eliminate the need to set the sample size a priori, but in many cases it requires high computational costs.

  8. Molecular adaptations in Antarctic fish and bacteria

    NASA Astrophysics Data System (ADS)

    Russo, Roberta; Riccio, Alessia; di Prisco, Guido; Verde, Cinzia; Giordano, Daniela

    2010-08-01

    Marine organisms, living in the cold waters of the Southern Ocean, are exposed to high oxygen concentrations. Cold-adapted organisms have developed networks of defence mechanisms to protect themselves against oxidative stress. The dominant suborder Notothenioidei of the Southern Ocean is one of the most interesting models, within vertebrates, to study the evolutionary biological responses to extreme environment. Within bacteria, the psychrophilic Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 gives the opportunity to explore the cellular strategies adopted in vivo by cold-adapted microorganisms to cope with cold and high oxygen concentration. Understanding the molecular mechanisms underlying how a range of Antarctic organisms have responded to climate change in the past will enable predictions as to how they and other species will adapt to global climate change, in terms of physiological function, distribution patterns and ecosystem balance.

  9. Adaptive Sampling in Hierarchical Simulation

    SciTech Connect

    Knap, J; Barton, N R; Hornung, R D; Arsenlis, A; Becker, R; Jefferson, D R

    2007-07-09

    We propose an adaptive sampling methodology for hierarchical multi-scale simulation. The method utilizes a moving kriging interpolation to significantly reduce the number of evaluations of finer-scale response functions to provide essential constitutive information to a coarser-scale simulation model. The underlying interpolation scheme is unstructured and adaptive to handle the transient nature of a simulation. To handle the dynamic construction and searching of a potentially large set of finer-scale response data, we employ a dynamic metric tree database. We study the performance of our adaptive sampling methodology for a two-level multi-scale model involving a coarse-scale finite element simulation and a finer-scale crystal plasticity based constitutive law.

  10. Automatic bio-sample bacteria detection system

    NASA Technical Reports Server (NTRS)

    Chappelle, E. W.; Colburn, M.; Kelbaugh, B. N.; Picciolo, G. L.

    1971-01-01

    Electromechanical device analyzes urine specimens in 15 minutes and processes one sample per minute. Instrument utilizes bioluminescent reaction between luciferase-luciferin mixture and adenosine triphosphate (ATP) to determine number of bacteria present in the sample. Device has potential application to analysis of other body fluids.

  11. Physiological adaptations of key oral bacteria.

    PubMed

    Douglas, C W Ian; Naylor, Kathryn; Phansopa, Chatchawal; Frey, Andrew M; Farmilo, Thomas; Stafford, Graham P

    2014-01-01

    Oral colonising bacteria are highly adapted to the various environmental niches harboured within the mouth, whether that means while contributing to one of the major oral diseases of caries, pulp infections, or gingival/periodontal disease or as part of a commensal lifestyle. Key to these infections is the ability to adhere to surfaces via a range of specialised adhesins targeted at both salivary and epithelial proteins, their glycans and to form biofilm. They must also resist the various physical stressors they are subjected to, including pH and oxidative stress. Possibly most strikingly, they have developed the ability to harvest both nutrient sources provided by the diet and those derived from the host, such as protein and surface glycans. We have attempted to review recent developments that have revealed much about the molecular mechanisms at work in shaping the physiology of oral bacteria and how we might use this information to design and implement new treatment strategies.

  12. Effect of adaptation and pulp density on bioleaching of mine waste using indigenous acidophilic bacteria

    NASA Astrophysics Data System (ADS)

    Cho, K.; Kim, B.; Lee, D.; Choi, N.; Park, C.

    2011-12-01

    Adaptation to environment is a natural phenomena that takes place in many animals, plants and microorganisms. These adapted organisms achieve stronger applicability than unadapted organisms after habitation in a specific environment for a long time. In the biohydrometallurgical industry, adaptation to special environment conditions by selective culturing is the most popular method for improving bioleaching activity of strains-although that is time consuming. This study investigated the influence of the bioleaching efficiency of mine waste under batch experimental conditions (adaptation and pulp density) using the indigenous acidophilic bacteria collected from acid mine drainage in Go-seong and Yeon-hwa, Korea. We conducted the batch experiments at the influences of parameters, such as the adaptation of bacteria and pulp density of the mine waste. In the adaptation case, the value of pH in 1'st adaptation bacteria sample exhibited lower than in 2'nd adaptation bacteria sample. And the content of both Cu and Zn at 1'st adaptation bacteria sample appeared lower than at 2'nd adaptation bacteria sample. In the SEM analysis, the rod-shaped bacteria with 1μm in length were observed on the filter paper (pore size - 0.45μm). The results of pulp density experiments revealed that the content of both Cu and Zn increased with increasing pulp density, since the increment of pulp density resulted in the enhancement of bioleaching capacity.

  13. Adaptive Peer Sampling with Newscast

    NASA Astrophysics Data System (ADS)

    Tölgyesi, Norbert; Jelasity, Márk

    The peer sampling service is a middleware service that provides random samples from a large decentralized network to support gossip-based applications such as multicast, data aggregation and overlay topology management. Lightweight gossip-based implementations of the peer sampling service have been shown to provide good quality random sampling while also being extremely robust to many failure scenarios, including node churn and catastrophic failure. We identify two problems with these approaches. The first problem is related to message drop failures: if a node experiences a higher-than-average message drop rate then the probability of sampling this node in the network will decrease. The second problem is that the application layer at different nodes might request random samples at very different rates which can result in very poor random sampling especially at nodes with high request rates. We propose solutions for both problems. We focus on Newscast, a robust implementation of the peer sampling service. Our solution is based on simple extensions of the protocol and an adaptive self-control mechanism for its parameters, namely—without involving failure detectors—nodes passively monitor local protocol events using them as feedback for a local control loop for self-tuning the protocol parameters. The proposed solution is evaluated by simulation experiments.

  14. Chemical markers for bacteria in extraterrestrial samples.

    PubMed

    Fox, Alvin

    2002-11-01

    Interplanetary missions to collect pristine Martian surface samples for analysis of organic molecules, and to search for evidence of life, are in the planning phases. The only extraterrestrial samples currently on Earth are lunar dust and rocks, brought back by the Apollo (U.S.) and Luna (Soviet Union) missions to the moon, and meteorites. Meteorites are contaminated when they pass through the Earth's atmosphere, and during environmental exposure on Earth. Lunar fines have been stored on Earth for over 30 years under conditions designed to avoid chemical but not microbiological contamination. It has been extremely difficult to draw firm conclusions about the origin of chemicals (including amino acids) in extraterrestrial samples. Of particular concern has been the possibility of bacterial contamination. Recent work using state-of-the-art gas chromatography tandem mass spectrometry (GC-MS/MS) has dramatically lowered the chemical background, allowing a clear demonstration that lunar fines are remarkably different from terrestrial dust in that they generally lack certain chemical markers (muramic acid and 3-hydroxy fatty acids) characteristic of Earth's bacteria. Thus, lunar dust might be used as a negative control, in conjunction with GC-MS/MS analyses, in future analytical studies of lunar dust and meteorites. Such analyses may also be important in studies designed to search for the presence of life on Mars.

  15. Accurate Biomass Estimation via Bayesian Adaptive Sampling

    NASA Technical Reports Server (NTRS)

    Wheeler, Kevin R.; Knuth, Kevin H.; Castle, Joseph P.; Lvov, Nikolay

    2005-01-01

    The following concepts were introduced: a) Bayesian adaptive sampling for solving biomass estimation; b) Characterization of MISR Rahman model parameters conditioned upon MODIS landcover. c) Rigorous non-parametric Bayesian approach to analytic mixture model determination. d) Unique U.S. asset for science product validation and verification.

  16. An Attempt to Sample Upper Atmospheric Bacteria.

    NASA Astrophysics Data System (ADS)

    Canales, D. R. J.; Edgar, B.; Lefer, B. L.; Dunbar, B.; Gamblin, R.; Ehteshami, A.; Nowling, M.; Ahmad, H.; Bias, C.; Pena, M.

    2015-12-01

    Attempts have been made over the last decade to find the density and diversity of living microorganisms in the stratosphere using both air planes and zero pressure balloons. Most of the published attempts to survey stratospheric microorganisms by the scientific community have involved heavy devices that could not be used on ultralight weight balloons, making this research expensive and thereby reducing the opportunities for sampling. In this project, we attempted to find how high a light weight balloon could collect microorganisms, and to bridge scientific study with hobbyist feasibility at lower cost. Our approach was to use hobbyist level items that lower the weight so that lighter weather balloons could be used. This approach will allow more sampling possibilities while also lowering cost of study. We have conducted two successful test flights. While there were no successful samples from the upper atmosphere, the fact that the system can capture surface organisms with the fact that sensors had viable data shows that anyone with interest can help find and study atmospheric microorganisms.

  17. Spatial adaptive sampling in multiscale simulation

    NASA Astrophysics Data System (ADS)

    Rouet-Leduc, Bertrand; Barros, Kipton; Cieren, Emmanuel; Elango, Venmugil; Junghans, Christoph; Lookman, Turab; Mohd-Yusof, Jamaludin; Pavel, Robert S.; Rivera, Axel Y.; Roehm, Dominic; McPherson, Allen L.; Germann, Timothy C.

    2014-07-01

    In a common approach to multiscale simulation, an incomplete set of macroscale equations must be supplemented with constitutive data provided by fine-scale simulation. Collecting statistics from these fine-scale simulations is typically the overwhelming computational cost. We reduce this cost by interpolating the results of fine-scale simulation over the spatial domain of the macro-solver. Unlike previous adaptive sampling strategies, we do not interpolate on the potentially very high dimensional space of inputs to the fine-scale simulation. Our approach is local in space and time, avoids the need for a central database, and is designed to parallelize well on large computer clusters. To demonstrate our method, we simulate one-dimensional elastodynamic shock propagation using the Heterogeneous Multiscale Method (HMM); we find that spatial adaptive sampling requires only ≈50×N0.14 fine-scale simulations to reconstruct the stress field at all N grid points. Related multiscale approaches, such as Equation Free methods, may also benefit from spatial adaptive sampling.

  18. Molecular adaptations in psychrophilic bacteria: potential for biotechnological applications.

    PubMed

    Russell, N J

    1998-01-01

    Bacteria which live in cold conditions are known as psychrophiles. Since so much of our planet is generally cold, i.e. below 5 degrees C, it is not surprising that they are very common amongst a wide variety of habitats. To enable them to survive and grow in cold environments, psychrophilic bacteria have evolved a complex range of adaptations to all of their cellular components, including their membranes, energy-generating systems, protein synthesis machinery, biodegradative enzymes and the components responsible for nutrient uptake. Whilst such a systems approach to the topic has its advantages, all of the changes can be described in terms of adaptive alterations in the proteins and lipids of the bacterial cell. The present review adopts the latter approach and, following a brief consideration of the definition of psychrophiles and description of their habitats, focuses on those adaptive changes in proteins and lipids, especially those which are either currently being explored for their biotechnological potential or might be so in the future. Such applications for proteins range from the use of cold-active enzymes in the detergent and food industries, in specific biotransformations and environmental bioremediations, to specialised uses in contact lens cleaning fluids and reducing the lactose content of milk; ice-nucleating proteins have potential uses in the manufacture of ice cream or artificial snow; for lipids, the uses include dietary supplements in the form of polyunsaturated fatty acids from some Antarctic marine psychrophiles.

  19. The versatility and adaptation of bacteria from the genus Stenotrophomonas

    SciTech Connect

    Ryan, R.P.; van der Lelie, D.; Monchy, S.; Cardinale, M.; Taghavi, S.; Crossman, L.; Avison, M. B.; Berg, G.; Dow, J. M.

    2009-07-01

    The genus Stenotrophomonas comprises at least eight species. These bacteria are found throughout the environment, particularly in close association with plants. Strains of the most predominant species, Stenotrophomonas maltophilia, have an extraordinary range of activities that include beneficial effects for plant growth and health, the breakdown of natural and man-made pollutants that are central to bioremediation and phytoremediation strategies and the production of biomolecules of economic value, as well as detrimental effects, such as multidrug resistance, in human pathogenic strains. Here, we discuss the versatility of the bacteria in the genus Stenotrophomonas and the insight that comparative genomic analysis of clinical and endophytic isolates of S. maltophilia has brought to our understanding of the adaptation of this genus to various niches.

  20. ADAPTATIONS OF INDIGENOUS BACTERIA TO FUEL CONTAMINATION IN KARST AQUIFERS IN SOUTH-CENTRAL KENTUCKY

    USGS Publications Warehouse

    Byl, Thomas D.; Metge, David W.; Daniel T. Agymang,; Bradley, Michael W.; Hileman, Gregg; Harvey, Ronald W.

    2014-01-01

    The karst aquifer systems in southern Kentucky can be dynamic and quick to change. Microorganisms that live in these unpredictable aquifers are constantly faced with environmental changes. Their survival depends upon adaptations to changes in water chemistry, taking advantage of positive stimuli and avoiding negative environmental conditions. The U.S. Geological Survey conducted a study in 2001 to determine the capability of bacteria to adapt in two distinct regions of water quality in a karst aquifer, an area of clean, oxygenated groundwater and an area where the groundwater was oxygen depleted and contaminated by jet fuel. Water samples containing bacteria were collected from one clean well and two jet fuel contaminated wells in a conduit-dominated karst aquifer. Bacterial concentrations, enumerated through direct count, ranged from 500,000 to 2.7 million bacteria per mL in the clean portion of the aquifer, and 200,000 to 3.2 million bacteria per mL in the contaminated portion of the aquifer over a twelve month period. Bacteria from the clean well ranged in size from 0.2 to 2.5 mm, whereas bacteria from one fuel-contaminated well were generally larger, ranging in size from 0.2 to 3.9 mm. Also, bacteria collected from the clean well had a higher density and, consequently, were more inclined to sink than bacteria collected from contaminated wells. Bacteria collected from the clean portion of the karst aquifer were predominantly (,95%) Gram-negative and more likely to have flagella present than bacteria collected from the contaminated wells, which included a substantial fraction (,30%) of Gram-positive varieties. The ability of the bacteria from the clean portion of the karst aquifer to biodegrade benzene and toluene was studied under aerobic and anaerobic conditions in laboratory microcosms. The rate of fuel biodegradation in laboratory studies was approximately 50 times faster under aerobic conditions as compared to anaerobic, sulfur-reducing conditions. The

  1. Fecal indicator bacteria variability in samples pumped from monitoring wells.

    PubMed

    Kozuskanich, J; Novakowski, K S; Anderson, B C

    2011-01-01

    The detection of microbiological contamination in drinking water from groundwater wells is often made with a limited number of samples that are collected using traditional geochemical sampling protocols. The objective of this study is to examine the variability of fecal indicator bacteria, as observed using discrete samples, due to pumping. Two wells were instrumented as multilevel piezometers in a bedrock aquifer, and bacterial enumeration was conducted on a total of 166 samples (for total coliform, fecal coliform, Escherichia coli, and fecal streptococci) using standard membrane filtration methods. Five tests were conducted using pumping rates ranging from 0.3 to 17 L/min in a variety of purging scenarios, which included constant and variable (incremental increase and decrease) flow. The results clearly show a rapid and reproducible, 1 to 2 log-unit decrease in fecal indicator bacteria at the onset of pumping to stabilized, low-level concentrations prior to the removal of three to five well volumes. The pumping rate was not found to be correlated with the magnitude of observed bacterial counts. Based on the results, we suggest sampling protocols for fecal indicator bacteria that include multiple collections during the course of pumping, including early-time samples, and consider other techniques such as microscopic enumeration when assessing the source of bacteria from the well-aquifer system.

  2. Adaptive importance sampling for network growth models

    PubMed Central

    Holmes, Susan P.

    2016-01-01

    Network Growth Models such as Preferential Attachment and Duplication/Divergence are popular generative models with which to study complex networks in biology, sociology, and computer science. However, analyzing them within the framework of model selection and statistical inference is often complicated and computationally difficult, particularly when comparing models that are not directly related or nested. In practice, ad hoc methods are often used with uncertain results. If possible, the use of standard likelihood-based statistical model selection techniques is desirable. With this in mind, we develop an Adaptive Importance Sampling algorithm for estimating likelihoods of Network Growth Models. We introduce the use of the classic Plackett-Luce model of rankings as a family of importance distributions. Updates to importance distributions are performed iteratively via the Cross-Entropy Method with an additional correction for degeneracy/over-fitting inspired by the Minimum Description Length principle. This correction can be applied to other estimation problems using the Cross-Entropy method for integration/approximate counting, and it provides an interpretation of Adaptive Importance Sampling as iterative model selection. Empirical results for the Preferential Attachment model are given, along with a comparison to an alternative established technique, Annealed Importance Sampling. PMID:27182098

  3. Feature Adaptive Sampling for Scanning Electron Microscopy

    PubMed Central

    Dahmen, Tim; Engstler, Michael; Pauly, Christoph; Trampert, Patrick; de Jonge, Niels; Mücklich, Frank; Slusallek, Philipp

    2016-01-01

    A new method for the image acquisition in scanning electron microscopy (SEM) was introduced. The method used adaptively increased pixel-dwell times to improve the signal-to-noise ratio (SNR) in areas of high detail. In areas of low detail, the electron dose was reduced on a per pixel basis, and a-posteriori image processing techniques were applied to remove the resulting noise. The technique was realized by scanning the sample twice. The first, quick scan used small pixel-dwell times to generate a first, noisy image using a low electron dose. This image was analyzed automatically, and a software algorithm generated a sparse pattern of regions of the image that require additional sampling. A second scan generated a sparse image of only these regions, but using a highly increased electron dose. By applying a selective low-pass filter and combining both datasets, a single image was generated. The resulting image exhibited a factor of ≈3 better SNR than an image acquired with uniform sampling on a Cartesian grid and the same total acquisition time. This result implies that the required electron dose (or acquisition time) for the adaptive scanning method is a factor of ten lower than for uniform scanning. PMID:27150131

  4. Multiple sample flow through immunomagnetic separator for concentrating pathogenic bacteria

    NASA Astrophysics Data System (ADS)

    Rotariu, Ovidiu; Ogden, Iain D.; MacRae, Marion; Udrea, Laura Elena; Strachan, Norval J. C.

    2005-06-01

    The standard method of immunomagnetic separation for isolating pathogenic bacteria from food and environmental matrices processes 1 ml volumes. Pathogens present at low levels (<0.5 pathogenic bacteria/g) will not be consistently detected by this method. Here a multiple sample flow through immunomagnetic separator has been designed and tested to process large volume samples (50 to 250 ml). Preliminary results show >97% recovery of polydisperse magnetic particles (diameter range 1 to 8 µm) containing 29-33% w/w Fe3O4 content. Between 70 and 130 times more of the pathogenic bacteria Escherichia coli O157 is recovered from PBS compared with the standard 1 ml method. Also, the recovery of E. coli O157 from beef mince homogenates, after a 4 h incubation at 42 °C, is between 80 and 180 times higher than the standard 1 ml method.

  5. Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments.

    PubMed

    Gorter, Florien A; Scanlan, Pauline D; Buckling, Angus

    2016-02-01

    Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium Pseudomonas fluorescens and its viral parasite bacteriophage Φ2. We coevolved replicate populations of bacteria and phages at three different temperatures, and determined their performance against coevolutionary partners from the same and different temperatures. Crucially, we measured performance at different assay temperatures, which allowed us to disentangle adaptation to biotic and abiotic habitat components. Our results show that bacteria and phages are more resistant and infectious, respectively, at the temperature at which they previously coevolved, confirming that local adaptation to abiotic conditions can play a crucial role in determining parasite infectivity and host resistance. Our work underlines the need to assess host-parasite interactions across multiple relevant abiotic environments, and suggests that microbial adaption to local temperatures can create ecological barriers to dispersal across temperature gradients.

  6. Real-time potentiometric detection of bacteria in complex samples.

    PubMed

    Zelada-Guillén, Gustavo A; Bhosale, Suryakant V; Riu, Jordi; Rius, F Xavier

    2010-11-15

    Detecting and identifying pathogen bacteria is essential to ensure quality at all stages of the food chain and to diagnose and control microbial infections. Traditional detection methods, including those based on cell culturing, are tedious and time-consuming, and their further application in real samples generally implies more complex pretreatment steps. Even though state-of-the-art techniques for detecting microorganisms enable the quantification of very low concentrations of bacteria, to date it has been difficult to obtain successful results in real samples in a simple, reliable, and rapid manner. In this Article, we demonstrate that the label-free detection and identification of living bacteria in real samples can be carried out in a couple of minutes and in a direct, simple, and selective way at concentration levels as low as 6 colony forming units/mL (CFU) in complex matrices such as milk or 26 CFU/mL in apple juice where the pretreatment step of samples is extremely easy. We chose Escherichia coli ( E. coli ) CECT 675 cells as a model organism as a nonpathogenic surrogate for pathogenic E. coli O157:H7 to test the effectiveness of a potentiometric aptamer-based biosensor. This biosensor uses single-walled carbon nanotubes (SWCNT) as excellent ion-to-electron transducers and covalently immobilized aptamers as biorecognition elements. The selective aptamer-target interaction significantly changes the electrical potential, thus allowing for both interspecies and interstrain selectivity and enabling the direct detection of the target. This technique is therefore a powerful tool for the immediate identification and detection of microorganisms. We demonstrate the highly selective detection of living bacteria with an immediate linear response of up to 10(4) CFU/mL. The biosensor can be easily built and used, is regenerated without difficulty, and can be used at least five times with no loss in the minimum amount of detected bacteria.

  7. Adaptive resistance to antibiotics in bacteria: a systems biology perspective.

    PubMed

    Sandoval-Motta, Santiago; Aldana, Maximino

    2016-05-01

    Despite all the major breakthroughs in antibiotic development and treatment procedures, there is still no long-term solution to the bacterial antibiotic resistance problem. Among all the known types of resistance, adaptive resistance (AdR) is particularly inconvenient. This phenotype is known to emerge as a consequence of concentration gradients, as well as contact with subinhibitory concentrations of antibiotics, both known to occur in human patients and livestock. Moreover, AdR has been repeatedly correlated with the appearance of multidrug resistance, although the biological processes behind its emergence and evolution are not well understood. Epigenetic inheritance, population structure and heterogeneity, high mutation rates, gene amplification, efflux pumps, and biofilm formation have all been reported as possible explanations for its development. Nonetheless, these concepts taken independently have not been sufficient to prevent AdR's fast emergence or to predict its low stability. New strains of resistant pathogens continue to appear, and none of the new approaches used to kill them (mixed antibiotics, sequential treatments, and efflux inhibitors) are completely efficient. With the advent of systems biology and its toolsets, integrative models that combine experimentally known features with computational simulations have significantly improved our understanding of the emergence and evolution of the adaptive-resistant phenotype. Apart from outlining these findings, we propose that one of the main cornerstones of AdR in bacteria, is the conjunction of two types of mechanisms: one rapidly responding to transient environmental challenges but not very efficient, and another much more effective and specific, but developing on longer time scales. WIREs Syst Biol Med 2016, 8:253-267. doi: 10.1002/wsbm.1335 For further resources related to this article, please visit the WIREs website. PMID:27103502

  8. Adaptation and tolerance of bacteria against acetic acid.

    PubMed

    Trček, Janja; Mira, Nuno Pereira; Jarboe, Laura R

    2015-08-01

    Acetic acid is a weak organic acid exerting a toxic effect to most microorganisms at concentrations as low as 0.5 wt%. This toxic effect results mostly from acetic acid dissociation inside microbial cells, causing a decrease of intracellular pH and metabolic disturbance by the anion, among other deleterious effects. These microbial inhibition mechanisms enable acetic acid to be used as a preservative, although its usefulness is limited by the emergence of highly tolerant spoilage strains. Several biotechnological processes are also inhibited by the accumulation of acetic acid in the growth medium including production of bioethanol from lignocellulosics, wine making, and microbe-based production of acetic acid itself. To design better preservation strategies based on acetic acid and to improve the robustness of industrial biotechnological processes limited by this acid's toxicity, it is essential to deepen the understanding of the underlying toxicity mechanisms. In this sense, adaptive responses that improve tolerance to acetic acid have been well studied in Escherichia coli and Saccharomyces cerevisiae. Strains highly tolerant to acetic acid, either isolated from natural environments or specifically engineered for this effect, represent a unique reservoir of information that could increase our understanding of acetic acid tolerance and contribute to the design of additional tolerance mechanisms. In this article, the mechanisms underlying the acetic acid tolerance exhibited by several bacterial strains are reviewed, with emphasis on the knowledge gathered in acetic acid bacteria and E. coli. A comparison of how these bacterial adaptive responses to acetic acid stress fit to those described in the yeast Saccharomyces cerevisiae is also performed. A systematic comparison of the similarities and dissimilarities of the ways by which different microbial systems surpass the deleterious effects of acetic acid toxicity has not been performed so far, although such exchange

  9. Adaptive resistance to antibiotics in bacteria: a systems biology perspective.

    PubMed

    Sandoval-Motta, Santiago; Aldana, Maximino

    2016-05-01

    Despite all the major breakthroughs in antibiotic development and treatment procedures, there is still no long-term solution to the bacterial antibiotic resistance problem. Among all the known types of resistance, adaptive resistance (AdR) is particularly inconvenient. This phenotype is known to emerge as a consequence of concentration gradients, as well as contact with subinhibitory concentrations of antibiotics, both known to occur in human patients and livestock. Moreover, AdR has been repeatedly correlated with the appearance of multidrug resistance, although the biological processes behind its emergence and evolution are not well understood. Epigenetic inheritance, population structure and heterogeneity, high mutation rates, gene amplification, efflux pumps, and biofilm formation have all been reported as possible explanations for its development. Nonetheless, these concepts taken independently have not been sufficient to prevent AdR's fast emergence or to predict its low stability. New strains of resistant pathogens continue to appear, and none of the new approaches used to kill them (mixed antibiotics, sequential treatments, and efflux inhibitors) are completely efficient. With the advent of systems biology and its toolsets, integrative models that combine experimentally known features with computational simulations have significantly improved our understanding of the emergence and evolution of the adaptive-resistant phenotype. Apart from outlining these findings, we propose that one of the main cornerstones of AdR in bacteria, is the conjunction of two types of mechanisms: one rapidly responding to transient environmental challenges but not very efficient, and another much more effective and specific, but developing on longer time scales. WIREs Syst Biol Med 2016, 8:253-267. doi: 10.1002/wsbm.1335 For further resources related to this article, please visit the WIREs website.

  10. Elucidating Microbial Adaptation Dynamics via Autonomous Exposure and Sampling

    NASA Astrophysics Data System (ADS)

    Grace, J. M.; Verseux, C.; Gentry, D.; Moffet, A.; Thayabaran, R.; Wong, N.; Rothschild, L.

    2013-12-01

    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[Wielgoss et al., 2013]. Although such studies inform fundamental questions about the way adaptation and even speciation occur, they are often limited by labor-intensive manual techniques[Wassmann et al., 2010]. 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[Alcántara-Díaz et al., 2004; Goldman and Travisano, 2011]. 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

  11. Automated measurement and quantification of heterotrophic bacteria in water samples based on the MPN method.

    PubMed

    Fuchsluger, C; Preims, M; Fritz, I

    2011-01-01

    Quantification of heterotrophic bacteria is a widely used measure for water analysis. Especially in terms of drinking water analysis, testing for microorganisms is strictly regulated by the European Drinking Water Directive, including quality criteria and detection limits. The quantification procedure presented in this study is based on the most probable number (MPN) method, which was adapted to comply with the need for a quick and easy screening tool for different kinds of water samples as well as varying microbial loads. Replacing tubes with 24-well titer plates for cultivation of bacteria drastically reduces the amount of culture media and also simplifies incubation. Automated photometric measurement of turbidity instead of visual evaluation of bacterial growth avoids misinterpretation by operators. Definition of a threshold ensures definite and user-independent determination of microbial growth. Calculation of the MPN itself is done using a program provided by the US Food and Drug Administration (FDA). For evaluation of the method, real water samples of different origins as well as pure cultures of bacteria were analyzed in parallel with the conventional plating methods. Thus, the procedure described requires less preparation time, reduces costs and ensures both stable and reliable results for water samples. PMID:20835882

  12. Density-dependent adaptive resistance allows swimming bacteria to colonize an antibiotic gradient.

    PubMed

    Hol, Felix J H; Hubert, Bert; Dekker, Cees; Keymer, Juan E

    2016-01-01

    During antibiotic treatment, antibiotic concentration gradients develop. Little is know regarding the effects of antibiotic gradients on populations of nonresistant bacteria. Using a microfluidic device, we show that high-density motile Escherichia coli populations composed of nonresistant bacteria can, unexpectedly, colonize environments where a lethal concentration of the antibiotic kanamycin is present. Colonizing bacteria establish an adaptively resistant population, which remains viable for over 24 h while exposed to the antibiotic. Quantitative analysis of multiple colonization events shows that collectively swimming bacteria need to exceed a critical population density in order to successfully colonize the antibiotic landscape. After colonization, bacteria are not dormant but show both growth and swimming motility under antibiotic stress. Our results highlight the importance of motility and population density in facilitating adaptive resistance, and indicate that adaptive resistance may be a first step to the emergence of genetically encoded resistance in landscapes of antibiotic gradients.

  13. Adaptive Metropolis Sampling with Product Distributions

    NASA Technical Reports Server (NTRS)

    Wolpert, David H.; Lee, Chiu Fan

    2005-01-01

    The Metropolis-Hastings (MH) algorithm is a way to sample a provided target distribution pi(z). It works by repeatedly sampling a separate proposal distribution T(x,x') to generate a random walk {x(t)}. We consider a modification of the MH algorithm in which T is dynamically updated during the walk. The update at time t uses the {x(t' less than t)} to estimate the product distribution that has the least Kullback-Leibler distance to pi. That estimate is the information-theoretically optimal mean-field approximation to pi. We demonstrate through computer experiments that our algorithm produces samples that are superior to those of the conventional MH algorithm.

  14. Quantum dot conjugates as labels for bacteria in environmental samples

    NASA Astrophysics Data System (ADS)

    Nadeau, Jay; Neal, Andrea; Holden, Patricia; Mielke, Randall

    Quantum dots (fluorescent semiconductor nanocrystals, QDs) have optical and physical properties that make them superior to fluorescent dyes for detection of microorganisms in environmental samples, especially in the field or in flight instruments where optical instrumentation is limited. They are extremely bright, providing a significant fluorescent signal even upon excitation with low-power LEDs. Their absorbance is broad, but their emission spectra are narrow, allowing for many colours to be excited with a single light source and the resulting emission to be readily deconvolved without output filters. They are both fluorescent and electron-dense, permitting them to be used for both fluorescence and electron microscopy. They are resistant to electron radiation and the oxidants most likely to be found on Mars. The challenge for their use in a potential wet-chemistry instrument is two-fold: first, to coat them with specific organic ligands for targeting bacteria in a non-Earth-centric fashion. Second, to ensure their stability during transport and determine potential false-positive results that may arise due to environmental conditions. We present some results on labelling of biofilm samples from the Canadian High Arctic, and some future plans for improvement of labelling techniques and targets that will address the goals of near-term Mars missions.

  15. Adaptive Importance Sampling for Control and Inference

    NASA Astrophysics Data System (ADS)

    Kappen, H. J.; Ruiz, H. C.

    2016-03-01

    Path integral (PI) control problems are a restricted class of non-linear control problems that can be solved formally as a Feynman-Kac PI and can be estimated using Monte Carlo sampling. In this contribution we review PI control theory in the finite horizon case. We subsequently focus on the problem how to compute and represent control solutions. We review the most commonly used methods in robotics and control. Within the PI theory, the question of how to compute becomes the question of importance sampling. Efficient importance samplers are state feedback controllers and the use of these requires an efficient representation. Learning and representing effective state-feedback controllers for non-linear stochastic control problems is a very challenging, and largely unsolved, problem. We show how to learn and represent such controllers using ideas from the cross entropy method. We derive a gradient descent method that allows to learn feed-back controllers using an arbitrary parametrisation. We refer to this method as the path integral cross entropy method or PICE. We illustrate this method for some simple examples. The PI control methods can be used to estimate the posterior distribution in latent state models. In neuroscience these problems arise when estimating connectivity from neural recording data using EM. We demonstrate the PI control method as an accurate alternative to particle filtering.

  16. Costs and Benefits of High Mutation Rates: Adaptive Evolution of Bacteria in the Mouse Gut

    NASA Astrophysics Data System (ADS)

    Giraud, Antoine; Matic, Ivan; Tenaillon, Olivier; Clara, Antonio; Radman, Miroslav; Fons, Michel; Taddei, François

    2001-03-01

    We have shown that bacterial mutation rates change during the experimental colonization of the mouse gut. A high mutation rate was initially beneficial because it allowed faster adaptation, but this benefit disappeared once adaptation was achieved. Mutator bacteria accumulated mutations that, although neutral in the mouse gut, are often deleterious in secondary environments. Consistently, the competitiveness of mutator bacteria is reduced during transmission to and re-colonization of similar hosts. The short-term advantages and long-term disadvantages of mutator bacteria could account for their frequency in nature.

  17. Irregular and adaptive sampling for automatic geophysic measure systems

    NASA Astrophysics Data System (ADS)

    Avagnina, Davide; Lo Presti, Letizia; Mulassano, Paolo

    2000-07-01

    In this paper a sampling method, based on an irregular and adaptive strategy, is described. It can be used as automatic guide for rovers designed to explore terrestrial and planetary environments. Starting from the hypothesis that a explorative vehicle is equipped with a payload able to acquire measurements of interesting quantities, the method is able to detect objects of interest from measured points and to realize an adaptive sampling, while badly describing the not interesting background.

  18. Studies on Bacteria?Like Particles Sampled from the Stratosphere

    SciTech Connect

    Wainwright, M; Weber, P; Smith, J; Hutcheon, I; Klyce, B; Wickramasinghe, N; Narlikar, J; Rajaratnam, P

    2004-07-16

    Bacteria-like particles recovered from the stratosphere and deposited on cellulose acetate membranes have been analyzed to confirm their bacterial nature. One particle appeared to be attached to an inorganic particle apparently by mucoid material typically produced by bacteria. A filamentous structure, morphologically similar to a fungal hypha, was also observed. EDS analysis showed that the particles were all non-mineral and therefore could be biological in nature. However, the composition several clumps of nanobacteria-sized particles were found, by SIMS analysis, to be inconsistent with that of bacteria. The results show that it is dangerous to assume that bacteria-like particles seen under scanning electron microscopy are necessarily bacteria.

  19. Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages.

    PubMed

    Bikard, David; Marraffini, Luciano A

    2012-02-01

    Bacteria are constantly challenged by bacteriophages (viruses that infect bacteria), the most abundant microorganism on earth. Bacteria have evolved a variety of immunity mechanisms to resist bacteriophage infection. In response, bacteriophages can evolve counter-resistance mechanisms and launch a 'virus versus host' evolutionary arms race. In this context, rapid evolution is fundamental for the survival of the bacterial cell. Programmed genetic variation mechanisms at loci involved in immunity against bacteriophages generate diversity at a much faster rate than random point mutation and enable bacteria to quickly adapt and repel infection. Diversity-generating retroelements (DGRs) and phase variation mechanisms enhance the generic (innate) immune response against bacteriophages. On the other hand, the integration of small bacteriophage sequences in CRISPR loci provide bacteria with a virus-specific and sequence-specific adaptive immune response. Therefore, although using different molecular mechanisms, both prokaryotes and higher organisms rely on programmed genetic variation to increase genetic diversity and fight rapidly evolving infectious agents.

  20. Comparison of the multiple-sample means with composite sample results for fecal indicator bacteria by quantitative PCR and culture.

    PubMed

    Converse, Reagan R; Wymer, Larry J; Dufour, Alfred P; Wade, Timothy J

    2012-10-01

    Few studies have addressed the efficacy of composite sampling for measuring indicator bacteria by quantitative PCR (qPCR). We compared results from composited samples with multiple-sample means for culture- and qPCR-based water quality monitoring. Results from composited samples for both methods were similarly correlated to multiple-sample means and predicted criteria exceedances equally.

  1. Harboring oil-degrading bacteria: a potential mechanism of adaptation and survival in corals inhabiting oil-contaminated reefs.

    PubMed

    Al-Dahash, Lulwa M; Mahmoud, Huda M

    2013-07-30

    Certain coral reef systems north of the Arabian Gulf are characterized by corals with a unique ability to thrive and flourish despite the presence of crude oil continuously seeping from natural cracks in the seabed. Harboring oil-degrading bacteria as a part of the holobiont has been investigated as a potential mechanism of adaptation and survival for corals in such systems. The use of conventional and molecular techniques verified a predominance of bacteria affiliated with Gammaproteobacteria, Actinobacteria and Firmicutes in the mucus and tissues of Acropora clathrata and Porites compressa. These bacteria were capable of degrading a wide range of aliphatic (C9-C28) aromatic hydrocarbons (Phenanthrene, Biphenyl, Naphthalene) and crude oil. In addition, microcosms supplied with coral samples and various concentrations of crude oil shifted their bacterial population toward the more advantageous types of oil degraders as oil concentrations increased.

  2. Two-stage sequential sampling: A neighborhood-free adaptive sampling procedure

    USGS Publications Warehouse

    Salehi, M.; Smith, D.R.

    2005-01-01

    Designing an efficient sampling scheme for a rare and clustered population is a challenging area of research. Adaptive cluster sampling, which has been shown to be viable for such a population, is based on sampling a neighborhood of units around a unit that meets a specified condition. However, the edge units produced by sampling neighborhoods have proven to limit the efficiency and applicability of adaptive cluster sampling. We propose a sampling design that is adaptive in the sense that the final sample depends on observed values, but it avoids the use of neighborhoods and the sampling of edge units. Unbiased estimators of population total and its variance are derived using Murthy's estimator. The modified two-stage sampling design is easy to implement and can be applied to a wider range of populations than adaptive cluster sampling. We evaluate the proposed sampling design by simulating sampling of two real biological populations and an artificial population for which the variable of interest took the value either 0 or 1 (e.g., indicating presence and absence of a rare event). We show that the proposed sampling design is more efficient than conventional sampling in nearly all cases. The approach used to derive estimators (Murthy's estimator) opens the door for unbiased estimators to be found for similar sequential sampling designs. ?? 2005 American Statistical Association and the International Biometric Society.

  3. The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis

    PubMed Central

    Bondarev, Vladimir; Richter, Michael; Romano, Stefano; Piel, Jörn; Schwedt, Anne; Schulz-Vogt, Heide N

    2013-01-01

    The majority of strains belonging to the genus Pseudovibrio have been isolated from marine invertebrates such as tunicates, corals and particularly sponges, but the physiology of these bacteria is poorly understood. In this study, we analyse for the first time the genomes of two Pseudovibrio strains – FO-BEG1 and JE062. The strain FO-BEG1 is a required symbiont of a cultivated Beggiatoa strain, a sulfide-oxidizing, autotrophic bacterium, which was initially isolated from a coral. Strain JE062 was isolated from a sponge. The presented data show that both strains are generalistic bacteria capable of importing and oxidizing a wide range of organic and inorganic compounds to meet their carbon, nitrogen, phosphorous and energy requirements under both, oxic and anoxic conditions. Several physiological traits encoded in the analysed genomes were verified in laboratory experiments with both isolates. Besides the versatile metabolic abilities of both Pseudovibrio strains, our study reveals a number of open reading frames and gene clusters in the genomes that seem to be involved in symbiont–host interactions. Both Pseudovibrio strains have the genomic potential to attach to host cells, interact with the eukaryotic cell machinery, produce secondary metabolites and supply the host with cofactors. PMID:23601235

  4. Adaptive Sampling for High Throughput Data Using Similarity Measures

    SciTech Connect

    Bulaevskaya, V.; Sales, A. P.

    2015-05-06

    The need for adaptive sampling arises in the context of high throughput data because the rates of data arrival are many orders of magnitude larger than the rates at which they can be analyzed. A very fast decision must therefore be made regarding the value of each incoming observation and its inclusion in the analysis. In this report we discuss one approach to adaptive sampling, based on the new data point’s similarity to the other data points being considered for inclusion. We present preliminary results for one real and one synthetic data set.

  5. COMPOSITE SAMPLING FOR DETECTION OF COLIFORM BACTERIA IN WATER SUPPLY

    EPA Science Inventory

    Low densities of coliform bacteria introduced into distribution systems may survive in protected habitats. These organisms may interfere with and cause confusion in the use of the coliforms as indicators of sewage contamination of drinking water. Methods of increasing the probabi...

  6. Biomass measurement of methane forming bacteria in environmental samples

    NASA Technical Reports Server (NTRS)

    Martz, R. F.; Sebacher, D. I.; White, D. C.

    1983-01-01

    Methane-forming bacteria contain unusual phytanylglycerol ether phospholipids which can be extracted from the bacteria in sediments and assayed quantitatively by high performance liquid chromatography (HPLC). In this procedure the lipids were extracted, the phospholipids recovered, hydrolyzed, purified by thin layer chromatography, derivatized and assayed by HPLC. Ether lipids were recovered quantitatively from Methanobacterium thermoautotrophicum and sediments at levels as low as 8 x 10(-14) moles. In freshwater and marine sediments the flux of methane to the atmosphere and the methane levels in the pore water reflects the recovery of the phytanyl glycerol ether lipid 'signature'. The proportion of the ether phospholipid to the total recoverable phospholipid was highest in anaerobic digester sewage sludge and deeper subsurface freshwater sediment horizons.

  7. Adaptive importance sampling of random walks on continuous state spaces

    SciTech Connect

    Baggerly, K.; Cox, D.; Picard, R.

    1998-11-01

    The authors consider adaptive importance sampling for a random walk with scoring in a general state space. Conditions under which exponential convergence occurs to the zero-variance solution are reviewed. These results generalize previous work for finite, discrete state spaces in Kollman (1993) and in Kollman, Baggerly, Cox, and Picard (1996). This paper is intended for nonstatisticians and includes considerable explanatory material.

  8. Several methods for concentrating bacteria in fluid samples

    NASA Technical Reports Server (NTRS)

    Thomas, R. R.

    1976-01-01

    The sensitivities of the firefly luciferase - ATP flow system and luminol flow system were established as 300,000 E. coli per milliliter and 10,000 E. coli per milliliter respectively. To achieve the detection limit of 1,000 bacteria per milliliter previously established, a method of concentrating microorganisms using a sartorius membrane filter system is investigated. Catalase in 50% ethanol is found to be a stable luminol standard and can be used up to 24 hours with only a 10% loss of activity. The luminol reagent is also stable over a 24 hour period. A method of preparing relatively inexpensive luciferase from desiccated firefly tails is developed.

  9. Adaptive video compressed sampling in the wavelet domain

    NASA Astrophysics Data System (ADS)

    Dai, Hui-dong; Gu, Guo-hua; He, Wei-ji; Chen, Qian; Mao, Tian-yi

    2016-07-01

    In this work, we propose a multiscale video acquisition framework called adaptive video compressed sampling (AVCS) that involves sparse sampling and motion estimation in the wavelet domain. Implementing a combination of a binary DMD and a single-pixel detector, AVCS acquires successively finer resolution sparse wavelet representations in moving regions directly based on extended wavelet trees, and alternately uses these representations to estimate the motion in the wavelet domain. Then, we can remove the spatial and temporal redundancies and provide a method to reconstruct video sequences from compressed measurements in real time. In addition, the proposed method allows adaptive control over the reconstructed video quality. The numerical simulation and experimental results indicate that AVCS performs better than the conventional CS-based methods at the same sampling rate even under the influence of noise, and the reconstruction time and measurements required can be significantly reduced.

  10. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.

    PubMed

    Goldstein, Richard A; Soyer, Orkun S

    2008-05-23

    Bacteria are able to sense and respond to a variety of external stimuli, with responses that vary from stimuli to stimuli and from species to species. The best-understood is chemotaxis in the model organism Escherichia coli, where the dynamics and the structure of the underlying pathway are well characterised. It is not clear, however, how well this detailed knowledge applies to mechanisms mediating responses to other stimuli or to pathways in other species. Furthermore, there is increasing experimental evidence that bacteria integrate responses from different stimuli to generate a coherent taxis response. We currently lack a full understanding of the different pathway structures and dynamics and how this integration is achieved. In order to explore different pathway structures and dynamics that can underlie taxis responses in bacteria, we perform a computational simulation of the evolution of taxis. This approach starts with a population of virtual bacteria that move in a virtual environment based on the dynamics of the simple biochemical pathways they harbour. As mutations lead to changes in pathway structure and dynamics, bacteria better able to localise with favourable conditions gain a selective advantage. We find that a certain dynamics evolves consistently under different model assumptions and environments. These dynamics, which we call non-adaptive dynamics, directly couple tumbling probability of the cell to increasing stimuli. Dynamics that are adaptive under a wide range of conditions, as seen in the chemotaxis pathway of E. coli, do not evolve in these evolutionary simulations. However, we find that stimulus scarcity and fluctuations during evolution results in complex pathway dynamics that result both in adaptive and non-adaptive dynamics depending on basal stimuli levels. Further analyses of evolved pathway structures show that effective taxis dynamics can be mediated with as few as two components. The non-adaptive dynamics mediating taxis responses

  11. Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions

    PubMed Central

    Shklarsh, Adi; Ariel, Gil; Schneidman, Elad; Ben-Jacob, Eshel

    2011-01-01

    Collective navigation and swarming have been studied in animal groups, such as fish schools, bird flocks, bacteria, and slime molds. Computer modeling has shown that collective behavior of simple agents can result from simple interactions between the agents, which include short range repulsion, intermediate range alignment, and long range attraction. Here we study collective navigation of bacteria-inspired smart agents in complex terrains, with adaptive interactions that depend on performance. More specifically, each agent adjusts its interactions with the other agents according to its local environment – by decreasing the peers' influence while navigating in a beneficial direction, and increasing it otherwise. We show that inclusion of such performance dependent adaptable interactions significantly improves the collective swarming performance, leading to highly efficient navigation, especially in complex terrains. Notably, to afford such adaptable interactions, each modeled agent requires only simple computational capabilities with short-term memory, which can easily be implemented in simple swarming robots. PMID:21980274

  12. Comparison of the Multiple-sample means with composite sample results for fecal indicator bacteria by quantitative PCR and culture

    EPA Science Inventory

    ABSTRACT: Few studies have addressed the efficacy of composite sampling for measurement of indicator bacteria by QPCR. In this study, composite results were compared to single sample results for culture- and QPCR-based water quality monitoring. Composite results for both methods ...

  13. Population Screening Using Sewage Reveals Pan-Resistant Bacteria in Hospital and Community Samples

    PubMed Central

    Mileguir, Fernando; Azar, Roberto; Smollan, Gill; Belausov, Natasha; Rahav, Galia; Shamiss, Ari; Mendelson, Ella; Keller, Nathan

    2016-01-01

    The presence of pan-resistant bacteria worldwide possesses a threat to global health. It is difficult to evaluate the extent of carriage of resistant bacteria in the population. Sewage sampling is a possible way to monitor populations. We evaluated the presence of pan-resistant bacteria in Israeli sewage collected from all over Israel, by modifying the pour plate method for heterotrophic plate count technique using commercial selective agar plates. This method enables convenient and fast sewage sampling and detection. We found that sewage in Israel contains multiple pan-resistant bacteria including carbapenemase resistant Enterobacteriacae carrying blaKPC and blaNDM-1, MRSA and VRE. blaKPC carrying Klebsiella pneumonia and Enterobacter cloacae were the most common Enterobacteriacae drug resistant bacteria found in the sewage locations we sampled. Klebsiella pneumonia, Enterobacter spp., Escherichia coli and Citrobacter spp. were the 4 main CRE isolated from Israeli sewage and also from clinical samples in our clinical microbiology laboratory. Hospitals and Community sewage had similar percentage of positive samplings for blaKPC and blaNDM-1. VRE was found to be more abundant in sewage in Israel than MRSA but there were more locations positive for MRSA and VRE bacteria in Hospital sewage than in the Community. Therefore, our upgrade of the pour plate method for heterotrophic plate count technique using commercial selective agar plates can be a useful tool for routine screening and monitoring of the population for pan-resistant bacteria using sewage. PMID:27780222

  14. Anti-Biofilm Activities from Marine Cold Adapted Bacteria Against Staphylococci and Pseudomonas aeruginosa

    PubMed Central

    Papa, Rosanna; Selan, Laura; Parrilli, Ermenegilda; Tilotta, Marco; Sannino, Filomena; Feller, Georges; Tutino, Maria L.; Artini, Marco

    2015-01-01

    Microbial biofilms have great negative impacts on the world’s economy and pose serious problems to industry, public health and medicine. The interest in the development of new approaches for the prevention and treatment of bacterial adhesion and biofilm formation has increased. Since, bacterial pathogens living in biofilm induce persistent chronic infections due to the resistance to antibiotics and host immune system. A viable approach should target adhesive properties without affecting bacterial vitality in order to avoid the appearance of resistant mutants. Many bacteria secrete anti-biofilm molecules that function in regulating biofilm architecture or mediating the release of cells from it during the dispersal stage of biofilm life cycle. Cold-adapted marine bacteria represent an untapped reservoir of biodiversity able to synthesize a broad range of bioactive compounds, including anti-biofilm molecules. The anti-biofilm activity of cell-free supernatants derived from sessile and planktonic cultures of cold-adapted bacteria belonging to Pseudoalteromonas, Psychrobacter, and Psychromonas species were tested against Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa strains. Reported results demonstrate that we have selected supernatants, from cold-adapted marine bacteria, containing non-biocidal agents able to destabilize biofilm matrix of all tested pathogens without killing cells. A preliminary physico-chemical characterization of supernatants was also performed, and these analyses highlighted the presence of molecules of different nature that act by inhibiting biofilm formation. Some of them are also able to impair the initial attachment of the bacterial cells to the surface, thus likely containing molecules acting as anti-biofilm surfactant molecules. The described ability of cold-adapted bacteria to produce effective anti-biofilm molecules paves the way to further characterization of the most promising molecules and to test their

  15. Anti-Biofilm Activities from Marine Cold Adapted Bacteria Against Staphylococci and Pseudomonas aeruginosa.

    PubMed

    Papa, Rosanna; Selan, Laura; Parrilli, Ermenegilda; Tilotta, Marco; Sannino, Filomena; Feller, Georges; Tutino, Maria L; Artini, Marco

    2015-01-01

    Microbial biofilms have great negative impacts on the world's economy and pose serious problems to industry, public health and medicine. The interest in the development of new approaches for the prevention and treatment of bacterial adhesion and biofilm formation has increased. Since, bacterial pathogens living in biofilm induce persistent chronic infections due to the resistance to antibiotics and host immune system. A viable approach should target adhesive properties without affecting bacterial vitality in order to avoid the appearance of resistant mutants. Many bacteria secrete anti-biofilm molecules that function in regulating biofilm architecture or mediating the release of cells from it during the dispersal stage of biofilm life cycle. Cold-adapted marine bacteria represent an untapped reservoir of biodiversity able to synthesize a broad range of bioactive compounds, including anti-biofilm molecules. The anti-biofilm activity of cell-free supernatants derived from sessile and planktonic cultures of cold-adapted bacteria belonging to Pseudoalteromonas, Psychrobacter, and Psychromonas species were tested against Staphylococcus aureus, Staphylococcus epidermidis, and Pseudomonas aeruginosa strains. Reported results demonstrate that we have selected supernatants, from cold-adapted marine bacteria, containing non-biocidal agents able to destabilize biofilm matrix of all tested pathogens without killing cells. A preliminary physico-chemical characterization of supernatants was also performed, and these analyses highlighted the presence of molecules of different nature that act by inhibiting biofilm formation. Some of them are also able to impair the initial attachment of the bacterial cells to the surface, thus likely containing molecules acting as anti-biofilm surfactant molecules. The described ability of cold-adapted bacteria to produce effective anti-biofilm molecules paves the way to further characterization of the most promising molecules and to test their

  16. Comparative Proteogenomics of Twelve Roseobacter Exoproteomes Reveals Different Adaptive Strategies Among These Marine Bacteria*

    PubMed Central

    Christie-Oleza, Joseph Alexander; Piña-Villalonga, Juana Maria; Bosch, Rafael; Nogales, Balbina; Armengaud, Jean

    2012-01-01

    Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port. The significance of this specific fraction of the exoproteome is discussed. PMID:22122883

  17. Adaptive Sampling Algorithms for Probabilistic Risk Assessment of Nuclear Simulations

    SciTech Connect

    Diego Mandelli; Dan Maljovec; Bei Wang; Valerio Pascucci; Peer-Timo Bremer

    2013-09-01

    Nuclear simulations are often computationally expensive, time-consuming, and high-dimensional with respect to the number of input parameters. Thus exploring the space of all possible simulation outcomes is infeasible using finite computing resources. During simulation-based probabilistic risk analysis, it is important to discover the relationship between a potentially large number of input parameters and the output of a simulation using as few simulation trials as possible. This is a typical context for performing adaptive sampling where a few observations are obtained from the simulation, a surrogate model is built to represent the simulation space, and new samples are selected based on the model constructed. The surrogate model is then updated based on the simulation results of the sampled points. In this way, we attempt to gain the most information possible with a small number of carefully selected sampled points, limiting the number of expensive trials needed to understand features of the simulation space. We analyze the specific use case of identifying the limit surface, i.e., the boundaries in the simulation space between system failure and system success. In this study, we explore several techniques for adaptively sampling the parameter space in order to reconstruct the limit surface. We focus on several adaptive sampling schemes. First, we seek to learn a global model of the entire simulation space using prediction models or neighborhood graphs and extract the limit surface as an iso-surface of the global model. Second, we estimate the limit surface by sampling in the neighborhood of the current estimate based on topological segmentations obtained locally. Our techniques draw inspirations from topological structure known as the Morse-Smale complex. We highlight the advantages and disadvantages of using a global prediction model versus local topological view of the simulation space, comparing several different strategies for adaptive sampling in both

  18. Stochastic, Adaptive Sampling of Information by Microvilli in Fly Photoreceptors

    PubMed Central

    Song, Zhuoyi; Postma, Marten; Billings, Stephen A.; Coca, Daniel; Hardie, Roger C.; Juusola, Mikko

    2012-01-01

    Summary Background In fly photoreceptors, light is focused onto a photosensitive waveguide, the rhabdomere, consisting of tens of thousands of microvilli. Each microvillus is capable of generating elementary responses, quantum bumps, in response to single photons using a stochastically operating phototransduction cascade. Whereas much is known about the cascade reactions, less is known about how the concerted action of the microvilli population encodes light changes into neural information and how the ultrastructure and biochemical machinery of photoreceptors of flies and other insects evolved in relation to the information sampling and processing they perform. Results We generated biophysically realistic fly photoreceptor models, which accurately simulate the encoding of visual information. By comparing stochastic simulations with single cell recordings from Drosophila photoreceptors, we show how adaptive sampling by 30,000 microvilli captures the temporal structure of natural contrast changes. Following each bump, individual microvilli are rendered briefly (∼100–200 ms) refractory, thereby reducing quantum efficiency with increasing intensity. The refractory period opposes saturation, dynamically and stochastically adjusting availability of microvilli (bump production rate: sample rate), whereas intracellular calcium and voltage adapt bump amplitude and waveform (sample size). These adapting sampling principles result in robust encoding of natural light changes, which both approximates perceptual contrast constancy and enhances novel events under different light conditions, and predict information processing across a range of species with different visual ecologies. Conclusions These results clarify why fly photoreceptors are structured the way they are and function as they do, linking sensory information to sensory evolution and revealing benefits of stochasticity for neural information processing. PMID:22704990

  19. Adaptive Sampling of Time Series During Remote Exploration

    NASA Technical Reports Server (NTRS)

    Thompson, David R.

    2012-01-01

    This work deals with the challenge of online adaptive data collection in a time series. A remote sensor or explorer agent adapts its rate of data collection in order to track anomalous events while obeying constraints on time and power. This problem is challenging because the agent has limited visibility (all its datapoints lie in the past) and limited control (it can only decide when to collect its next datapoint). This problem is treated from an information-theoretic perspective, fitting a probabilistic model to collected data and optimizing the future sampling strategy to maximize information gain. The performance characteristics of stationary and nonstationary Gaussian process models are compared. Self-throttling sensors could benefit environmental sensor networks and monitoring as well as robotic exploration. Explorer agents can improve performance by adjusting their data collection rate, preserving scarce power or bandwidth resources during uninteresting times while fully covering anomalous events of interest. For example, a remote earthquake sensor could conserve power by limiting its measurements during normal conditions and increasing its cadence during rare earthquake events. A similar capability could improve sensor platforms traversing a fixed trajectory, such as an exploration rover transect or a deep space flyby. These agents can adapt observation times to improve sample coverage during moments of rapid change. An adaptive sampling approach couples sensor autonomy, instrument interpretation, and sampling. The challenge is addressed as an active learning problem, which already has extensive theoretical treatment in the statistics and machine learning literature. A statistical Gaussian process (GP) model is employed to guide sample decisions that maximize information gain. Nonsta tion - ary (e.g., time-varying) covariance relationships permit the system to represent and track local anomalies, in contrast with current GP approaches. Most common GP models

  20. Distributed database kriging for adaptive sampling (D²KAS)

    DOE PAGES

    Roehm, Dominic; Pavel, Robert S.; Barros, Kipton; Rouet-Leduc, Bertrand; McPherson, Allen L.; Germann, Timothy C.; Junghans, Christoph

    2015-03-18

    We present an adaptive sampling method supplemented by a distributed database and a prediction method for multiscale simulations using the Heterogeneous Multiscale Method. A finite-volume scheme integrates the macro-scale conservation laws for elastodynamics, which are closed by momentum and energy fluxes evaluated at the micro-scale. In the original approach, molecular dynamics (MD) simulations are launched for every macro-scale volume element. Our adaptive sampling scheme replaces a large fraction of costly micro-scale MD simulations with fast table lookup and prediction. The cloud database Redis provides the plain table lookup, and with locality aware hashing we gather input data for our predictionmore » scheme. For the latter we use kriging, which estimates an unknown value and its uncertainty (error) at a specific location in parameter space by using weighted averages of the neighboring points. We find that our adaptive scheme significantly improves simulation performance by a factor of 2.5 to 25, while retaining high accuracy for various choices of the algorithm parameters.« less

  1. Distributed database kriging for adaptive sampling (D²KAS)

    SciTech Connect

    Roehm, Dominic; Pavel, Robert S.; Barros, Kipton; Rouet-Leduc, Bertrand; McPherson, Allen L.; Germann, Timothy C.; Junghans, Christoph

    2015-03-18

    We present an adaptive sampling method supplemented by a distributed database and a prediction method for multiscale simulations using the Heterogeneous Multiscale Method. A finite-volume scheme integrates the macro-scale conservation laws for elastodynamics, which are closed by momentum and energy fluxes evaluated at the micro-scale. In the original approach, molecular dynamics (MD) simulations are launched for every macro-scale volume element. Our adaptive sampling scheme replaces a large fraction of costly micro-scale MD simulations with fast table lookup and prediction. The cloud database Redis provides the plain table lookup, and with locality aware hashing we gather input data for our prediction scheme. For the latter we use kriging, which estimates an unknown value and its uncertainty (error) at a specific location in parameter space by using weighted averages of the neighboring points. We find that our adaptive scheme significantly improves simulation performance by a factor of 2.5 to 25, while retaining high accuracy for various choices of the algorithm parameters.

  2. Learning Adaptive Forecasting Models from Irregularly Sampled Multivariate Clinical Data

    PubMed Central

    Liu, Zitao; Hauskrecht, Milos

    2016-01-01

    Building accurate predictive models of clinical multivariate time series is crucial for understanding of the patient condition, the dynamics of a disease, and clinical decision making. A challenging aspect of this process is that the model should be flexible and adaptive to reflect well patient-specific temporal behaviors and this also in the case when the available patient-specific data are sparse and short span. To address this problem we propose and develop an adaptive two-stage forecasting approach for modeling multivariate, irregularly sampled clinical time series of varying lengths. The proposed model (1) learns the population trend from a collection of time series for past patients; (2) captures individual-specific short-term multivariate variability; and (3) adapts by automatically adjusting its predictions based on new observations. The proposed forecasting model is evaluated on a real-world clinical time series dataset. The results demonstrate the benefits of our approach on the prediction tasks for multivariate, irregularly sampled clinical time series, and show that it can outperform both the population based and patient-specific time series prediction models in terms of prediction accuracy. PMID:27525189

  3. Distributed Database Kriging for Adaptive Sampling (D2 KAS)

    NASA Astrophysics Data System (ADS)

    Roehm, Dominic; Pavel, Robert S.; Barros, Kipton; Rouet-Leduc, Bertrand; McPherson, Allen L.; Germann, Timothy C.; Junghans, Christoph

    2015-07-01

    We present an adaptive sampling method supplemented by a distributed database and a prediction method for multiscale simulations using the Heterogeneous Multiscale Method. A finite-volume scheme integrates the macro-scale conservation laws for elastodynamics, which are closed by momentum and energy fluxes evaluated at the micro-scale. In the original approach, molecular dynamics (MD) simulations are launched for every macro-scale volume element. Our adaptive sampling scheme replaces a large fraction of costly micro-scale MD simulations with fast table lookup and prediction. The cloud database Redis provides the plain table lookup, and with locality aware hashing we gather input data for our prediction scheme. For the latter we use kriging, which estimates an unknown value and its uncertainty (error) at a specific location in parameter space by using weighted averages of the neighboring points. We find that our adaptive scheme significantly improves simulation performance by a factor of 2.5-25, while retaining high accuracy for various choices of the algorithm parameters.

  4. Adaptive Sampling for Learning Gaussian Processes Using Mobile Sensor Networks

    PubMed Central

    Xu, Yunfei; Choi, Jongeun

    2011-01-01

    This paper presents a novel class of self-organizing sensing agents that adaptively learn an anisotropic, spatio-temporal Gaussian process using noisy measurements and move in order to improve the quality of the estimated covariance function. This approach is based on a class of anisotropic covariance functions of Gaussian processes introduced to model a broad range of spatio-temporal physical phenomena. The covariance function is assumed to be unknown a priori. Hence, it is estimated by the maximum a posteriori probability (MAP) estimator. The prediction of the field of interest is then obtained based on the MAP estimate of the covariance function. An optimal sampling strategy is proposed to minimize the information-theoretic cost function of the Fisher Information Matrix. Simulation results demonstrate the effectiveness and the adaptability of the proposed scheme. PMID:22163785

  5. Recognition of Extracellular Bacteria by NLRs and Its Role in the Development of Adaptive Immunity

    PubMed Central

    Ferrand, Jonathan; Ferrero, Richard Louis

    2013-01-01

    Innate immune recognition of bacteria is the first requirement for mounting an effective immune response able to control infection. Over the previous decade, the general paradigm was that extracellular bacteria were only sensed by cell surface-expressed Toll-like receptors (TLRs), whereas cytoplasmic sensors, including members of the Nod-like receptor (NLR) family, were specific to pathogens capable of breaching the host cell membrane. It has become apparent, however, that intracellular innate immune molecules, such as the NLRs, play key roles in the sensing of not only intracellular, but also extracellular bacterial pathogens or their components. In this review, we will discuss the various mechanisms used by bacteria to activate NLR signaling in host cells. These mechanisms include bacterial secretion systems, pore-forming toxins, and outer membrane vesicles. We will then focus on the influence of NLR activation on the development of adaptive immune responses in different cell types. PMID:24155747

  6. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria.

    PubMed

    Veith, Nadine; Feldman-Salit, Anna; Cojocaru, Vlad; Henrich, Stefan; Kummer, Ursula; Wade, Rebecca C

    2013-01-01

    Pyruvate kinase (PYK) is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric activation may

  7. [Quantitative use of fluorescence in situ hybridization to detect syntrophic acetogenic bacteria in anaerobic environmental samples].

    PubMed

    Li, Yan-Na; Xu, Ke-Wei; Du, Guo-Cheng; Chen, Jian; Liu, He

    2007-12-01

    Syntrophic acetogenic bacteria, an important functional one in anaerobic habitats, were detected and counted by fluorescence in situ hybridization (FISH) technology by using 16S rRNA-based oligonucleotide probes. For enumeration and quantification of the targeted bacteria, an attempt was made to optimize the hybridization conditions. The optimum conditions are as follows: a fixation time of 19h, a dehydrated time of 5 min, and a formamide concentration of 55% in hybridized solution. The abundance of syntrophic acetogenic bacteria of different environmental samples were quantified by FISH and the results showed that Upflow Anaerobic Sludge Reactor (UASB) treating STHZ high-concentration organic wastewater and the digestive tract of some animals were the main habitats of syntrophic acetogenic bacteria. The numbers of syntrophic acetogenic bacteria in UASB and cattle manure were 1.70 x 10(9) cells/mL sample and 6.50 x 10(8) cells/mL sample, respectively. Meanwhile, the sediments of rivers and lakes existed less of the bacteria and the contents of them were just about 1.20 x 10(8) cells/mL sample in Taihu lake.

  8. Effect of imperfect detectability on adaptive and conventional sampling: simulated sampling of freshwater mussels in the upper Mississippi River.

    PubMed

    Smith, David R; Gray, Brian R; Newton, Teresa J; Nichols, Doug

    2010-11-01

    Adaptive sampling designs are recommended where, as is typical with freshwater mussels, the outcome of interest is rare and clustered. However, the performance of adaptive designs has not been investigated when outcomes are not only rare and clustered but also imperfectly detected. We address this combination of challenges using data simulated to mimic properties of freshwater mussels from a reach of the upper Mississippi River. Simulations were conducted under a range of sample sizes and detection probabilities. Under perfect detection, efficiency of the adaptive sampling design increased relative to the conventional design as sample size increased and as density decreased. Also, the probability of sampling occupied habitat was four times higher for adaptive than conventional sampling of the lowest density population examined. However, imperfect detection resulted in substantial biases in sample means and variances under both adaptive sampling and conventional designs. The efficiency of adaptive sampling declined with decreasing detectability. Also, the probability of encountering an occupied unit during adaptive sampling, relative to conventional sampling declined with decreasing detectability. Thus, the potential gains in the application of adaptive sampling to rare and clustered populations relative to conventional sampling are reduced when detection is imperfect. The results highlight the need to increase or estimate detection to improve performance of conventional and adaptive sampling designs.

  9. Gut bacteria facilitate adaptation to crop rotation in the western corn rootworm.

    PubMed

    Chu, Chia-Ching; Spencer, Joseph L; Curzi, Matías J; Zavala, Jorge A; Seufferheld, Manfredo J

    2013-07-16

    Insects are constantly adapting to human-driven landscape changes; however, the roles of their gut microbiota in these processes remain largely unknown. The western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) (Coleoptera: Chrysomelidae) is a major corn pest that has been controlled via annual rotation between corn (Zea mays) and nonhost soybean (Glycine max) in the United States. This practice selected for a "rotation-resistant" variant (RR-WCR) with reduced ovipositional fidelity to cornfields. When in soybean fields, RR-WCRs also exhibit an elevated tolerance of antiherbivory defenses (i.e., cysteine protease inhibitors) expressed in soybean foliage. Here we show that gut bacterial microbiota is an important factor facilitating this corn specialist's (WCR's) physiological adaptation to brief soybean herbivory. Comparisons of gut microbiota between RR- and wild-type WCR (WT-WCR) revealed concomitant shifts in bacterial community structure with host adaptation to soybean diets. Antibiotic suppression of gut bacteria significantly reduced RR-WCR tolerance of soybean herbivory to the level of WT-WCR, whereas WT-WCR were unaffected. Our findings demonstrate that gut bacteria help to facilitate rapid adaptation of insects in managed ecosystems.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. Use of quantitative PCR to evaluate methods of bacteria sampling in periodontal patients.

    PubMed

    Masunaga, Hiroshi; Tsutae, Wataru; Oh, Hyun; Shinozuka, Naoki; Kishimoto, Noriyoshi; Ogata, Yorimasa

    2010-12-01

    Periodontal disease is associated with specific periodontal pathogens and may persist as gingivitis or progress to more severe disease. The bacteria involved in disease initiation and progression have not been identified. We used quantitative polymerase chain reaction (PCR) to compare the levels of Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, and total bacteria detected by different sampling methods. On the basis of the results of clinical examinations, 57 patients were divided into 3 groups: healthy group (group A), gingivitis group (group B), and periodontitis group (group C). Bacterial samples were collected from saliva, mouthwash, and by paper-point sampling of gingival crevicular fluid (GCF), and the samples were analyzed with quantitative PCR targeting 16S rRNA. The numbers of total bacteria in samples of GCF, saliva, and mouthwash were 10⁵ to 10⁶, 10⁸, and 10⁷, respectively, per milliliter. The number of P. gingivalis in GCF samples was lower than 10 in group A; however, in groups B and C, the values were 10³ and 10⁴, respectively, indicating that the number of P. gingivalis increased with worsening clinical status. Findings were similar in the samples of saliva and mouthwash. The numbers of T. forsythia showed a pattern similar to that of P. gingivalis in all 3 samples. These results suggest that saliva and mouthwash samples are clinically useful for bacterial testing of periodontal diseases by quantitative PCR. In addition, mouthwash sampling is more feasible and straightforward than saliva sampling.

  12. Coincident plasmids and antimicrobial resistance in marine bacteria isolated from polluted and unpolluted Atlantic Ocean Samples

    SciTech Connect

    Baya, A.M.; Brayton, P.R.; Brown, V.L.; Grimes, D.J.; Russek-Cohen, E.; Colwell, R.R.

    1986-06-01

    Sewage effluent and outfall confluence samples were collected at the Barceloneta Regional Treatment Plant in Barceloneta, Puerto Rico; outfall confluence samples at Ocean City, Md., were also collected. Samples from uncontaminated open ocean areas served as clean-water controls. Bacteria were enriched in marine broth 2216 amended with 1 ..mu..g of one of a set of chemical selected for study per ml: nitrobenzene, dibutyl phthalate, m-cresol, o-cresol, 4-nitroaniline, bis(tributyltin) oxide, and quinone. MICs of the chemicals were determined individually for all isolates. Bacterial isolates were evaluated for resistance to nine different antibiotics and for the presence of plasmid DNA. Treated sewage was found to contain large numbers of bacteria simultaneously possessing antibiotic resistance, chemical resistance, and multiple bands of plasmic DNA. Bacteria resistant to penicillin, erythromycin, nalidixic acid, ampicillin, m-cresol, quinone, and bis(tributyltin) oxide were detected in nearly all samples, but only sewage outfall confluence samples yielded bacterial isolates that were resistant to streptomycin. Bacteria resistant to a combination of antibiotics, including kanamycin, chloramphenicol, gentamicin, and tetracycline, were isolated only from sewage effluent samples. It is concluded that bacterial isolates derived from toxic chemical wastes more frequently contain plasmid DNA and demonstrate antimicrobial resistance than do bacterial isolates from domestic sewage-impacted waters or from uncontaminated open ocean sites.

  13. Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria.

    PubMed

    Zhu, Bo; Ibrahim, Muhammad; Cui, Zhouqi; Xie, Guanlin; Jin, Gulei; Kube, Michael; Li, Bin; Zhou, Xueping

    2016-08-01

    Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria. PMID:26859773

  14. Fluorescence in situ hybridization rapidly detects three different pathogenic bacteria in urinary tract infection samples.

    PubMed

    Wu, Qing; Li, Yan; Wang, Ming; Pan, Xiao P; Tang, Yong F

    2010-11-01

    The detection of pathogenic bacteria in urine is an important criterion for diagnosing urinary tract infections (UTIs). By using fluorescence in situ hybridization (FISH) with rRNA-targeted, fluorescently labeled oligonucleotide probes, bacterial pathogens present in urine samples were identified within 3-4 h. In this study, three probes that are specific for Escherichia coli, Enterococcus faecalis and Staphylococcus aureus were designed based on the conserved 16S RNA sequences, whereas probe Eub338 broadly recognizes all bacteria. We collected a total of 1000 urine samples, and 325 of these samples tested positive for a UTI via traditional culturing techniques; additionally, all 325 of these samples tested positive with the Eub338 probe in FISH analysis. FISH analyses with species-specific probes were performed in parallel to the test the ability to differentiate among several pathogenic bacteria. The samples for these experiments included 76 E. coli infected samples, 32 E. faecalis infected samples and 9 S. aureus infected samples. Compared to conventional methods of bacterial identification, the FISH method produced positive results for >90% of the samples tested. FISH has the potential to become an extremely useful diagnostic tool for UTIs because it has a quick turnaround time and high accuracy.

  15. Acetic acid bacteria genomes reveal functional traits for adaptation to life in insect guts.

    PubMed

    Chouaia, Bessem; Gaiarsa, Stefano; Crotti, Elena; Comandatore, Francesco; Degli Esposti, Mauro; Ricci, Irene; Alma, Alberto; Favia, Guido; Bandi, Claudio; Daffonchio, Daniele

    2014-04-01

    Acetic acid bacteria (AAB) live in sugar rich environments, including food matrices, plant tissues, and the gut of sugar-feeding insects. By comparing the newly sequenced genomes of Asaia platycodi and Saccharibacter sp., symbionts of Anopheles stephensi and Apis mellifera, respectively, with those of 14 other AAB, we provide a genomic view of the evolutionary pattern of this bacterial group and clues on traits that explain the success of AAB as insect symbionts. A specific pre-adaptive trait, cytochrome bo3 ubiquinol oxidase, appears ancestral in AAB and shows a phylogeny that is congruent with that of the genomes. The functional properties of this terminal oxidase might have allowed AAB to adapt to the diverse oxygen levels of arthropod guts.

  16. Acetic Acid Bacteria Genomes Reveal Functional Traits for Adaptation to Life in Insect Guts

    PubMed Central

    Chouaia, Bessem; Gaiarsa, Stefano; Crotti, Elena; Comandatore, Francesco; Degli Esposti, Mauro; Ricci, Irene; Alma, Alberto; Favia, Guido; Bandi, Claudio; Daffonchio, Daniele

    2014-01-01

    Acetic acid bacteria (AAB) live in sugar rich environments, including food matrices, plant tissues, and the gut of sugar-feeding insects. By comparing the newly sequenced genomes of Asaia platycodi and Saccharibacter sp., symbionts of Anopheles stephensi and Apis mellifera, respectively, with those of 14 other AAB, we provide a genomic view of the evolutionary pattern of this bacterial group and clues on traits that explain the success of AAB as insect symbionts. A specific pre-adaptive trait, cytochrome bo3 ubiquinol oxidase, appears ancestral in AAB and shows a phylogeny that is congruent with that of the genomes. The functional properties of this terminal oxidase might have allowed AAB to adapt to the diverse oxygen levels of arthropod guts. PMID:24682158

  17. Rapid, culture-independent, optical diagnostics of centrifugally captured bacteria from urine samples

    PubMed Central

    Schröder, Ulrich-Christian; Bokeloh, Frank; O'Sullivan, Mary; Glaser, Uwe; Wolf, Katharina; Pfister, Wolfgang; Popp, Jürgen; Ducrée, Jens; Neugebauer, Ute

    2015-01-01

    This work presents a polymeric centrifugal microfluidic platform for the rapid and sensitive identification of bacteria directly from urine, thus eliminating time-consuming cultivation steps. This “Lab-on-a-Disc” platform utilizes the rotationally induced centrifugal field to efficiently capture bacteria directly from suspension within a glass-polymer hybrid chip. Once trapped in an array of small V-shaped structures, the bacteria are readily available for spectroscopic characterization, such as Raman spectroscopic fingerprinting, providing valuable information on the characteristics of the captured bacteria. Utilising fluorescence microscopy, quantification of the bacterial load has been achieved for concentrations above 2 × 10−7 cells ml−1 within a 4 μl sample. As a pilot application, we characterize urine samples from patients with urinary tract infections. Following minimal sample preparation, Raman spectra of the bacteria are recorded following centrifugal capture in stopped-flow sedimentation mode. Utilizing advanced analysis algorithms, including extended multiplicative scattering correction, high-quality Raman spectra of different pathogens, such as Escherichia coli or Enterococcus faecalis, are obtained from the analyzed patient samples. The whole procedure, including sample preparation, requires about 1 h to obtain a valuable result, marking a significant reduction in diagnosis time when compared to the 24 h and more typically required for standard microbiological methods. As this cost-efficient centrifugal cartridge can be operated using low-complexity, widely automated instrumentation, while providing valuable bacterial identification in urine samples in a greatly reduced time-period, our opto-microfluidic Lab-on-a-Disc device demonstrates great potential for next-generation patient diagnostics at the of point-of-care. PMID:26339318

  18. An efficient sampling algorithm with adaptations for Bayesian variable selection.

    PubMed

    Araki, Takamitsu; Ikeda, Kazushi; Akaho, Shotaro

    2015-01-01

    In Bayesian variable selection, indicator model selection (IMS) is a class of well-known sampling algorithms, which has been used in various models. The IMS is a class of methods that uses pseudo-priors and it contains specific methods such as Gibbs variable selection (GVS) and Kuo and Mallick's (KM) method. However, the efficiency of the IMS strongly depends on the parameters of a proposal distribution and the pseudo-priors. Specifically, the GVS determines their parameters based on a pilot run for a full model and the KM method sets their parameters as those of priors, which often leads to slow mixings of them. In this paper, we propose an algorithm that adapts the parameters of the IMS during running. The parameters obtained on the fly provide an appropriate proposal distribution and pseudo-priors, which improve the mixing of the algorithm. We also prove the convergence theorem of the proposed algorithm, and confirm that the algorithm is more efficient than the conventional algorithms by experiments of the Bayesian variable selection.

  19. Molecular Adaptation Mechanisms Employed by Ethanologenic Bacteria in Response to Lignocellulose-derived Inhibitory Compounds

    PubMed Central

    Ibraheem, Omodele; Ndimba, Bongani K.

    2013-01-01

    Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains. PMID:23847442

  20. Molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds.

    PubMed

    Ibraheem, Omodele; Ndimba, Bongani K

    2013-01-01

    Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains. PMID:23847442

  1. Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids

    PubMed Central

    Pazos-Perez, Nicolas; Pazos, Elena; Catala, Carme; Mir-Simon, Bernat; Gómez-de Pedro, Sara; Sagales, Juan; Villanueva, Carlos; Vila, Jordi; Soriano, Alex; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

    2016-01-01

    Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints. PMID:27364357

  2. PNA-based fluorescence in situ hybridization for identification of bacteria in clinical samples.

    PubMed

    Fazli, Mustafa; Bjarnsholt, Thomas; Høiby, Niels; Givskov, Michael; Tolker-Nielsen, Tim

    2014-01-01

    Fluorescence in situ hybridization with PNA probes (PNA-FISH) that target specific bacterial ribosomal RNA sequences is a powerful and rapid tool for identification of bacteria in clinical samples. PNA can diffuse readily through the bacterial cell wall due to its uncharged backbone, and PNA-FISH can be performed with high specificity due to the extraordinary thermal stability of RNA-PNA hybrid complexes. We describe a PNA-FISH procedure and provide examples of the application of PNA-FISH for the identification of bacteria in chronic wounds, cystic fibrosis lungs, and soft tissue fillers. In all these cases, bacteria can be identified in biofilm aggregates, which may explain their recalcitrance to antibiotic treatment.

  3. Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids

    NASA Astrophysics Data System (ADS)

    Pazos-Perez, Nicolas; Pazos, Elena; Catala, Carme; Mir-Simon, Bernat; Gómez-de Pedro, Sara; Sagales, Juan; Villanueva, Carlos; Vila, Jordi; Soriano, Alex; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

    2016-07-01

    Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints.

  4. Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present.

    PubMed

    Kepner, R L; Pratt, J R

    1994-12-01

    Understanding the role of bacteria in microbial food webs is intimately connected to the methods applied in the direct enumeration of bacteria. We have examined over 220 papers describing studies in which fluorochrome staining followed by epifluorescent microscopic direct counts was used to estimate total bacterial abundances. In this review, we summarize patterns in the use of 3,6-bis[dimethylamino]acridinium chloride (acridine orange) and 4',6-diamidino-2-phenylindole (DAPI), the two stains most frequently used in bacterial enumeration. The staining of samples with these fluorochromes, followed by filtration and direct counting of bacterial cells on filter surfaces, has become routine over the past 10 years. We examine trends in features of the standard direct count methods, such as sample preservation and preparation techniques, membrane filter types used, applied stain concentrations, duration of staining, and counting strategies, in relation to the types of samples being examined. The high variability in bacterial counts observed within similar sample types may be partially accounted for by differences in methods. Synthesizing review findings, we include a recommended method for the direct enumeration of bacteria in environmental samples. PMID:7854248

  5. Multiplex Detection of Bacteria in Complex Clinical and Environmental Samples using Oligonucleotide-coupled Fluorescent Microspheres

    PubMed Central

    Dumonceaux, Tim J.; Town, Jennifer R.; Hill, Janet E.; Chaban, Bonnie L.; Hemmingsen, Sean M.

    2011-01-01

    multiplex method is expandable well beyond the range of current quantitative PCR assays for particular organisms, which is currently limited to 5 or 6 different assays in a single sample14. Importantly, the method is not limited to the detection of bacteria in vaginal swabs and can be easily adapted to rapidly profile nearly any microbial community of interest. For example, we have recently begun to apply this methodology to the development of diagnostic tools for use in wastewater treatment plants. PMID:22041586

  6. Ecophysiological adaptations of anaerobic bacteria to low pH. [Sarcina ventriculi; Lactobacillus helveticus

    SciTech Connect

    Goodwin, S.D.

    1986-01-01

    The ecological and physiological adaptations of anaerobic bacteria to low pH were investigated in field and laboratory studies. Determinations of hydrogen kinetic parameters demonstrated that overall hydrogen metabolism was inhibited in acid ecosystems. In particular, hydrogen metabolism became progressively uncoupled at low pH. This uncoupling resulted in a slowing of carbon flow during anaerobic digestion and the accumulation of intermediary metabolites. The addition of carbon electron donors to acid bog sediments resulted in the accumulation of hydrogen and a slowing of the overall rates of anaerobic digestion. As an adaptation to low pH, anaerobic bacterial populations shifted from production of acid intermediary metabolites (e.g. acetate and lactate) to the production of neutral intermediary metabolites (e.g. ethanol). This shift was observed both in situ and in pure cultures of hydrolytic strains isolated from bog sediments. Detailed physiological studies of Sarcina ventriculi showed an adaptation to growth at low pH by mechanisms which allowed the continued production of ethanol from glucose and the maintenance of a proton motive force at low cytoplasmic pH values. Further physiological studies Lactobacillus helveticus showed that the accumulation of acidic end-product (lactic acid) strongly influenced cellular electrochemical parameters. Based on the results of computer simulations and laboratory studies of the physiology of the organism in the presence of organic acids, a new model for the passive coupling of energy conservation to the efflux of lactic acid in an electroneutral process is proposed.

  7. Rapid evolutionary adaptation to elevated salt concentrations in pathogenic freshwater bacteria Serratia marcescens.

    PubMed

    Ketola, Tarmo; Hiltunen, Teppo

    2014-10-01

    Rapid evolutionary adaptions to new and previously detrimental environmental conditions can increase the risk of invasion by novel pathogens. We tested this hypothesis with a 133-day-long evolutionary experiment studying the evolution of the pathogenic Serratia marcescens bacterium at salinity niche boundary and in fluctuating conditions. We found that S. marcescens evolved at harsh (80 g/L) and extreme (100 g/L) salt conditions had clearly improved salt tolerance than those evolved in the other three treatments (ancestral conditions, nonsaline conditions, and fluctuating salt conditions). Evolutionary theories suggest that fastest evolutionary changes could be observed in intermediate selection pressures. Therefore, we originally hypothesized that extreme conditions, such as our 100 g/L salinity treatment, could lead to slower adaptation due to low population sizes. However, no evolutionary differences were observed between populations evolved in harsh and extreme conditions. This suggests that in the study presented here, low population sizes did not prevent evolution in the long run. On the whole, the adaptive potential observed here could be important for the transition of pathogenic S. marcescens bacteria from human-impacted freshwater environments, such as wastewater treatment plants, to marine habitats, where they are known to infect and kill corals (e.g., through white pox disease).

  8. Preferential Osmolyte Accumulation: a Mechanism of Osmotic Stress Adaptation in Diazotrophic Bacteria

    PubMed Central

    Madkour, Magdy A.; Smith, Linda Tombras; Smith, Gary M.

    1990-01-01

    A common cellular mechanism of osmotic-stress adaptation is the intracellular accumulation of organic solutes (osmolytes). We investigated the mechanism of osmotic adaptation in the diazotrophic bacteria Azotobacter chroococcum, Azospirillum brasilense, and Klebsiella pneumoniae, which are adversely affected by high osmotic strength (i.e., soil salinity and/or drought). We used natural-abundance 13C nuclear magnetic resonance spectroscopy to identify all the osmolytes accumulating in these strains during osmotic stress generated by 0.5 M NaCl. Evidence is presented for the accumulation of trehalose and glutamate in Azotobacter chroococcum ZSM4, proline and glutamate in Azospirillum brasilense SHS6, and trehalose and proline in K. pneumoniae. Glycine betaine was accumulated in all strains grown in culture media containing yeast extract as the sole nitrogen source. Alternative nitrogen sources (e.g., NH4Cl or casamino acids) in the culture medium did not result in measurable glycine betaine accumulation. We suggest that the mechanism of osmotic adaptation in these organisms entails the accumulation of osmolytes in hyperosmotically stressed cells resulting from either enhanced uptake from the medium (of glycine betaine, proline, and glutamate) or increased net biosynthesis (of trehalose, proline, and glutamate) or both. The preferred osmolyte in Azotobacter chroococcum ZSM4 shifted from glutamate to trehalose as a consequence of a prolonged osmotic stress. Also, the dominant osmolyte in Azospirillum brasilense SHS6 shifted from glutamate to proline accumulation as the osmotic strength of the medium increased. PMID:16348295

  9. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

    PubMed Central

    Marraffini, Luciano A.; Sontheimer, Erik J.

    2010-01-01

    Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs — small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway. PMID:20125085

  10. Adaptive response of bacteria: Multiple hurdles, cross-tolerance and tools to illustrate underlying mechanisms

    NASA Astrophysics Data System (ADS)

    Paramythiotis, Spyridon; Skandamis, Panagiotis N.

    2015-01-01

    A basic principle in the bacterial resistance against lethal stresses is that exposure of microbial cells to a sublethal hurdle (e.g., pH 5.0, 3% NaCl, or 48°C) may induce resistance to lethal level of the same or different stress. The latter is called "cross-tolerance" and the bacteria experiencing such situations are termed "stress-hardened". The majority of scientific reports on the adaptive responses of bacteria to stresses have recently addressed the need to elucidate the underlying mechanisms controlling bacterial stress response. This in turn, will assist in the efficient application of the multiple hurdle approach, e.g., by selecting specific sanitizers, combining stress treatments or antimicrobials, especially in mild processing, against specific cellular targets, eliminating the possibility of the development of stress adapted cells. Common scientific approaches for studying the link between phenotype (e.g., inactivation, survival, or growth) and physiology is the assessment of global transcriptional changes (up- or down-regulation) or those of certain genes, as well as of proteins involved in certain metabolic pathways, occurring during exposure to stress. This may also be performed in parallel to comparative evaluation of the phenotypic response of wild and mutant strains. The post-genomics research on foodborne pathogens has extended our knowledge beyond their phenotypic behavior and may offer mechanistic insights in the following: (i) the top-down approach (induction), which is the search of the underlying mechanisms (low level) responsible for a specific phenotype based on "-omic" studies; and (ii) the bottom-up approach (deduction), which starts from intracellular level and forms a mechanistic (functional) basis for the cellular response. All these may eventually enable the development of mechanistic microbial models and efficient strategies for controlling survival and growth of pathogens in foods.

  11. Key Role for Efflux in the Preservative Susceptibility and Adaptive Resistance of Burkholderia cepacia Complex Bacteria

    PubMed Central

    Rushton, Laura; Sass, Andrea; Baldwin, Adam; Dowson, Christopher G.; Donoghue, Denise

    2013-01-01

    Bacteria from the Burkholderia cepacia complex (Bcc) are encountered as industrial contaminants, and little is known about the species involved or their mechanisms of preservative resistance. Multilocus sequence typing (MLST) revealed that multiple Bcc species may cause contamination, with B. lata (n = 17) and B. cenocepacia (n = 11) dominant within the collection examined. At the strain level, 11 of the 31 industrial sequence types identified had also been recovered from either natural environments or clinical infections. Minimal inhibitory (MIC) and minimum bactericidal (MBC) preservative concentrations varied across 83 selected Bcc strains, with industrial strains demonstrating increased tolerance for dimethylol dimethyl hydantoin (DMDMH). Benzisothiazolinone (BIT), DMDMH, methylisothiazolinone (MIT), a blend of 3:1 methylisothiazolinone-chloromethylisothiazolinone (M-CMIT), methyl paraben (MP), and phenoxyethanol (PH), were all effective anti-Bcc preservatives; benzethonium chloride (BC) and sodium benzoate (SB) were least effective. Since B. lata was the dominant industrial Bcc species, the type strain, 383T (LMG 22485T), was used to study preservative tolerance. Strain 383 developed stable preservative tolerance for M-CMIT, MIT, BIT, and BC, which resulted in preservative cross-resistance and altered antibiotic susceptibility, motility, and biofilm formation. Transcriptomic analysis of the B. lata 383 M-CMIT-adapted strain demonstrated that efflux played a key role in its M-CMIT tolerance and elevated fluoroquinolone resistance. The role of efflux was corroborated using the inhibitor l-Phe-Arg-β-napthylamide, which reduced the MICs of M-CMIT and ciprofloxacin. In summary, intrinsic preservative tolerance and stable adaptive changes, such as enhanced efflux, play a role in the ability of Bcc bacteria to cause industrial contamination. PMID:23587949

  12. Key role for efflux in the preservative susceptibility and adaptive resistance of Burkholderia cepacia complex bacteria.

    PubMed

    Rushton, Laura; Sass, Andrea; Baldwin, Adam; Dowson, Christopher G; Donoghue, Denise; Mahenthiralingam, Eshwar

    2013-07-01

    Bacteria from the Burkholderia cepacia complex (Bcc) are encountered as industrial contaminants, and little is known about the species involved or their mechanisms of preservative resistance. Multilocus sequence typing (MLST) revealed that multiple Bcc species may cause contamination, with B. lata (n = 17) and B. cenocepacia (n = 11) dominant within the collection examined. At the strain level, 11 of the 31 industrial sequence types identified had also been recovered from either natural environments or clinical infections. Minimal inhibitory (MIC) and minimum bactericidal (MBC) preservative concentrations varied across 83 selected Bcc strains, with industrial strains demonstrating increased tolerance for dimethylol dimethyl hydantoin (DMDMH). Benzisothiazolinone (BIT), DMDMH, methylisothiazolinone (MIT), a blend of 3:1 methylisothiazolinone-chloromethylisothiazolinone (M-CMIT), methyl paraben (MP), and phenoxyethanol (PH), were all effective anti-Bcc preservatives; benzethonium chloride (BC) and sodium benzoate (SB) were least effective. Since B. lata was the dominant industrial Bcc species, the type strain, 383(T) (LMG 22485(T)), was used to study preservative tolerance. Strain 383 developed stable preservative tolerance for M-CMIT, MIT, BIT, and BC, which resulted in preservative cross-resistance and altered antibiotic susceptibility, motility, and biofilm formation. Transcriptomic analysis of the B. lata 383 M-CMIT-adapted strain demonstrated that efflux played a key role in its M-CMIT tolerance and elevated fluoroquinolone resistance. The role of efflux was corroborated using the inhibitor l-Phe-Arg-β-napthylamide, which reduced the MICs of M-CMIT and ciprofloxacin. In summary, intrinsic preservative tolerance and stable adaptive changes, such as enhanced efflux, play a role in the ability of Bcc bacteria to cause industrial contamination.

  13. Autonomous spatially adaptive sampling in experiments based on curvature, statistical error and sample spacing with applications in LDA measurements

    NASA Astrophysics Data System (ADS)

    Theunissen, Raf; Kadosh, Jesse S.; Allen, Christian B.

    2015-06-01

    Spatially varying signals are typically sampled by collecting uniformly spaced samples irrespective of the signal content. For signals with inhomogeneous information content, this leads to unnecessarily dense sampling in regions of low interest or insufficient sample density at important features, or both. A new adaptive sampling technique is presented directing sample collection in proportion to local information content, capturing adequately the short-period features while sparsely sampling less dynamic regions. The proposed method incorporates a data-adapted sampling strategy on the basis of signal curvature, sample space-filling, variable experimental uncertainty and iterative improvement. Numerical assessment has indicated a reduction in the number of samples required to achieve a predefined uncertainty level overall while improving local accuracy for important features. The potential of the proposed method has been further demonstrated on the basis of Laser Doppler Anemometry experiments examining the wake behind a NACA0012 airfoil and the boundary layer characterisation of a flat plate.

  14. Investigating the presence of predatory bacteria on algal bloom samples using a T6SS gene marker.

    NASA Astrophysics Data System (ADS)

    Hendricks, J.; Sison-Mangus, M.; Mehic, S.; McMahon, E.

    2015-12-01

    Predation is considered to be a major driving force in evolution and ecology, which has been observed affecting individual organisms, communities, and entire ecosystems. The type VI secretion system (T6SS) is an intermembranal protein complex identified in certain bacteria, which appears to have evolved strictly as a mechanism of predation. The effects of bacteria on phytoplankton physiology are still understudied, however, studies have shown that the interactions between bacteria that inhabit the phycosphere of phytoplankton can possibly result in coevolution of native host and microbiota. It is unclear if bacteria can prey upon other bacteria to gain advantages during periods of high phytoplankton density. Here, we investigate the predatory interactions between bacteria and analyze environmental samples for the presence of predatory bacterial genes in an effort to understand bacteria-bacteria and phytoplankton interactions during algal blooms. DNA were extracted from bacterial samples collected weekly from size-fractionated samples using 3.0 um and 0.2 um membrane filters at the Santa Cruz wharf. PCR amplification and gel visualization for the presence of T6SS gene was carried out on bloom and non-bloom samples. Moreover, we carried out a lab- based experiment to observe bacteria-bacteria interaction that may hint for the presence of predatory behavior between bacterial taxa. We observed what appeared to be a predatory biofilm formation between certain bacterial species. These bacteria, however, did not contain the T6SS genes. On the contrary the T6SS gene was discovered in some of the bloom samples gathered from the Santa Cruz wharf. It is still unclear if the predatory mechanisms facilitate the abundance of certain groups of bacteria that contain the T6SS genes during algal blooms, but our evidence suggest that bacterial predation through T6SS mechanism is present during bloom events.

  15. Levels and complexity of IgA antibody against oral bacteria in samples of human colostrum.

    PubMed

    Petrechen, L N; Zago, F H; Sesso, M L T; Bertoldo, B B; Silva, C B; Azevedo, K P; de Lima Pereira, S A; Geraldo-Martins, V R; Ferriani, V P L; Nogueira, R D

    2015-01-01

    Streptococcus mutans (SM) have three main virulence antigens: glucan binding protein B (gbpB), glucosyltransferase (Gtf) and antigens I/II (Ag I/II) envolved in the capacity of those bacteria to adhere and accumulate in the dental biofilm. Also, the glycosyltransferases 153 kDa of Streptococcus gordonii (SGO) and 170kDa of Streptococcus sanguinis (SSA) were important antigens associated with the accumulation of those bacterias. Streptococcus mitis (SMI) present IgA1 protease of 202 kDa. We investigated the specificity and levels IgA against those antigens of virulence in samples of human colostrum. This study involved 77 samples of colostrum that were analyzed for levels of immunoglobulian A, M and G by Elisa. The specificity of IgA against extracts of SM and initials colonizators (SSA, SMI, SGO) were analyzed by the Western blot. The mean concentration of IgA was 2850.2 (±2567.2) mg/100 mL followed by IgM and IgG (respectively 321.8±90.3 and 88.3±51.5), statistically different (p<0.05). Results showed that the majority of samples had detectable levels of IgA antibodies to extracts of bacteria antigens and theirs virulence antigens. To SM, the GbpB was significantly lower detected than others antigens of SM (p<0.05). High complexities of response to Ags were identified in the samples. There were no significant differences in the mean number of IgA-reactive Ags between the antigens (p>0.4). So, the breast milk from first hours after birth presented significant levels of IgA specific against important virulence of antigens those oral streptococci, which can disrupt the installation and accumulation process of these microorganisms in the oral cavity.

  16. Quantification of Gram-positive bacteria: adaptation and evaluation of a preparation strategy using high amounts of clinical tissue

    PubMed Central

    2014-01-01

    Background A preparation method for quantification of bacteria in tissues is obligatory to reduce tissue mass, concentrate the target, purify, remove inhibitory substances and to achieve constant target recovery rates. No preparation method has been available until now for a high mass of tissue applicable for routine use and analytical veterinary diagnostics. Results This study describes an easy-to-use tissue preparation protocol to quantify Gram-positive bacteria from a large volume of tissue matrix. A previously published sample preparation method (Matrix-Lysis) from food science was successfully adapted for clinical use on tissues from pigs, including cerebrum, spinal cord, lung, liver, ileum, colon, caecum, kidney and muscle tissue. This tissue preparation method now permits quantification of pathogens from 5 g of organic matrix, which is a 20–200 fold increase by weight compared to other methods. It is based on solubilization of the sample matrix with either a chaotrope plus detergent or divalent salts as solubilization agents. The method was designed as a modular system, offering the possibility to change lysis buffers, according to tissue solubilization characteristics and the intended detection method (molecular or culture). Using Listeria monocytogenes as model organism, viable cell quantification or DNA extraction and quantitative real-time PCR were performed after Matrix-Lysis to determine recovery rates and detection limit (LOD). The adapted Matrix-Lysis protocol resulted in high recovery rates (mean value: 76% ± 39%) for all tested organs, except kidney, and recovery was constant over 5 log scales for all tested buffer systems. The LOD for Matrix-Lysis with subsequent plate count method (PCM) was as low as 1 CFU/5 g, while for qPCR based detection the LOD was 102 bacterial cell equivalents (BCE)/5 g for two buffer systems. Conclusions This tissue preparation is inexpensive and can be easily used for routine and analytical veterinary

  17. Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

    NASA Astrophysics Data System (ADS)

    Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

    2013-04-01

    Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

  18. Physical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System

    PubMed Central

    Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

    2013-01-01

    Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population. PMID:23492852

  19. Probiogenomics as a tool to obtain genetic insights into adaptation of probiotic bacteria to the human gut.

    PubMed

    Ventura, Marco; Turroni, Francesca; van Sinderen, Douwe

    2012-01-01

    Bifidobacteria and lactobacilli are widely exploited as health-promoting bacteria in many functional foods. However, the molecular mechanisms as to how these bacteria positively impact on host health are far from completely understood. For this reason these microorganisms represent a growing area of interest with respect to their genomics, molecular biology and genetics. Recent genome sequencing of a large number of strains of bifidobacteria and lactobacilli has allowed access to the complete genetic makeup of representative members of these bacteria. Here, we will discuss how the analysis of genomic data has helped us to understand the mechanisms by which these bacteria adapt to the specific environment of the gastrointestinal tract, while also revealing genetic functions that mediate specific host-microbe interactions. PMID:22095053

  20. Application of adaptive cluster sampling to low-density populations of freshwater mussels

    USGS Publications Warehouse

    Smith, D.R.; Villella, R.F.; Lemarie, D.P.

    2003-01-01

    Freshwater mussels appear to be promising candidates for adaptive cluster sampling because they are benthic macroinvertebrates that cluster spatially and are frequently found at low densities. We applied adaptive cluster sampling to estimate density of freshwater mussels at 24 sites along the Cacapon River, WV, where a preliminary timed search indicated that mussels were present at low density. Adaptive cluster sampling increased yield of individual mussels and detection of uncommon species; however, it did not improve precision of density estimates. Because finding uncommon species, collecting individuals of those species, and estimating their densities are important conservation activities, additional research is warranted on application of adaptive cluster sampling to freshwater mussels. However, at this time we do not recommend routine application of adaptive cluster sampling to freshwater mussel populations. The ultimate, and currently unanswered, question is how to tell when adaptive cluster sampling should be used, i.e., when is a population sufficiently rare and clustered for adaptive cluster sampling to be efficient and practical? A cost-effective procedure needs to be developed to identify biological populations for which adaptive cluster sampling is appropriate.

  1. Impact of processing method on recovery of bacteria from wipes used in biological surface sampling.

    PubMed

    Downey, Autumn S; Da Silva, Sandra M; Olson, Nathan D; Filliben, James J; Morrow, Jayne B

    2012-08-01

    Environmental sampling for microbiological contaminants is a key component of hygiene monitoring and risk characterization practices utilized across diverse fields of application. However, confidence in surface sampling results, both in the field and in controlled laboratory studies, has been undermined by large variation in sampling performance results. Sources of variation include controlled parameters, such as sampling materials and processing methods, which often differ among studies, as well as random and systematic errors; however, the relative contributions of these factors remain unclear. The objective of this study was to determine the relative impacts of sample processing methods, including extraction solution and physical dissociation method (vortexing and sonication), on recovery of Gram-positive (Bacillus cereus) and Gram-negative (Burkholderia thailandensis and Escherichia coli) bacteria from directly inoculated wipes. This work showed that target organism had the largest impact on extraction efficiency and recovery precision, as measured by traditional colony counts. The physical dissociation method (PDM) had negligible impact, while the effect of the extraction solution was organism dependent. Overall, however, extraction of organisms from wipes using phosphate-buffered saline with 0.04% Tween 80 (PBST) resulted in the highest mean recovery across all three organisms. The results from this study contribute to a better understanding of the factors that influence sampling performance, which is critical to the development of efficient and reliable sampling methodologies relevant to public health and biodefense.

  2. Adopting Bacteria in Order to Adapt to Water-How Reed Beetles Colonized the Wetlands (Coleoptera, Chrysomelidae, Donaciinae).

    PubMed

    Kleinschmidt, Birgit; Kölsch, Gregor

    2011-12-09

    The present paper reviews the biology of reed beetles (Donaciinae), presents experimental data on the role of specific symbiotic bacteria, and describes a molecular method for the detection of those bacteria. Reed beetles are herbivores living on wetland plants, each species being mono- or oligo-phagous. They lay their eggs on the host plant and the larvae live underwater in the sediment attached to its roots. The larvae pupate there in a water-tight cocoon, which they build using a secretion that is produced by symbiotic bacteria. The bacteria are located in four blind sacs at the foregut of the larvae; in (female) adults they colonize two out of the six Malpighian tubules. Tetracycline treatment of larvae reduced their pupation rate, although the bacteria could not be fully eliminated. When the small amount of bacterial mass attached to eggs was experimentally removed before hatching, symbiont free larvae resulted, showing the external transmission of the bacteria to the offspring. Specific primers were designed to detect the bacteria, and to confirm their absence in manipulated larvae. The pupation underwater enabled the reed beetles to permanently colonize the wetlands and to diversify in this habitat underexploited by herbivorous insects (adaptive radiation).

  3. Modification of Fatty acids in membranes of bacteria: implication for an adaptive mechanism to the toxicity of carbon nanotubes.

    PubMed

    Zhu, Baotong; Xia, Xinghui; Xia, Na; Zhang, Shangwei; Guo, Xuejun

    2014-04-01

    We explored whether bacteria could respond adaptively to the presence of carbon nanotubes (CNTs) by investigating the influence of CNTs on the viability, composition of fatty acids, and cytoplasmic membrane fluidity of bacteria in aqueous medium for 24 h exposure. The CNTs included long single-walled carbon nanotubes (L-SWCNTs), short single-walled carbon nanotubes (S-SWCNTs), short carboxyl single-walled carbon nanotubes (S-SWCNT-COOH), and aligned multiwalled carbon nanotubes (A-MWCNTs). The bacteria included three common model bacteria, Staphyloccocus aureus (Gram-positive), Bacillus subtilis (Gram-positive), and Escherichia coli (Gram-negative), and one polybrominated diphenyl ether degrading strain, Ochrobactrum sp. (Gram-negative). Generally, L-SWCNTs were the most toxic to bacteria, whereas S-SWCNT-COOH showed the mildest bacterial toxicity. Ochrobactrum sp. was more susceptible to the toxic effect of CNTs than E. coli. Compared to the control in the absence of CNTs, the viability of Ochrobactrum sp. decreased from 71.6-81.4% to 41.8-70.2%, and E. coli from 93.7-104.0% to 67.7-91.0% when CNT concentration increased from 10 to 50 mg L(-1). The cytoplasmic membrane fluidity of bacteria increased with CNT concentration, and a significant negative correlation existed between the bacterial viabilities and membrane fluidity for E. coli and Ochrobactrum sp. (p < 0.05), indicating that the increase in membrane fluidity induced by CNTs was an important factor causing the inactivation of bacteria. In the presence of CNTs, E. coli and Ochrobactrum sp. showed elevation in the level of saturated fatty acids accompanied with reduction in unsaturated fatty acids, compensating for the fluidizing effect of CNTs. This demonstrated that bacteria could modify their composition of fatty acids to adapt to the toxicity of CNTs. In contrast, S. aureus and B. subtilis exposed to CNTs increased the proportion of branched-chain fatty acids and decreased the level of straight

  4. Identification of Cellulose Breaking Bacteria in Landfill Samples for Organic Waste Management

    NASA Astrophysics Data System (ADS)

    Chan, P. M.; Leung, F. C.

    2015-12-01

    According to the Hong Kong Environmental Protection Department, the citizens of Hong Kong disposes 13,500 tonnes of waste to the landfill everyday. Out of the 13,500 tonnes, 3600 tonnes consist of organic waste. Furthermore, due to the limited supply of land for landfills in Hong Kong, it is estimated that landfills will be full by about 2020. Currently, organic wastes at landfills undergo anaerobic respiration, where methane gas, one of the most harmful green house gases, will be released. The management of such waste is a pressing issue, as possible solutions must be presented in this crucial period of time. The Independent Schools Foundation Academy introduced their very own method to manage the waste produced by the students. With an approximate of 1500 students on campus, the school produces 27 metric tonnes of food waste each academic year. The installation of the rocket food composter provides an alternate method of disposable of organic waste the school produces, for the aerobic environment allows for different by-products to be produced, namely compost that can be used for organic farming by the primary school students and subsequently carbon dioxide, a less harmful greenhouse gas. This research is an extension on the current work, as another natural factor is considered. It evaluates the microorganism community present in leachate samples collected from the North East New Territories Landfill, for the bacteria in the area exhibits special characteristics in the process of decomposition. Through the sequencing and analysis of the genome of the bacteria, the identification of the bacteria might lead to a break through on the current issue. Some bacteria demonstrate the ability to degrade lignin cellulose, or assist in the production of methane gas in aerobic respirations. These characteristics can hopefully be utilized in the future in waste managements across the globe.

  5. Identification and antimicrobial susceptibility of obligate anaerobic bacteria from clinical samples of animal origin.

    PubMed

    Mayorga, Melissa; Rodríguez-Cavallini, Evelyn; López-Ureña, Diana; Barquero-Calvo, Elías; Quesada-Gómez, Carlos

    2015-12-01

    The etiology of veterinary infectious diseases has been the focus of considerable research, yet relatively little is known about the causative agents of anaerobic infections. Susceptibility studies have documented the emergence of antimicrobial resistance and indicate distinct differences in resistance patterns related to veterinary hospitals, geographic regions, and antibiotic-prescribing regimens. The aim of the present study was to identify the obligate anaerobic bacteria from veterinary clinical samples and to determinate the in vitro susceptibility to eight antimicrobials and their resistance-associated genes. 81 clinical specimens obtained from food-producing animals, pets and wild animals were examined to determine the relative prevalence of obligate anaerobic bacteria, and the species represented. Bacteroides spp, Prevotella spp and Clostridium spp represented approximately 80% of all anaerobic isolates. Resistance to metronidazole, clindamycin, tetracycline and fluoroquinolones was found in strains isolated from food-producing animals. Ciprofloxacin, enrofloxacin and cephalotin showed the highest resistance in all isolates. In 17%, 4% and 14% of tetracycline-resistant isolates, the resistance genes tetL, tetM and tetW were respectively amplified by PCR whereas in 4% of clindamycin-resistant strains the ermG gene was detected. 26% of the isolates were positive for cepA, while only 6% harbored the cfxA (resistance-conferring genes to beta-lactams). In this study, the obligate anaerobic bacteria from Costa Rica showed a high degree of resistance to most antimicrobials tested. Nevertheless, in the majority of cases this resistance was not related to the resistance acquired genes usually described in anaerobes. It is important to address and regulate the use of antimicrobials in the agricultural industry and the empirical therapy in anaerobic bacterial infections in veterinary medicine, especially since antibiotics and resistant bacteria can persist in the

  6. Pentaplex PCR assay for detection of hemorrhagic bacteria from stool samples.

    PubMed

    Al-Talib, Hassanain; Latif, Baha; Mohd-Zain, Zaini

    2014-09-01

    Diarrheal diseases cause illness and death among children younger than 10 years in developing countries. Conventional testing for the detection of hemorrhagic bacteria takes 2 to 5 days to yield complete information on the organism and its antibiotic sensitivity pattern. Hence, in the present study, we developed a molecular-based diagnostic assay that identifies common hemorrhagic bacteria in stool samples. A set of specific primers were designed for the detection of Salmonella spp., Shigella spp., enterohemorrhagic Escherichia coli (EHEC), and Campylobacter spp., suitable for use in a one-tube PCR assay. The assay in the present study simultaneously detected five genes, namely, ompC for the Salmonella genus, virA for the Shigella genus, eaeA for EHEC, 16S rRNA for the Campylobacter genus, and hemA for an internal control. Specific primer pairs were successfully designed and simultaneously amplified the targeted genes. Validation with 20 Gram-negative and 17 Gram-positive strains yielded 100% specificity. The limit of detection of the multiplex PCR assay was 1 × 10(3) CFU at the bacterial cell level and 100 pg at the genomic DNA level. Further evaluation of the multiplex PCR with 223 bacterium-spiked stool specimens revealed 100% sensitivity and specificity. We conclude that the developed multiplex PCR assay was rapid, giving results within 4 h, which is essential for the identification of hemorrhagic bacteria, and it might be useful as an additional diagnostic tool whenever time is important in the diagnosis of hemorrhagic bacteria that cause diarrhea. In addition, the presence of an internal control in the multiplex PCR assay is important for excluding false-negative cases.

  7. POF-Darts: Geometric adaptive sampling for probability of failure

    DOE PAGES

    Ebeida, Mohamed S.; Mitchell, Scott A.; Swiler, Laura P.; Romero, Vicente J.; Rushdi, Ahmad A.

    2016-06-18

    We introduce a novel technique, POF-Darts, to estimate the Probability Of Failure based on random disk-packing in the uncertain parameter space. POF-Darts uses hyperplane sampling to explore the unexplored part of the uncertain space. We use the function evaluation at a sample point to determine whether it belongs to failure or non-failure regions, and surround it with a protection sphere region to avoid clustering. We decompose the domain into Voronoi cells around the function evaluations as seeds and choose the radius of the protection sphere depending on the local Lipschitz continuity. As sampling proceeds, regions uncovered with spheres will shrink,more » improving the estimation accuracy. After exhausting the function evaluation budget, we build a surrogate model using the function evaluations associated with the sample points and estimate the probability of failure by exhaustive sampling of that surrogate. In comparison to other similar methods, our algorithm has the advantages of decoupling the sampling step from the surrogate construction one, the ability to reach target POF values with fewer samples, and the capability of estimating the number and locations of disconnected failure regions, not just the POF value. Furthermore, we present various examples to demonstrate the efficiency of our novel approach.« less

  8. Microwave irradiation for shortening the processing time of samples of flagellated bacteria for scanning electron microscopy.

    PubMed

    Hernández-Chavarría, Francisco

    2004-01-01

    Microwave irradiation (MWI) has been applied to the development of rapid methods to process biological samples for scanning electron microscopy (SEM). In this paper we propose two simple and quick techniques for processing bacteria (Proteus mirabilis and Vibrio mimicus) for SEM using MWI. In the simplest methodology, the bacteria were placed on a cover-glass, air-dried, and submitted to conductivity stain. The reagent used for the conductivity stain was the mordant of a light microscopy staining method (10 ml of 5% carbolic acid solution, 2 g of tannic acid, and 10 ml of saturated aluminum sulfate 12-H2O). In the second method the samples were double fixed (glutaraldehyde and then osmium), submitted to conductivity stain, dehydrated through a series of ethanol solutions of increasing concentration, treated with hexamethyldisilazine (HMDS), and dried at 35 degrees C for 5 minutes. In both methods the steps from fixation to treatment with HMDS were done under MWI for 2 minutes in an ice-water bath, in order to dissipate the heat generated by the MWI. Although both techniques preserve bacterial morphology adequately, the latter, technique showed the best preservation, including the appearance of flagella, and that process was completed in less than 2 hours at temperatures of MWI between 4 to 5 degrees C. PMID:17061527

  9. How Magnetotactic Bacteria Respond to Radiation Induced Stress and Damage: Comparative Genomics Evidences for Evolutionary Adaptation

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Pan, Y.

    2015-12-01

    Solar radiation and galactic cosmic radiation is believed to be major restriction factors influencing survival and evolution of life. On planet earth, geomagnetic field along with atmosphere protect living beings from the harmful radiation. During a geomagnetic reversal or excursion, however, the efflux of charged particles on earth surface would increase as the shielding effect of magnetic field decrease. The stratospheric ozone can also be partially stripped away by solar wind when the strength of the field is weak, leading to an increasing ultraviolet radiation penetration to the earth surface. However, studies on the mechanism of radiation induced stress and damage are focused only on bacteria that have no response to magnetic field. This study was motivated by the need to fill the gap upon knowledge of that on magnetic field sensitive microorganism. Magnetotactic bacteria (MTB) are a group of microbes that are able to synthesis intracellular nano-sized magnetic particles (named magnetosomes). These chain-arranged magnetosomes help MTB sense and swim along the magnetic field to find their optimal living environment efficiently. In this paper, in silico prediction of stress and damage repair genes in response to different radiation were carried out on the complete genome of four nonmagnetotactic and four magnetotactic spirilla. In silico analyses of the genomes of magnetic field sensitive and non-sensitive spirilla revealed: 1) all strains contain genes for regulate responses superoxide and peroxide stress, DNA pyrimidine dimer and string breaks; 2) non-magnetotactic spirilla have more genes dealing with oxidative stress, while magnetotactic spirilla may benefit from magnetotaxis by swimming into oxic-anoxic zone away from oxidative stress and direct radiation damage; yet, the lipid hydroperoxide peroxidase gene in MTB may be responsible for possible ROS generated by the membrane enveloped magnetite magnetosome; 3) magnetotactic spirilla possess SOS rec

  10. Antibiotic resistance among bacteria isolated from seawater and penguin fecal samples collected near Palmer Station, Antarctica.

    PubMed

    Miller, Robert V; Gammon, Katharine; Day, Martin J

    2009-01-01

    Antibiotic resistance in aquatic bacteria has increased steadily as a consequence of the widespread use of antibiotics, but practice and international treaty should have limited antibiotic contamination in Antarctica. We estimated antibiotic resistance in microorganisms isolated from the Antarctic marine waters and a penguin rookery, for 2 reasons: (i) as a measure of human impact and (ii) as a potential "snapshot" of the preantibiotic world. Samples were taken at 4 established sampling sites near Palmer Station, which is situated at the southern end of the Palmer Archipelago (64 degrees 10'S, 61 degrees 50'W). Sites were chosen to provide different potentials for human contamination. Forty 50 mL samples of seawater were collected and colony-forming units (CFU)/mL were determined at 6 and 20 degrees C. For this study, presumed psychrophiles (growth at 6 degrees C) were assumed to be native to Antarctic waters, whereas presumed mesophiles (growth at 20 degrees C but not at 6 degrees C) were taken to represent introduced organisms. The 20-6 degrees C CFU/mL ratio was used as a measure of the relative impact to the ecosystem of presumably introduced organisms. This ratio was highest at the site nearest to Palmer Station and decreased with distance from it, suggesting that human presence has impacted the natural microbial flora of the site. The frequency of resistance to 5 common antibiotics was determined in each group of isolates. Overall drug resistance was higher among the presumed mesophiles than the presumed psychrophiles and increased with proximity to Palmer Station, with the presumed mesophiles showing higher frequencies of single and multiple drug resistance than the psychrophile population. The frequency of multidrug resistance followed the same pattern. It appears that multidrug resistance is low among native Antarctic bacteria but is increased by human habitation.

  11. Adaptive Sampling of Spatiotemporal Phenomena with Optimization Criteria

    NASA Technical Reports Server (NTRS)

    Chien, Steve A.; Thompson, David R.; Hsiang, Kian

    2013-01-01

    This work was designed to find a way to optimally (or near optimally) sample spatiotemporal phenomena based on limited sensing capability, and to create a model that can be run to estimate uncertainties, as well as to estimate covariances. The goal was to maximize (or minimize) some function of the overall uncertainty. The uncertainties and covariances were modeled presuming a parametric distribution, and then the model was used to approximate the overall information gain, and consequently, the objective function from each potential sense. These candidate sensings were then crosschecked against operation costs and feasibility. Consequently, an operations plan was derived that combined both operational constraints/costs and sensing gain. Probabilistic modeling was used to perform an approximate inversion of the model, which enabled calculation of sensing gains, and subsequent combination with operational costs. This incorporation of operations models to assess cost and feasibility for specific classes of vehicles is unique.

  12. Enumeration of total bacteria and bacteria with genes for proteolytic activity in pure cultures and in environmental samples by quantitative PCR mediated amplification.

    PubMed

    Bach, H-J; Tomanova, J; Schloter, M; Munch, J C

    2002-05-01

    Real-time quantitative PCR assays were developed for the absolute quantification of different groups of bacteria in pure cultures and in environmental samples. 16S rRNA genes were used as markers for eubacteria, and genes for extracellular peptidases were used as markers for potentially proteolytic bacteria. For the designed 16S rDNA TaqMan assay, specificity of the designed primer-probe combination for eubacteria, a high amplification efficiency over a wide range of starting copy numbers and a high reproducibility is demonstrated. Cell concentrations of Bacillus cereus, B. subtilis and Pseudomonas fluorescens in liquid culture were monitored by TaqMan-PCR using the 16S rDNA target sequence of Escherichia coli as external standard for quantification. Results agree with plate counts and microscopic counts of DAPI stained cells. The significance of 16S rRNA operon multiplicity to the quantification of bacteria is discussed.Furthermore, three sets of primer pair together with probe previously designed for targeting different classes of bacterial extracellular peptidases were tested for their suitability for TaqMan-PCR based quantification of proteolytic bacteria. Since high degeneracy of the probes did not allow accurate quantification, SybrGreen was used instead of molecular probes to visualize and quantify PCR products during PCR. The correlation between fluorescence and starting copy number was of the same high quality as for the 16S rDNA TaqMan assay for all the three peptidase gene classes. The detected amount of genes for neutral metallopeptidase of B. cereus, for subtilisin of B. subtilis and for alkaline metallopeptidase of P. fluorescens corresponded exactly to the numbers of bacteria investigated by the 16S rDNA targeting assay. The developed assays were applied for the quantification of bacteria in soil samples.

  13. Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples

    PubMed Central

    Kumar, Nikhil; Lin, Mingqun; Zhao, Xuechu; Ott, Sandra; Santana-Cruz, Ivette; Daugherty, Sean; Rikihisa, Yasuko; Sadzewicz, Lisa; Tallon, Luke J.; Fraser, Claire M.; Dunning Hotopp, Julie C.

    2016-01-01

    Despite numerous advances in genomics and bioinformatics, technological hurdles remain to examine host-microbe transcriptomics. Sometimes the transcriptome of either or both can be ascertained merely by generating more sequencing reads. However, many cases exist where bacterial mRNA needs to be enriched further to enable cost-effective sequencing of the pathogen or endosymbiont. While a suitable method is commercially available for mammalian samples of this type, development of such methods has languished for invertebrate samples. Furthermore, a common method across multiple taxa would facilitate comparisons between bacteria in invertebrate vectors and their vertebrate hosts. Here, a method is described to concurrently remove polyadenylated transcripts, prokaryotic rRNA, and eukaryotic rRNA, including those with low amounts of starting material (e.g. 100 ng). In a Wolbachia-Drosophila system, this bacterial mRNA enrichment yielded a 3-fold increase in Wolbachia mRNA abundance and a concomitant 3.3-fold increase in the percentage of transcripts detected. More specifically, 70% of the genome could be recovered by transcriptome sequencing compared to 21% in the total RNA. Sequencing of similar bacterial mRNA-enriched samples generated from Ehrlichia-infected canine cells covers 93% of the Ehrlichia genome, suggesting ubiquitous transcription across the entire Ehrlichia chaffeensis genome. This technique can potentially be used to enrich bacterial mRNA in many studies of host-microbe interactions. PMID:27713560

  14. Phylogeography, Salinity Adaptations and Metabolic Potential of the Candidate Division KB1 Bacteria Based on a Partial Single Cell Genome.

    PubMed

    Nigro, Lisa M; Hyde, Andrew S; MacGregor, Barbara J; Teske, Andreas

    2016-01-01

    Deep-sea hypersaline anoxic basins and other hypersaline environments contain abundant and diverse microbial life that has adapted to these extreme conditions. The bacterial Candidate Division KB1 represents one of several uncultured groups that have been consistently observed in hypersaline microbial diversity studies. Here we report the phylogeography of KB1, its phylogenetic relationships to Candidate Division OP1 Bacteria, and its potential metabolic and osmotic stress adaptations based on a partial single cell amplified genome of KB1 from Orca Basin, the largest hypersaline seafloor brine basin in the Gulf of Mexico. Our results are consistent with the hypothesis - previously developed based on (14)C incorporation experiments with mixed-species enrichments from Mediterranean seafloor brines - that KB1 has adapted its proteins to elevated intracellular salinity, but at the same time KB1 apparently imports glycine betaine; this compatible solute is potentially not limited to osmoregulation but could also serve as a carbon and energy source. PMID:27597842

  15. Phylogeography, Salinity Adaptations and Metabolic Potential of the Candidate Division KB1 Bacteria Based on a Partial Single Cell Genome

    PubMed Central

    Nigro, Lisa M.; Hyde, Andrew S.; MacGregor, Barbara J.; Teske, Andreas

    2016-01-01

    Deep-sea hypersaline anoxic basins and other hypersaline environments contain abundant and diverse microbial life that has adapted to these extreme conditions. The bacterial Candidate Division KB1 represents one of several uncultured groups that have been consistently observed in hypersaline microbial diversity studies. Here we report the phylogeography of KB1, its phylogenetic relationships to Candidate Division OP1 Bacteria, and its potential metabolic and osmotic stress adaptations based on a partial single cell amplified genome of KB1 from Orca Basin, the largest hypersaline seafloor brine basin in the Gulf of Mexico. Our results are consistent with the hypothesis – previously developed based on 14C incorporation experiments with mixed-species enrichments from Mediterranean seafloor brines – that KB1 has adapted its proteins to elevated intracellular salinity, but at the same time KB1 apparently imports glycine betaine; this compatible solute is potentially not limited to osmoregulation but could also serve as a carbon and energy source.

  16. Molecular identification of multi drug resistant bacteria from urinary tract infected urine samples.

    PubMed

    Kumar, M S; Das, A P

    2016-09-01

    Urinary tract infections (UTIs) are of great concern in both developing and developed countries all over the world. Even though the infections are more common in women and children, they are at a considerable rate in men and of all ages. The uropathogens causing the infections are spread through various routes. The treatment generally recommended by the physicians is antibiotic usage. But, most of the uropathogens have evolved antibiotic resistance mechanisms. This makes the present situation hectic in control and prevention of UTIs. The present study aims to illustrate the multidrug resistance patterns among isolated bacterial strains from infected urine samples in Odisha state, India. Four bacterial strains were isolated and identified as Proteus sp. SK3, Pseudomonas sp. ADMK77, Proteus sp. BLKB2 and Enterobacter hormaechei strain CW-3 by 16S rRNA gene sequencing. Phylogenetc analysis indicated the strains belong to three various genera namely, Proteus, Pseudomonas and Enterobacter. The evolutionary timeline of the bacteria was studied by constructing phylogenetic trees by Neighborhood Joining method. The presence of ESBL gene and biofilm forming capability were studied for the four strains. Antibiotic susceptibility patterns of the isolates were studied toward the commonly recommended antibiotics. Both the Proteus strains were found commonly susceptible to aminoglycoside and sulphonamide groups. Pseudomonas strain was found to be susceptible to cephems, aminoglycosides and fluoroquinolones. Enterobacter sp was found to be resistant to almost all antibiotic groups and susceptible to only sulphonamides group. The antibiotic susceptibility patterns of the bacteria help in choosing the empirical antibiotic treatment for UTI. PMID:27354209

  17. Isolation and characterization of entomopathogenic bacteria from soil samples from the western region of Cuba.

    PubMed

    González, Aileen; Rodríguez, Graciela; Bruzón, Rosa Y; Díaz, Manuel; Companionis, Ariamys; Menéndez, Zulema; Gato, René

    2013-06-01

    The use of insect pathogens is a viable alternative for insect control because of their relative specificity and lower environmental impact. The search for wild strains against dipterans could have an impact on mosquito control programs. We have made an extensive screening of soil in western Cuba to find bacteria with larvicidal activity against mosquitoes. A total of 150 soil samples were collected and isolates were identifying using the API 50 CHB gallery. Phenotypic characteristics were analyzed by hierarchical ascending classification. Quantitative bioassays were conducted under laboratory conditions following the World Health Organization protocol in order to ascertain the toxicity and efficacy of isolates. The protein profiles of the crystal components were determined by SDS-PAGE. Eight hundred and eighty-one bacterial isolates were obtained, and 13 isolates with entomopathogenic activity were isolated from nine samples. Nine isolates displayed higher entomopathogenic activity against both Cx. quinquefasciatus and Ae. aegypti compared with the reference strain 266/2. All toxic isolates showed higher biological potency than the 266/2 strain. These isolates with high entomopathogenic activity displayed a protein pattern similar to the B. thuringiensis var. israelensis IPS-82 and 266/2 strains. These results are a valuable tool for the control of Diptera of medical importance. PMID:23701606

  18. Rapid detection and typing of live bacteria from human joint fluid samples by utilizing an integrated microfluidic system.

    PubMed

    Chang, Wen-Hsin; Wang, Chih-Hung; Lin, Chih-Lin; Wu, Jiunn-Jong; Lee, Mel S; Lee, Gwo-Bin

    2015-04-15

    Periprosthetic joint infection (PJI) is one of the most dreading complications that hinder the merits of an arthroplasty. A prerequisite for treatment of the above procedure is rapid detection of live bacteria to prevent its recurrence and proper choice of antibiotics. Conventional culture methods are time-consuming and associated with a high false negative rate. Amplification of bacterial genetic materials requires a tedious process but is associated with a high false positive rate. An integrated microfluidic system capable of molecular diagnosis for detecting live bacteria was reported in our previous work. However, the system could not provide detailed information about infectious bacteria for the subsequent antibiotic choices. Furthermore, it took at least 55min to finish the entire process. In this work, a microfluidic platform using ethidium monoazide (EMA) which can only penetrate into dead bacteria is presented for live bacteria detection and typing within a short period of time (30min for the detection of live bacteria and another 40min for the typing of bacteria strains). We tested the proposed system by using human joint fluid samples and found its limit of detection for bacterial detection equal to 10(2)CFU (colony formation unit) for live bacteria detection with gold nanoparticle probes and 10(2)-10(4)CFU for typing bacteria by an on-chip polymerase chain reaction. The whole procedure of the integrated microfluidic system is automated with little human intervention. Moreover, this is the first time that sequential live bacteria detection and typing are demonstrated on the same microfluidic platform. Based on the promising results, the proposed system may become in the near future an auxiliary tool for immediate medical decision and choice of antibiotics in routine arthroplasties or PJI's.

  19. Isolation and culture of anammox bacteria adapted to livestock wastewater environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Research was conducted to develop process applications for anaerobic ammonium oxidation (anammox) bacteria acclimated to animal wastewater conditions using microbial immobilization techniques. In the anammox reaction, under anaerobic and autotrophic conditions, ammonium (NH4+) serves as the electron...

  20. Destruction-free procedure for the isolation of bacteria from sputum samples for Raman spectroscopic analysis.

    PubMed

    Kloß, Sandra; Lorenz, Björn; Dees, Stefan; Labugger, Ines; Rösch, Petra; Popp, Jürgen

    2015-11-01

    Lower respiratory tract infections are the fourth leading cause of death worldwide. Here, a timely identification of the causing pathogens is crucial to the success of the treatment. Raman spectroscopy allows for quick identification of bacterial cells without the need for time-consuming cultivation steps, which is the current gold standard to detect pathogens. However, before Raman spectroscopy can be used to identify pathogens, they have to be isolated from the sample matrix, i.e., sputum in case of lower respiratory tract infections. In this study, we report an isolation protocol for single bacterial cells from sputum samples for Raman spectroscopic identification. Prior to the isolation, a liquefaction step using the proteolytic enzyme mixture Pronase E is required in order to deal with the high viscosity of sputum. The extraction of the bacteria was subsequently performed via different filtration and centrifugation steps, whereby isolation ratios between 46 and 57 % were achieved for sputa spiked with 6·10(7) to 6·10(4) CFU/mL of Staphylococcus aureus. The compatibility of such a liquefaction and isolation procedure towards a Raman spectroscopic classification was shown for five different model species, namely S. aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Klebsiella pneumoniae, and Pseudomonas aeruginosa. A classification of single-cell Raman spectra of these five species with an accuracy of 98.5 % could be achieved on the basis of a principal component analysis (PCA) followed by a linear discriminant analysis (LDA). These classification results could be validated with an independent test dataset, where 97.4 % of all spectra were identified correctly. Graphical Abstract Development of an isolation protocol of bacterial cells out of sputum samples followed by Raman spectroscopic measurement and species identification using chemometrical models. PMID:26041453

  1. Effects of Calibration Sample Size and Item Bank Size on Ability Estimation in Computerized Adaptive Testing

    ERIC Educational Resources Information Center

    Sahin, Alper; Weiss, David J.

    2015-01-01

    This study aimed to investigate the effects of calibration sample size and item bank size on examinee ability estimation in computerized adaptive testing (CAT). For this purpose, a 500-item bank pre-calibrated using the three-parameter logistic model with 10,000 examinees was simulated. Calibration samples of varying sizes (150, 250, 350, 500,…

  2. A robust adaptive sampling method for faster acquisition of MR images.

    PubMed

    Vellagoundar, Jaganathan; Machireddy, Ramasubba Reddy

    2015-06-01

    A robust adaptive k-space sampling method is proposed for faster acquisition and reconstruction of MR images. In this method, undersampling patterns are generated based on magnitude profile of a fully acquired 2-D k-space data. Images are reconstructed using compressive sampling reconstruction algorithm. Simulation experiments are done to assess the performance of the proposed method under various signal-to-noise ratio (SNR) levels. The performance of the method is better than non-adaptive variable density sampling method when k-space SNR is greater than 10dB. The method is implemented on a fully acquired multi-slice raw k-space data and a quality assurance phantom data. Data reduction of up to 60% is achieved in the multi-slice imaging data and 75% is achieved in the phantom imaging data. The results show that reconstruction accuracy is improved over non-adaptive or conventional variable density sampling method. The proposed sampling method is signal dependent and the estimation of sampling locations is robust to noise. As a result, it eliminates the necessity of mathematical model and parameter tuning to compute k-space sampling patterns as required in non-adaptive sampling methods.

  3. [Bacteria isolated from urine and renal tissue samples and their relation to renal histology].

    PubMed

    Gökalp, A; Gültekin, E Y; Bakici, M Z; Ozdeşlik, B

    1988-01-01

    The bacteria from the urine and renal biopsy specimens of 40 patients undergoing renal surgery were isolated and their relations with renal histology investigated. The urine cultures were positive in 14 patients, the same organisms being isolated from the renal tissue in 7 cases. In 6 patients with negative urine cultures, bacteria were isolated from renal tissues. Of the 28 cases pathologically diagnosed as chronic pyelonephritis, bacteria were isolated from the renal tissue in 13 cases, the urine cultures being positive in only 11 cases. E. coli was the most commonly encountered bacteria in both the urine and renal tissues.

  4. Dual-Track Clearance of Circulating Bacteria Balances Rapid Restoration of Blood Sterility with Induction of Adaptive Immunity.

    PubMed

    Broadley, Steven P; Plaumann, Ann; Coletti, Raffaele; Lehmann, Christin; Wanisch, Andreas; Seidlmeier, Amelie; Esser, Knud; Luo, Shanshan; Rämer, Patrick C; Massberg, Steffen; Busch, Dirk H; van Lookeren Campagne, Menno; Verschoor, Admar

    2016-07-13

    Efficient clearance of bacteremia prevents life-threatening disease. Platelet binding to intravascular bacteria, a process involving platelet glycoprotein GPIb and bacterial opsonization with activated complement C3, influences blood clearance and anti-infective immunity. Using intravital microscopy of the bloodstream of mice infected with Listeria monocytogenes, we show that bacterial clearance is not a uniform process but a "dual-track" mechanism consisting of parallel "fast" and "slow" pathways. "Slow clearance" is regulated by time-dependent bacterial opsonization, stochastic platelet binding, and capture of bacteria-platelet-complexes via the complement receptor of the immunoglobulin superfamily, CRIg. The mechanism spares some bacteria from "fast clearance" and rapid destruction in the liver via Kupffer cell scavenger receptors, keeping them available for adaptive immunity induction by splenic CD8α(+) dendritic cells. We consistently find "fast" and "slow" clearance patterns for a broad panel of other Gram+ and Gram- bacteria. Thus, dual-track clearance balances rapid restoration of blood sterility with induction of specific antibacterial immunity.

  5. Dual-Track Clearance of Circulating Bacteria Balances Rapid Restoration of Blood Sterility with Induction of Adaptive Immunity.

    PubMed

    Broadley, Steven P; Plaumann, Ann; Coletti, Raffaele; Lehmann, Christin; Wanisch, Andreas; Seidlmeier, Amelie; Esser, Knud; Luo, Shanshan; Rämer, Patrick C; Massberg, Steffen; Busch, Dirk H; van Lookeren Campagne, Menno; Verschoor, Admar

    2016-07-13

    Efficient clearance of bacteremia prevents life-threatening disease. Platelet binding to intravascular bacteria, a process involving platelet glycoprotein GPIb and bacterial opsonization with activated complement C3, influences blood clearance and anti-infective immunity. Using intravital microscopy of the bloodstream of mice infected with Listeria monocytogenes, we show that bacterial clearance is not a uniform process but a "dual-track" mechanism consisting of parallel "fast" and "slow" pathways. "Slow clearance" is regulated by time-dependent bacterial opsonization, stochastic platelet binding, and capture of bacteria-platelet-complexes via the complement receptor of the immunoglobulin superfamily, CRIg. The mechanism spares some bacteria from "fast clearance" and rapid destruction in the liver via Kupffer cell scavenger receptors, keeping them available for adaptive immunity induction by splenic CD8α(+) dendritic cells. We consistently find "fast" and "slow" clearance patterns for a broad panel of other Gram+ and Gram- bacteria. Thus, dual-track clearance balances rapid restoration of blood sterility with induction of specific antibacterial immunity. PMID:27345696

  6. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  7. Organic solvent adaptation of Gram positive bacteria: applications and biotechnological potentials.

    PubMed

    Torres, Sebastian; Pandey, Ashok; Castro, Guillermo R

    2011-01-01

    Organic-solvent-tolerant bacteria are considered extremophiles with different tolerance levels that change among species and strains, but also depend on the inherent toxicity of the solvent. Extensive studies to understand the mechanisms of organic solvent tolerance have been done in Gram-negative bacteria. On the contrary, the information on the solvent tolerance mechanisms in Gram-positive bacteria remains scarce. Possible shared mechanisms among Gram-(-) and Gram-(+) microorganisms include: energy-dependent active efflux pumps that export toxic organic solvents to the external medium; cis-to-trans isomerization of unsaturated membrane fatty acids and modifications in the membrane phospholipid headgroups; formation of vesicles loaded with toxic compounds; and changes in the biosynthesis rate of phospholipids to accelerate repair processes. However, additional physiological responses of Gram-(+) bacteria to organic solvents seem to be specific. The aim of the present work is to review the state of the art of responsible mechanisms for organic solvent tolerance in Gram-positive bacteria, and their industrial and environmental biotechnology potential. PMID:21504787

  8. Detection of and discrimination between gram-positive and gram-negative bacteria in intraocular samples by using nested PCR.

    PubMed

    Carroll, N M; Jaeger, E E; Choudhury, S; Dunlop, A A; Matheson, M M; Adamson, P; Okhravi, N; Lightman, S

    2000-05-01

    A nested PCR protocol has been developed for the detection of and discrimination between 14 species of gram-positive and -negative bacteria in samples of ocular fluids. First-round PCR with pan-bacterial oligonucleotide primers, based on conserved sequences of the 16S ribosomal gene, was followed by a gram-negative-organism-specific PCR, which resulted in a single 985-bp amplification product, and a multiplex PCR which resulted in two PCR products: a 1,025 bp amplicon (all bacteria) and a 355 bp amplicon (gram-positive bacteria only). All products were detected by gel electrophoresis. The sensitivity of the assay was between 10 fg and 1 pg of bacterial DNA, depending on the species tested, equivalent to between 24 and 4 live bacteria spiked in water. The identification was complete in 3.5 h. The molecular techniques were subsequently applied to four samples of intraocular fluid, (three vitreous and one aqueous) from three patients with clinical signs of bacterial endophthalmitis (test samples) and two samples of vitreous from a patient with chronic intraocular inflammation (control samples). In all culture-positive samples (two of three vitreous and one of one aqueous), a complete concordance was observed between molecular methods and culture results. PCR correctly identified the gram stain classification of the organisms. The bacterial etiology was also identified in a culture-negative patient with clinical history and signs highly suggestive of bacterial endophthalmitis. Furthermore, control samples from a patient with chronic intraocular inflammation remained PCR negative. In summary, this protocol has demonstrated potential as a rapid diagnostic test in confirming the diagnosis of infection and also determining the Gram status of bacteria with high specificity and sensitivity.

  9. Rapid detection of bacteria in urine samples by the "three-plug-injection" method using capillary electrophoresis.

    PubMed

    Song, Lin; Li, Wanchen; Li, Guoxia; Wei, Dianjun; Ge, Peng; Li, Guizhen; Zheng, Fang; Sun, Xuguo

    2013-09-15

    This study explored a method that can rapidly detect bacteria in urine samples for the auxiliary determination of urinary tract infections (UTIs). Urine samples from patients with UTIs (230 cases) were obtained using aseptic technique. The urine biochemical assay was then carried out using an automated urine analyzer for all the urine samples. Bacterial species were identified by a combination of bacterial culture technique, morphological observation and the BACT-IST microbial identification/susceptibility analysis system. The most common seven species of bacteria in the study included Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, Enterococcus faecalis, Staphylococcus aureus and Staphylococcus epidermidis. Bacterial samples were suspended in sample buffer solutions and separated by the "three-plug-injection" method using capillary electrophoresis (CE). Each species of bacteria appeared as a bacterial peak. The mixture of the seven species also provided only one peak. Further analysis showed that the concentration limit for the "three-plug-injection" method is 10(6) colony forming units (CFU)/mL, and there is a good linear relationship between the peak height and bacterial concentration (R(2)=0.99). The effect of urine composition on CE results was also investigated. The results showed that urine composition, i.e., proteins, white blood cells (WBCs) and red blood cells (RBCs), affected the peak retention time but could not affect the separation of bacteria. The results demonstrated that the bacteria in urine samples can be detected within 10min by the "three-plug-injection" method using CE. The "three-plug-injection" method is therefore suitable for the rapid detection of organisms in clinical urine samples from UTIs.

  10. On efficient two-stage adaptive designs for clinical trials with sample size adjustment.

    PubMed

    Liu, Qing; Li, Gang; Anderson, Keaven M; Lim, Pilar

    2012-01-01

    Group sequential designs are rarely used for clinical trials with substantial over running due to fast enrollment or long duration of treatment and follow-up. Traditionally, such trials rely on fixed sample size designs. Recently, various two-stage adaptive designs have been introduced to allow sample size adjustment to increase statistical power or avoid unnecessarily large trials. However, these adaptive designs can be seriously inefficient. To address this infamous problem, we propose a likelihood-based two-stage adaptive design where sample size adjustment is derived from a pseudo group sequential design using cumulative conditional power. We show through numerical examples that this design cannot be improved by group sequential designs. In addition, the approach may uniformly improve any existing two-stage adaptive designs with sample size adjustment. For statistical inference, we provide methods for sequential p-values and confidence intervals, as well as median unbiased and minimum variance unbiased estimates. We show that the claim of inefficiency of adaptive designs by Tsiatis and Mehta ( 2003 ) is logically flawed, and thereby provide a strong defense of Cui et al. ( 1999 ). PMID:22651105

  11. Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A.

    PubMed

    Bunker, Jeffrey J; Flynn, Theodore M; Koval, Jason C; Shaw, Dustin G; Meisel, Marlies; McDonald, Benjamin D; Ishizuka, Isabel E; Dent, Alexander L; Wilson, Patrick C; Jabri, Bana; Antonopoulos, Dionysios A; Bendelac, Albert

    2015-09-15

    Immunoglobulin A (IgA) is prominently secreted at mucosal surfaces and coats a fraction of the intestinal microbiota. However, the commensal bacteria bound by IgA are poorly characterized and the type of humoral immunity they elicit remains elusive. We used bacterial flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in murine models of immunodeficiency to identify IgA-bound bacteria and elucidate mechanisms of commensal IgA targeting. We found that residence in the small intestine, rather than bacterial identity, dictated induction of specific IgA. Most commensals elicited strong T-independent (TI) responses that originated from the orphan B1b lineage and from B2 cells, but excluded natural antibacterial B1a specificities. Atypical commensals including segmented filamentous bacteria and Mucispirillum evaded TI responses but elicited T-dependent IgA. These data demonstrate exquisite targeting of distinct commensal bacteria by multiple layers of humoral immunity and reveal a specialized function of the B1b lineage in TI mucosal IgA responses.

  12. Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A.

    PubMed

    Bunker, Jeffrey J; Flynn, Theodore M; Koval, Jason C; Shaw, Dustin G; Meisel, Marlies; McDonald, Benjamin D; Ishizuka, Isabel E; Dent, Alexander L; Wilson, Patrick C; Jabri, Bana; Antonopoulos, Dionysios A; Bendelac, Albert

    2015-09-15

    Immunoglobulin A (IgA) is prominently secreted at mucosal surfaces and coats a fraction of the intestinal microbiota. However, the commensal bacteria bound by IgA are poorly characterized and the type of humoral immunity they elicit remains elusive. We used bacterial flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in murine models of immunodeficiency to identify IgA-bound bacteria and elucidate mechanisms of commensal IgA targeting. We found that residence in the small intestine, rather than bacterial identity, dictated induction of specific IgA. Most commensals elicited strong T-independent (TI) responses that originated from the orphan B1b lineage and from B2 cells, but excluded natural antibacterial B1a specificities. Atypical commensals including segmented filamentous bacteria and Mucispirillum evaded TI responses but elicited T-dependent IgA. These data demonstrate exquisite targeting of distinct commensal bacteria by multiple layers of humoral immunity and reveal a specialized function of the B1b lineage in TI mucosal IgA responses. PMID:26320660

  13. Changes in Endosymbiotic Bacteria of Brown Planthoppers During the Process of Adaptation to Different Resistant Rice Varieties.

    PubMed

    Hong-Xing, Xu; Xu-Song, Zheng; Ya-Jun, Yang; Jun-Ce, Tian; Qiang, Fu; Gong-Yin, Ye; Zhong-Xian, Lu

    2015-06-01

    The specific primers of five species of endosymbiotic bacteria were designed to determine their numbers in three virulent populations of brown planthopper, Nilapavata lugens Stål, and to assess changes during adaptation to different resistant varieties using fluorescent quantitative PCR. The results showed that Chryseobacterium was the dominant bacteria in all three populations of brown planthopper, followed by Acinetobacter in TN1 population, Arsenophonus and Serratia in Mudgo population, and Arthrobacter and Acinetobacter in ASD7 population. When the TN1 population of brown planthopper was transferred to ASD7 (with resistant gene bph2) rice plants, Chryseobacterium was still the dominant bacteria, but the originally subdominant Acinetobacter declined to a level that was not significantly different from that of other endosymbiotic bacteria. After they were transferred to Mudgo (with resistant gene Bph1), Serratia and Arsenophonus increased significantly and became the dominant bacteria. However, they declined to a level that was not significantly different from that of the three other species after two generations. When ASD7 and Mudgo populations of brown planthopper were transferred to the susceptible variety TN1, the community of endosymbiotic bacteria in the ASD7 population of brown planthopper showed no significant changes. However, the numbers of Acinetobacter and Arthrobacter in the Mudgo population of brown planthopper exhibited a transient increase and returned to their original levels after two generations. After the Mudgo population of brown planthopper was transferred to ASD7 rice plants, the quantity of endosymbiotic bacteria fluctuated, but the bacterial structure did not change significantly. However, after the ASD7 population of brown planthopper was transferred to the Mudgo rice plants, the bacterial structure changed significantly. Serratia and Arsenophonus increased significantly and became dominant. Although Serratia and Arsenophonus decreased

  14. Changes in Endosymbiotic Bacteria of Brown Planthoppers During the Process of Adaptation to Different Resistant Rice Varieties.

    PubMed

    Hong-Xing, Xu; Xu-Song, Zheng; Ya-Jun, Yang; Jun-Ce, Tian; Qiang, Fu; Gong-Yin, Ye; Zhong-Xian, Lu

    2015-06-01

    The specific primers of five species of endosymbiotic bacteria were designed to determine their numbers in three virulent populations of brown planthopper, Nilapavata lugens Stål, and to assess changes during adaptation to different resistant varieties using fluorescent quantitative PCR. The results showed that Chryseobacterium was the dominant bacteria in all three populations of brown planthopper, followed by Acinetobacter in TN1 population, Arsenophonus and Serratia in Mudgo population, and Arthrobacter and Acinetobacter in ASD7 population. When the TN1 population of brown planthopper was transferred to ASD7 (with resistant gene bph2) rice plants, Chryseobacterium was still the dominant bacteria, but the originally subdominant Acinetobacter declined to a level that was not significantly different from that of other endosymbiotic bacteria. After they were transferred to Mudgo (with resistant gene Bph1), Serratia and Arsenophonus increased significantly and became the dominant bacteria. However, they declined to a level that was not significantly different from that of the three other species after two generations. When ASD7 and Mudgo populations of brown planthopper were transferred to the susceptible variety TN1, the community of endosymbiotic bacteria in the ASD7 population of brown planthopper showed no significant changes. However, the numbers of Acinetobacter and Arthrobacter in the Mudgo population of brown planthopper exhibited a transient increase and returned to their original levels after two generations. After the Mudgo population of brown planthopper was transferred to ASD7 rice plants, the quantity of endosymbiotic bacteria fluctuated, but the bacterial structure did not change significantly. However, after the ASD7 population of brown planthopper was transferred to the Mudgo rice plants, the bacterial structure changed significantly. Serratia and Arsenophonus increased significantly and became dominant. Although Serratia and Arsenophonus decreased

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

    PubMed Central

    Dziewit, Lukasz; Bartosik, Dariusz

    2014-01-01

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

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

    PubMed

    Dziewit, Lukasz; Bartosik, Dariusz

    2014-01-01

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

  17. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

    PubMed Central

    Barroso-Batista, João; Demengeot, Jocelyne; Gordo, Isabel

    2015-01-01

    Co-evolution between the mammalian immune system and the gut microbiota is believed to have shaped the microbiota's astonishing diversity. Here we test the corollary hypothesis that the adaptive immune system, directly or indirectly, influences the evolution of commensal species. We compare the evolution of Escherichia coli upon colonization of the gut of wild-type and Rag2−/− mice, which lack lymphocytes. We show that bacterial adaptation is slower in immune-compromised animals, a phenomenon explained by differences in the action of natural selection within each host. Emerging mutations exhibit strong beneficial effects in healthy hosts but substantial antagonistic pleiotropy in immune-deficient mice. This feature is due to changes in the composition of the gut microbiota, which differs according to the immune status of the host. Our results indicate that the adaptive immune system influences the tempo and predictability of E. coli adaptation to the mouse gut. PMID:26615893

  18. Isolation and preliminary characterization of aerobic heterotrophic bacteria isolated from sub-glacial Antarctic water samples

    NASA Astrophysics Data System (ADS)

    Palma-Alvarez, R.; Lanoil, B. D.

    2002-05-01

    Recently, evidence has been accumulating supporting the presence of biogeochemically active microbial communities in cold, dark, and isolated subglacial environments. These environments are important sites of rock weathering, provide insight into global biogeochemistry during glacial periods, and are potential analogues for ancient Snowball Earth events and the ice-covered oceans of the Jovian moon, Europa. However, the extent of microbial influence on subglacial geochemistry is unclear. As part of an ongoing project to address the extent of that influence, we isolated aerobic heterotrophic bacteria from sediment-laden water from beneath Ice Stream C, a fast moving region of the Western Antarctic Ice Sheet (WAIS). Plates of a standard environmental media (R2A) were prepared at three dilutions (1x, 0.1x, 0.01x) and inoculated in duplicate in a HEPA-filtered environment. One replicate was incubated at 4oC, the other at room temperature in the dark. All plates showed abundant growth, although colony size was positively correlated with media concentration. One-hundred eighty-one colonies total were picked, grown in liquid R2A (1x concentration) at the same initial temperature, and characterized for Gram character, cell shape, cell size, and production of a diffusible yellow pigment with similar chemical characteristics to the siderophore, pyoverdine. Based on these characters, a moderate level of diversity was observed in these isolates. A few types dominated the samples, with several others found only rarely. Further characterization of these isolates is ongoing, and results of these studies and their possible implications for sub-glacial biogeochemistry are discussed.

  19. Adaptive Sampling-Based Information Collection for Wireless Body Area Networks.

    PubMed

    Xu, Xiaobin; Zhao, Fang; Wang, Wendong; Tian, Hui

    2016-08-31

    To collect important health information, WBAN applications typically sense data at a high frequency. However, limited by the quality of wireless link, the uploading of sensed data has an upper frequency. To reduce upload frequency, most of the existing WBAN data collection approaches collect data with a tolerable error. These approaches can guarantee precision of the collected data, but they are not able to ensure that the upload frequency is within the upper frequency. Some traditional sampling based approaches can control upload frequency directly, however, they usually have a high loss of information. Since the core task of WBAN applications is to collect health information, this paper aims to collect optimized information under the limitation of upload frequency. The importance of sensed data is defined according to information theory for the first time. Information-aware adaptive sampling is proposed to collect uniformly distributed data. Then we propose Adaptive Sampling-based Information Collection (ASIC) which consists of two algorithms. An adaptive sampling probability algorithm is proposed to compute sampling probabilities of different sensed values. A multiple uniform sampling algorithm provides uniform samplings for values in different intervals. Experiments based on a real dataset show that the proposed approach has higher performance in terms of data coverage and information quantity. The parameter analysis shows the optimized parameter settings and the discussion shows the underlying reason of high performance in the proposed approach.

  20. Adaptive Sampling-Based Information Collection for Wireless Body Area Networks

    PubMed Central

    Xu, Xiaobin; Zhao, Fang; Wang, Wendong; Tian, Hui

    2016-01-01

    To collect important health information, WBAN applications typically sense data at a high frequency. However, limited by the quality of wireless link, the uploading of sensed data has an upper frequency. To reduce upload frequency, most of the existing WBAN data collection approaches collect data with a tolerable error. These approaches can guarantee precision of the collected data, but they are not able to ensure that the upload frequency is within the upper frequency. Some traditional sampling based approaches can control upload frequency directly, however, they usually have a high loss of information. Since the core task of WBAN applications is to collect health information, this paper aims to collect optimized information under the limitation of upload frequency. The importance of sensed data is defined according to information theory for the first time. Information-aware adaptive sampling is proposed to collect uniformly distributed data. Then we propose Adaptive Sampling-based Information Collection (ASIC) which consists of two algorithms. An adaptive sampling probability algorithm is proposed to compute sampling probabilities of different sensed values. A multiple uniform sampling algorithm provides uniform samplings for values in different intervals. Experiments based on a real dataset show that the proposed approach has higher performance in terms of data coverage and information quantity. The parameter analysis shows the optimized parameter settings and the discussion shows the underlying reason of high performance in the proposed approach. PMID:27589758

  1. Adaptive Sampling-Based Information Collection for Wireless Body Area Networks.

    PubMed

    Xu, Xiaobin; Zhao, Fang; Wang, Wendong; Tian, Hui

    2016-01-01

    To collect important health information, WBAN applications typically sense data at a high frequency. However, limited by the quality of wireless link, the uploading of sensed data has an upper frequency. To reduce upload frequency, most of the existing WBAN data collection approaches collect data with a tolerable error. These approaches can guarantee precision of the collected data, but they are not able to ensure that the upload frequency is within the upper frequency. Some traditional sampling based approaches can control upload frequency directly, however, they usually have a high loss of information. Since the core task of WBAN applications is to collect health information, this paper aims to collect optimized information under the limitation of upload frequency. The importance of sensed data is defined according to information theory for the first time. Information-aware adaptive sampling is proposed to collect uniformly distributed data. Then we propose Adaptive Sampling-based Information Collection (ASIC) which consists of two algorithms. An adaptive sampling probability algorithm is proposed to compute sampling probabilities of different sensed values. A multiple uniform sampling algorithm provides uniform samplings for values in different intervals. Experiments based on a real dataset show that the proposed approach has higher performance in terms of data coverage and information quantity. The parameter analysis shows the optimized parameter settings and the discussion shows the underlying reason of high performance in the proposed approach. PMID:27589758

  2. Temporally Adaptive Sampling: A Case Study in Rare Species Survey Design with Marbled Salamanders (Ambystoma opacum)

    PubMed Central

    Charney, Noah D.; Kubel, Jacob E.; Eiseman, Charles S.

    2015-01-01

    Improving detection rates for elusive species with clumped distributions is often accomplished through adaptive sampling designs. This approach can be extended to include species with temporally variable detection probabilities. By concentrating survey effort in years when the focal species are most abundant or visible, overall detection rates can be improved. This requires either long-term monitoring at a few locations where the species are known to occur or models capable of predicting population trends using climatic and demographic data. For marbled salamanders (Ambystoma opacum) in Massachusetts, we demonstrate that annual variation in detection probability of larvae is regionally correlated. In our data, the difference in survey success between years was far more important than the difference among the three survey methods we employed: diurnal surveys, nocturnal surveys, and dipnet surveys. Based on these data, we simulate future surveys to locate unknown populations under a temporally adaptive sampling framework. In the simulations, when pond dynamics are correlated over the focal region, the temporally adaptive design improved mean survey success by as much as 26% over a non-adaptive sampling design. Employing a temporally adaptive strategy costs very little, is simple, and has the potential to substantially improve the efficient use of scarce conservation funds. PMID:25799224

  3. Temporally adaptive sampling: a case study in rare species survey design with marbled salamanders (Ambystoma opacum).

    PubMed

    Charney, Noah D; Kubel, Jacob E; Eiseman, Charles S

    2015-01-01

    Improving detection rates for elusive species with clumped distributions is often accomplished through adaptive sampling designs. This approach can be extended to include species with temporally variable detection probabilities. By concentrating survey effort in years when the focal species are most abundant or visible, overall detection rates can be improved. This requires either long-term monitoring at a few locations where the species are known to occur or models capable of predicting population trends using climatic and demographic data. For marbled salamanders (Ambystoma opacum) in Massachusetts, we demonstrate that annual variation in detection probability of larvae is regionally correlated. In our data, the difference in survey success between years was far more important than the difference among the three survey methods we employed: diurnal surveys, nocturnal surveys, and dipnet surveys. Based on these data, we simulate future surveys to locate unknown populations under a temporally adaptive sampling framework. In the simulations, when pond dynamics are correlated over the focal region, the temporally adaptive design improved mean survey success by as much as 26% over a non-adaptive sampling design. Employing a temporally adaptive strategy costs very little, is simple, and has the potential to substantially improve the efficient use of scarce conservation funds. PMID:25799224

  4. Temporally adaptive sampling: a case study in rare species survey design with marbled salamanders (Ambystoma opacum).

    PubMed

    Charney, Noah D; Kubel, Jacob E; Eiseman, Charles S

    2015-01-01

    Improving detection rates for elusive species with clumped distributions is often accomplished through adaptive sampling designs. This approach can be extended to include species with temporally variable detection probabilities. By concentrating survey effort in years when the focal species are most abundant or visible, overall detection rates can be improved. This requires either long-term monitoring at a few locations where the species are known to occur or models capable of predicting population trends using climatic and demographic data. For marbled salamanders (Ambystoma opacum) in Massachusetts, we demonstrate that annual variation in detection probability of larvae is regionally correlated. In our data, the difference in survey success between years was far more important than the difference among the three survey methods we employed: diurnal surveys, nocturnal surveys, and dipnet surveys. Based on these data, we simulate future surveys to locate unknown populations under a temporally adaptive sampling framework. In the simulations, when pond dynamics are correlated over the focal region, the temporally adaptive design improved mean survey success by as much as 26% over a non-adaptive sampling design. Employing a temporally adaptive strategy costs very little, is simple, and has the potential to substantially improve the efficient use of scarce conservation funds.

  5. Development of a membrane-array method for the detection of human intestinal bacteria in fecal samples.

    PubMed

    Wang, R F; Kim, S-J; Robertson, L H; Cerniglia, C E

    2002-10-01

    A membrane-array method was developed for the detection of human intestinal bacteria in fecal samples without using the expensive microarray-arrayer and laser-scanner. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to nitrocellulose membranes. Digoxigenin (DIG)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or pure cultured bacteria using two universal primers, and were hybridized to the membrane-array. Hybridization signals were read by NBT/BCIP color development. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, B. vulgatus, B. fragilis, B. distasonis, Clostridium clostridiiforme, C. leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, R. bromii, R. callidus, R. albus, Bifidobacterium longum, B. adolescentis, B. infantis, Eubacterium biforme, E. aerofaciens, Lactobacillus acidophilus,Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the membrane-array method is a reliable technique for the detection of predominant human intestinal bacteria in the fecal samples. The result was also confirmed by using specific PCR methods for these bacteria.

  6. Career Adapt-Abilities Scale in a French-Speaking Swiss Sample: Psychometric Properties and Relationships to Personality and Work Engagement

    ERIC Educational Resources Information Center

    Rossier, Jerome; Zecca, Gregory; Stauffer, Sarah D.; Maggiori, Christian; Dauwalder, Jean-Pierre

    2012-01-01

    The aim of this study was to analyze the psychometric properties of the Career Adapt-Abilities Scale (CAAS) in a French-speaking Swiss sample and its relationship with personality dimensions and work engagement. The heterogeneous sample of 391 participants (M[subscript age] = 39.59, SD = 12.30) completed the CAAS-International and a short version…

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

    PubMed

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

    2006-04-01

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

  8. [Cloning and expression of endoglucanase of marine cold-adapted bacteria Pseudoalteromonas sp. MB-1].

    PubMed

    You, Yin-wei; Wang, Tian-hong

    2005-02-01

    The cold-adapted gram-negative rod bacterium MB-1 which could secret cellulase was screened from mud of the bottom of the Huanghai. According to the sequence of 16S rDNA, this bacterium screened was identified as one species of Pseudoalteromonas and was named as Pseudoalteromonas sp. MB-1. The gene celA encoding cold-adapted endogluanase was cloned and then jointed to pGEX-4T-1 to construct expression plasmid pGEX-celA which was expressed in E. coli BL21. Analysis to the supernatant of E. coli sonicate revealed that the concentration of GST-CelA was about 78.5 mg/L. Properties of the fusion enzyme of GST-CelA including the optimum temperature at 35 degrees C and the optimum pH about 7.2, showed that this fusion enzyme still belonged to cold-adapted enzyme and neutral enzyme. The result lays solid base for the fundamental theory and application research on cold-adapted cellulase from Pseudoalteromonas sp. MB-1.

  9. Phylogeography, Salinity Adaptations and Metabolic Potential of the Candidate Division KB1 Bacteria Based on a Partial Single Cell Genome

    PubMed Central

    Nigro, Lisa M.; Hyde, Andrew S.; MacGregor, Barbara J.; Teske, Andreas

    2016-01-01

    Deep-sea hypersaline anoxic basins and other hypersaline environments contain abundant and diverse microbial life that has adapted to these extreme conditions. The bacterial Candidate Division KB1 represents one of several uncultured groups that have been consistently observed in hypersaline microbial diversity studies. Here we report the phylogeography of KB1, its phylogenetic relationships to Candidate Division OP1 Bacteria, and its potential metabolic and osmotic stress adaptations based on a partial single cell amplified genome of KB1 from Orca Basin, the largest hypersaline seafloor brine basin in the Gulf of Mexico. Our results are consistent with the hypothesis – previously developed based on 14C incorporation experiments with mixed-species enrichments from Mediterranean seafloor brines – that KB1 has adapted its proteins to elevated intracellular salinity, but at the same time KB1 apparently imports glycine betaine; this compatible solute is potentially not limited to osmoregulation but could also serve as a carbon and energy source. PMID:27597842

  10. Control of growth and adaptation to nutritional shifts for bacteria exposed to amino acid-limiting environments

    NASA Astrophysics Data System (ADS)

    Mateescu, Eduard M.; Hwa, Terence

    2007-03-01

    In order to grow at the highest rate sustainable by the environment, bacteria turn on different metabolic pathways and utilize a myriad of adaptive strategies. The macromolecular composition (RNA, DNA, protein) and overall cell size (mass) can be very different in different environments. Surprisingly however, these differences appear to depend only on the growth rate and not on the growth medium itself. As the nutritional environment changes in time, the cells quickly adapt their composition to the one corresponding to the new conditions. Here, we propose a phenomenological model of growth and adaptation control for the bacterial cell, based on a simplified formulation of the central dogma and a simplified implementation of the stringent response. The core model contains no free parameters and provides a simple intuitive understanding of cell growth control. The results generated by the model, physiological state of the cell as well as the characteristics of the transition between optimized states of growth, are in qualitative and semi-quantitative agreement (i.e. within a factor of 2) with the experimental observations.

  11. Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates.

    PubMed Central

    Lowe, S E; Jain, M K; Zeikus, J G

    1993-01-01

    Anaerobic bacteria include diverse species that can grow at environmental extremes of temperature, pH, salinity, substrate toxicity, or available free energy. The first evolved archaebacterial and eubacterial species appear to have been anaerobes adapted to high temperatures. Thermoanaerobes and their stable enzymes have served as model systems for basic and applied studies of microbial cellulose and starch degradation, methanogenesis, ethanologenesis, acetogenesis, autotrophic CO2 fixation, saccharidases, hydrogenases, and alcohol dehydrogenases. Anaerobes, unlike aerobes, appear to have evolved more energy-conserving mechanisms for physiological adaptation to environmental stresses such as novel enzyme activities and stabilities and novel membrane lipid compositions and functions. Anaerobic syntrophs do not have similar aerobic bacterial counterparts. The metabolic end products of syntrophs are potent thermodynamic inhibitors of energy conservation mechanisms, and they require coordinated consumption by a second partner organism for species growth. Anaerobes adapted to environmental stresses and their enzymes have biotechnological applications in organic waste treatment systems and chemical and fuel production systems based on biomass-derived substrates or syngas. These kinds of anaerobes have only recently been examined by biologists, and considerably more study is required before they are fully appreciated by science and technology. Images PMID:8336675

  12. An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

    SciTech Connect

    Li, Weixuan; Lin, Guang

    2015-03-21

    Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes’ rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle these challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.

  13. An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

    SciTech Connect

    Li, Weixuan; Lin, Guang

    2015-08-01

    Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes' rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle these challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.

  14. An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

    DOE PAGES

    Li, Weixuan; Lin, Guang

    2015-03-21

    Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes’ rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle thesemore » challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.« less

  15. Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe

    PubMed Central

    Postolache, Dragos; Lascoux, Martin; Drouzas, Andreas D.; Källman, Thomas; Leonarduzzi, Cristina; Liepelt, Sascha; Piotti, Andrea; Popescu, Flaviu; Roschanski, Anna M.; Zhelev, Peter; Fady, Bruno; Vendramin, Giovanni Giuseppe

    2016-01-01

    Background Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical ‘within-site’ approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species’ southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales. PMID:27392065

  16. Region and edge-adaptive sampling and boundary completion for segmentation

    SciTech Connect

    Dillard, Scott E; Prasad, Lakshman; Grazzini, Jacopo A

    2010-01-01

    Edge detection produces a set of points that are likely to lie on discontinuities between objects within an image. We consider faces of the Gabriel graph of these points, a sub-graph of the Delaunay triangulation. Features are extracted by merging these faces using size, shape and color cues. We measure regional properties of faces using a novel shape-dependant sampling method that overcomes undesirable sampling bias of the Delaunay triangles. Instead, sampling is biased so as to smooth regional statistics within the detected object boundaries, and this smoothing adapts to local geometric features of the shape such as curvature, thickness and straightness.

  17. The Vineland Adaptive Behavior Scale in a sample of normal French Children: a research note.

    PubMed

    Fombonne, E; Achard, S

    1993-09-01

    The Vineland Adaptive Behavior scale (survey form) was used in a sample of 151 normal children under age 18. Standardized mean scores of French children were comparable to those of the American normative sample. From the age of 6 onwards, French children scored consistently lower in the Daily Living Skills domain though the magnitude of this difference remained moderate. While the overall findings support the cross-cultural stability of the psychometric properties of this instrument, attention is drawn to potential problems in the use of the Vineland scales, with special reference to autistic samples.

  18. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

    PubMed Central

    Dziewit, Lukasz; Pyzik, Adam; Szuplewska, Magdalena; Matlakowska, Renata; Mielnicki, Sebastian; Wibberg, Daniel; Schlüter, Andreas; Pühler, Alfred; Bartosik, Dariusz

    2015-01-01

    The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface. PMID:26074880

  19. Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.

    PubMed

    Wielgoss, Sébastien; Bergmiller, Tobias; Bischofberger, Anna M; Hall, Alex R

    2016-03-01

    Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.

  20. Detection of airborne bacteria in a duck production facility with two different personal air sampling devices for an exposure assessment.

    PubMed

    Martin, Elena; Dziurowitz, Nico; Jäckel, Udo; Schäfer, Jenny

    2015-01-01

    Prevalent airborne microorganisms are not well characterized in industrial animal production buildings with respect to their quantity or quality. To investigate the work-related microbial exposure, personal bioaerosol sampling during the whole working day is recommended. Therefore, bioaerosol sampling in a duck hatchery and a duck house with two personal air sampling devices, a filter-based PGP and a NIOSH particle size separator, was performed. Subsequent, quantitative and qualitative analyses were carried out with" culture independent methods. Total cell concentrations (TCC) determined via fluorescence microscopy showed no difference between the two devices. In average, 8 × 10(6) cells/m(3) were determined in the air of the duck hatchery and 5 × 10(7) cells/m(3) in the air of the duck house. A Generated Restriction Fragment Length Polymorphism (RFLP) pattern revealed deviant bacterial compositions comparing samples collected with both devices. Clone library analyses based on 16S rRNA gene sequence analysis from the hatchery's air showed 65% similarity between the two sampling devices. Detailed 16S rRNA gene sequence analyses showed the occurrence of bacterial species like Acinetobacter baumannii, Enterococcus faecalis, Escherichia sp., and Shigella sp.; and a group of Staphylococcus delphini, S. intermedius, and S. pseudintermedius that provided the evidence of potential exposure to risk group 2 bacteria at the hatchery workplace. Size fractionated sampling with the developed by the Institute for Occupational Safety and Health of the German Social Accident Insurance (IFA) device revealed that pathogenic bacteria would deposit in the inhalable, the thorax, and possibly alveolar dust fraction according to EN481. TCC analysis showed the deposition of bacterial cells in the third stage (< 1μm) at the NIOSH device which implies that bacteria can reach deep into the lungs and contaminate the alveolus after inhalation. Nevertheless, both personal sampling devices

  1. Patterns of local adaptation in space and time among soil bacteria.

    PubMed

    Kraemer, Susanne A; Kassen, Rees

    2015-03-01

    Our understanding of microbial biogeography has been governed by the dictum "Everything is everywhere, but the environment selects." In other words, the distribution of microbes is thought to occur in a regime of extensive dispersal and strong selection, generating local adaptation. However, direct tests of these assumptions are rare. Here, we investigate the extent of local adaptation in space and time of a collection of soil-derived microbial isolates, most belonging to the genus Pseudomonas, across a growing season from a deciduous forest in western Quebec, Canada, using a reciprocal transplant design. Average performance of all clones varied substantially in both space and time, in line with the expectation of strong selection in both dimensions. The behavior of genotype-by-environment variance in fitness and its components, responsiveness and inconsistency, in space and through time suggests that the strength of divergent selection increases as sites become more distant from each other in both dimensions. However, divergent selection was not strong enough to maintain different specialized types across the environments studied, which suggests that Pseudomonas and their close relatives are not locally adapted to the prevailing conditions of growth.

  2. Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria

    PubMed Central

    Ishii, Eiji; Chiba, Shinobu; Hashimoto, Narimasa; Kojima, Seiji; Homma, Michio; Ito, Koreaki; Akiyama, Yoshinori; Mori, Hiroyuki

    2015-01-01

    SecDF interacts with the SecYEG translocon in bacteria and enhances protein export in a proton-motive-force-dependent manner. Vibrio alginolyticus, a marine-estuarine bacterium, contains two SecDF paralogs, V.SecDF1 and V.SecDF2. Here, we show that the export-enhancing function of V.SecDF1 requires Na+ instead of H+, whereas V.SecDF2 is Na+-independent, presumably requiring H+. In accord with the cation-preference difference, V.SecDF2 was only expressed under limited Na+ concentrations whereas V.SecDF1 was constitutive. However, it is not the decreased concentration of Na+ per se that the bacterium senses to up-regulate the V.SecDF2 expression, because marked up-regulation of the V.SecDF2 synthesis was observed irrespective of Na+ concentrations under certain genetic/physiological conditions: (i) when the secDF1VA gene was deleted and (ii) whenever the Sec export machinery was inhibited. VemP (Vibrio export monitoring polypeptide), a secretory polypeptide encoded by the upstream ORF of secDF2VA, plays the primary role in this regulation by undergoing regulated translational elongation arrest, which leads to unfolding of the Shine–Dalgarno sequence for translation of secDF2VA. Genetic analysis of V. alginolyticus established that the VemP-mediated regulation of SecDF2 is essential for the survival of this marine bacterium in low-salinity environments. These results reveal that a class of marine bacteria exploits nascent-chain ribosome interactions to optimize their protein export pathways to propagate efficiently under different ionic environments that they face in their life cycles. PMID:26392525

  3. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

    PubMed Central

    Ricard, Guénola; McEwan, Neil R; Dutilh, Bas E; Jouany, Jean-Pierre; Macheboeuf, Didier; Mitsumori, Makoto; McIntosh, Freda M; Michalowski, Tadeusz; Nagamine, Takafumi; Nelson, Nancy; Newbold, Charles J; Nsabimana, Eli; Takenaka, Akio; Thomas, Nadine A; Ushida, Kazunari; Hackstein, Johannes HP; Huynen, Martijn A

    2006-01-01

    Background The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium). Results A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates. Conclusion Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches. PMID:16472398

  4. Genomic and exoproteomic analyses of cold- and alkaline-adapted bacteria reveal an abundance of secreted subtilisin-like proteases.

    PubMed

    Lylloff, Jeanette E; Hansen, Lea B S; Jepsen, Morten; Sanggaard, Kristian W; Vester, Jan K; Enghild, Jan J; Sørensen, Søren J; Stougaard, Peter; Glaring, Mikkel A

    2016-03-01

    Proteases active at low temperature or high pH are used in many commercial applications, including the detergent, food and feed industries, and bacteria specifically adapted to these conditions are a potential source of novel proteases. Environments combining these two extremes are very rare, but offer the promise of proteases ideally suited to work at both high pH and low temperature. In this report, bacteria from two cold and alkaline environments, the ikaite columns in Greenland and alkaline ponds in the McMurdo Dry Valley region, Antarctica, were screened for extracellular protease activity. Two isolates, Arsukibacterium ikkense from Greenland and a related strain, Arsukibacterium sp. MJ3, from Antarctica, were further characterized with respect to protease production. Genome sequencing identified a range of potential extracellular proteases including a number of putative secreted subtilisins. An extensive liquid chromatography-tandem mass spectrometry analysis of proteins secreted by A. ikkense identified six subtilisin-like proteases as abundant components of the exoproteome in addition to other peptidases potentially involved in complete degradation of extracellular protein. Screening of Arsukibacterium genome libraries in Escherichia coli identified two orthologous secreted subtilisins active at pH 10 and 20 °C, which were also present in the A. ikkense exoproteome. Recombinant production of both proteases confirmed the observed activity. PMID:26834075

  5. Using continuous in-situ measurements to adaptively trigger urban storm water samples

    NASA Astrophysics Data System (ADS)

    Wong, B. P.; Kerkez, B.

    2015-12-01

    Until cost-effective in-situ sensors are available for biological parameters, nutrients and metals, automated samplers will continue to be the primary source of reliable water quality measurements. Given limited samples bottles, however, autosamplers often obscure insights on nutrient sources and biogeochemical processes which would otherwise be captured using a continuous sampling approach. To that end, we evaluate the efficacy a novel method to measure first-flush nutrient dynamics in flashy, urban watersheds. Our approach reduces the number of samples required to capture water quality dynamics by leveraging an internet-connected sensor node, which is equipped with a suite of continuous in-situ sensors and an automated sampler. To capture both the initial baseflow as well as storm concentrations, a cloud-hosted adaptive algorithm analyzes the high-resolution sensor data along with local weather forecasts to optimize a sampling schedule. The method was tested in a highly developed urban catchment in Ann Arbor, Michigan and collected samples of nitrate, phosphorus, and suspended solids throughout several storm events. Results indicate that the watershed does not exhibit first flush dynamics, a behavior that would have been obscured when using a non-adaptive sampling approach.

  6. An adapted tissue microarray for the development of a matrix arrangement of tissue samples.

    PubMed

    Gurgel, Daniel C; Dornelas, Conceição A; Lima-Júnior, Roberto C P; Ribeiro, Ronaldo A; Almeida, Paulo R C

    2012-03-15

    The arrangement of tissue samples in a matrix, known as the tissue microarray (TMA) method, is a well-recognized method worldwide. This technique makes it possible to assess the expression of molecular markers on a large scale with high yields in terms of time, costs, and archived material. Some researchers are trying to adapt the technique to expand the research possibilities. This study proposes an adaptive simplification of low-cost instruments for obtaining samples that will be used in the construction of the TMA. The use of a manual leather puncher, which has a very low cost and a long expected life and eliminates the need to use a press machine, is a simple and effective alternative to building blocks of tissue microarrays.

  7. The Evolution of Two-Component Systems in Bacteria RevealsDifferent Strategies for Niche Adaptation

    SciTech Connect

    Alm, Eric; Huang, Katherine; Arkin, Adam

    2006-09-13

    Two-component systems including histidine protein kinasesrepresent the primary signal transduction paradigm in prokaryoticorganisms. To understand how these systems adapt to allow organisms todetect niche-specific signals, we analyzed the phylogenetic distributionof nearly 5000 histidine protein kinases from 207 sequenced prokaryoticgenomes. We found that many genomes carry a large repertoire of recentlyevolved signaling genes, which may reflect selective pressure to adapt tonew environmental conditions. Both lineage-specific gene family expansionand horizontal gene transfer play major roles in the introduction of newhistidine kinases into genomes; however, there are differences in howthese two evolutionary forces act. Genes imported via horizontal transferare more likely to retain their original functionality as inferred from asimilar complement of signaling domains, while gene family expansionaccompanied by domain shuffling appears to be a major source of novelgenetic diversity. Family expansion is the dominantsource of newhistidine kinase genes in the genomes most enriched in signalingproteins, and detailed analysis reveals that divergence in domainstructure and changes in expression patterns are hallmarks of recentexpansions. Finally, while these two modes of gene acquisition arewidespread across bacterial taxa, there are clear species-specificpreferences for which mode is used.

  8. Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria.

    PubMed

    Liu, Shuai; Hu, Baolan; He, Zhanfei; Zhang, Bin; Tian, Guangming; Zheng, Ping; Fang, Fang

    2015-10-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05). PMID:26099334

  9. Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria.

    PubMed

    Liu, Shuai; Hu, Baolan; He, Zhanfei; Zhang, Bin; Tian, Guangming; Zheng, Ping; Fang, Fang

    2015-10-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05).

  10. Adaptation and Validation of the Sexual Assertiveness Scale (SAS) in a Sample of Male Drug Users.

    PubMed

    Vallejo-Medina, Pablo; Sierra, Juan Carlos

    2015-04-21

    The aim of the present study was to adapt and validate the Sexual Assertiveness Scale (SAS) in a sample of male drug users. A sample of 326 male drug users and 322 non-clinical males was selected by cluster sampling and convenience sampling, respectively. Results showed that the scale had good psychometric properties and adequate internal consistency reliability (Initiation = .66, Refusal = .74 and STD-P = .79). An evaluation of the invariance showed strong factor equivalence between both samples. A high and moderate effect of Differential Item Functioning was only found in items 1 and 14 (∆R 2 Nagelkerke = .076 and .037, respectively). We strongly recommend not using item 1 if the goal is to compare the scores of both groups, otherwise the comparison will be biased. Correlations obtained between the CSFQ-14 and the safe sex ratio and the SAS subscales were significant (CI = 95%) and indicated good concurrent validity. Scores of male drug users were similar to those of non-clinical males. Therefore, the adaptation of the SAS to drug users provides enough guarantees for reliable and valid use in both clinical practice and research, although care should be taken with item 1.

  11. Adaptation and Validation of the Sexual Assertiveness Scale (SAS) in a Sample of Male Drug Users.

    PubMed

    Vallejo-Medina, Pablo; Sierra, Juan Carlos

    2015-01-01

    The aim of the present study was to adapt and validate the Sexual Assertiveness Scale (SAS) in a sample of male drug users. A sample of 326 male drug users and 322 non-clinical males was selected by cluster sampling and convenience sampling, respectively. Results showed that the scale had good psychometric properties and adequate internal consistency reliability (Initiation = .66, Refusal = .74 and STD-P = .79). An evaluation of the invariance showed strong factor equivalence between both samples. A high and moderate effect of Differential Item Functioning was only found in items 1 and 14 (∆R 2 Nagelkerke = .076 and .037, respectively). We strongly recommend not using item 1 if the goal is to compare the scores of both groups, otherwise the comparison will be biased. Correlations obtained between the CSFQ-14 and the safe sex ratio and the SAS subscales were significant (CI = 95%) and indicated good concurrent validity. Scores of male drug users were similar to those of non-clinical males. Therefore, the adaptation of the SAS to drug users provides enough guarantees for reliable and valid use in both clinical practice and research, although care should be taken with item 1. PMID:25896498

  12. Adaptive k-space sampling design for edge-enhanced DCE-MRI using compressed sensing.

    PubMed

    Raja, Rajikha; Sinha, Neelam

    2014-09-01

    The critical challenge in dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is the trade-off between spatial and temporal resolution due to the limited availability of acquisition time. To address this, it is imperative to under-sample k-space and to develop specific reconstruction techniques. Our proposed method reconstructs high-quality images from under-sampled dynamic k-space data by proposing two main improvements; i) design of an adaptive k-space sampling lattice and ii) edge-enhanced reconstruction technique. A high-resolution data set obtained before the start of the dynamic phase is utilized. The sampling pattern is designed to adapt to the nature of k-space energy distribution obtained from the static high-resolution data. For image reconstruction, the well-known compressed sensing-based total variation (TV) minimization constrained reconstruction scheme is utilized by incorporating the gradient information obtained from the static high-resolution data. The proposed method is tested on seven real dynamic time series consisting of 2 breast data sets and 5 abdomen data sets spanning 1196 images in all. For data availability of only 10%, performance improvement is seen across various quality metrics. Average improvements in Universal Image Quality Index and Structural Similarity Index Metric of up to 28% and 24% on breast data and about 17% and 9% on abdomen data, respectively, are obtained for the proposed method as against the baseline TV reconstruction with variable density random sampling pattern.

  13. A Predictive Approach to Nonparametric Inference for Adaptive Sequential Sampling of Psychophysical Experiments

    PubMed Central

    Benner, Philipp; Elze, Tobias

    2012-01-01

    We present a predictive account on adaptive sequential sampling of stimulus-response relations in psychophysical experiments. Our discussion applies to experimental situations with ordinal stimuli when there is only weak structural knowledge available such that parametric modeling is no option. By introducing a certain form of partial exchangeability, we successively develop a hierarchical Bayesian model based on a mixture of Pólya urn processes. Suitable utility measures permit us to optimize the overall experimental sampling process. We provide several measures that are either based on simple count statistics or more elaborate information theoretic quantities. The actual computation of information theoretic utilities often turns out to be infeasible. This is not the case with our sampling method, which relies on an efficient algorithm to compute exact solutions of our posterior predictions and utility measures. Finally, we demonstrate the advantages of our framework on a hypothetical sampling problem. PMID:22822269

  14. Evaluation of dry sheet medium culture plate (Compactdry TC) method for determining numbers of bacteria in food samples.

    PubMed

    Mizuochi, S; Kodaka, H

    2000-05-01

    The Compactdry, a ready-to-use and self-diffusible dry medium sheet culture system, has been developed by the Nissui Pharmaceutical Co. Ltd. for enumerating bacteria in food. The Compactdry consists of special spread sheet with culture medium that is the same as standard method nutrients, a cold water-soluble gelling agent, and a unique plastic dish. The procedure for bacterial examination in a sample solution (1 ml) is to just inoculate a test solution into the center of the self-diffusible medium and incubate at 35 degrees C for 48 h. The Compactdry TC (CTC) for the enumeration of total aerobic bacteria from 97 food samples was compared with the standard plate count (SPC) method and 3M Petrifilm aerobic count plates (PAC). The correlation coefficients between the CTC and SPC method, the CTC and PAC, and the PAC and SPC method were 0.97, 0.99, and 0.97, respectively. The Compactdry system is useful for the enumeration of total aerobic bacteria in food and may be a possible suitable alternative to the conventional pour-plate or the Petrifilm plate methods.

  15. A proteomics workflow for quantitative and time-resolved analysis of adaptation reactions of internalized bacteria.

    PubMed

    Pförtner, Henrike; Wagner, Juliane; Surmann, Kristin; Hildebrandt, Petra; Ernst, Sandra; Bernhardt, Jörg; Schurmann, Claudia; Gutjahr, Melanie; Depke, Maren; Jehmlich, Ulrike; Dhople, Vishnu; Hammer, Elke; Steil, Leif; Völker, Uwe; Schmidt, Frank

    2013-06-15

    The development of a mass spectrometric workflow for the sensitive identification and quantitation of the kinetics of changes in metaproteomes, or in particular bacterial pathogens after internalization by host cells, is described. This procedure employs three essential stages: (i) SILAC pulse-chase labeling and infection assay; (ii) isolation of bacteria by GFP-assisted cell sorting; (iii) mass spectrometry-based proteome analysis. This approach displays greater sensitivity than techniques relying on conventional cell sorting and protein separation, due to an efficient combination of a filtration-based purification and an on-membrane digestion. We exemplary describe the use of the workflow for the identification and quantitation of the proteome of 10⁶ cells of Staphylococcus aureus after internalization by S9 human bronchial epithelial cells. With minor modifications, the workflow described can be applied for the characterization of other host-pathogen pairs, permitting identification and quantitation of hundreds of bacterial proteins over a time range of several hours post infection.

  16. Quick Detection of Sulfur Bacteria in Environmental Water Sample with SEM(scanning electron microscopy) coupled with Energy Dispersive X-ray Spectrometry

    NASA Astrophysics Data System (ADS)

    Sun, C.; Ding, H.; Wang, Y.; Jiang, F.; Li, X.; Gao, W.; Yin, X.

    2015-12-01

    Sulfur-oxidizing bacteria play important roles in global sulfur cycle. Sulfur bacteria detection has been largely dependent on targeted gene sequencing technology or traditional cell cultivation which usually takes from days to months to finish. This cannot meet the requirements of some time-sensitive samples and/or complicated environmental samples. Since Energy-Dispersive X-ray Spectrometry (EDS) can be used to simultaneously detect multiple elements including sulfur in a sample with minimal sample treatment, the technology was applied to detect sulfur bacteria through the high sulfur content in the bacteria cell. We report the application of SEM (scanning electron microscopy) imaging coupled with EDS mapping for direct and quick detection of sulfur oxidizer in contaminated environmental water samples. The presence of sulfur bacteria can be confirmed within 24 hours after sampling. Subsequent 16S RNA gene sequencing results found the bacteria detected had over 99% similarity to Chromatium Okenii, confirming the bacterium was a sulfur oxidizer. The developed technique made it possible to quickly detect sulfur oxidizer in environmental sample and could have wide applications in sulfur bacteria detection in environmental water samples.

  17. Investigation of N-acyl homoserine lactone (AHL) molecule production in Gram-negative bacteria isolated from cooling tower water and biofilm samples.

    PubMed

    Haslan, Ezgi; Kimiran-Erdem, Ayten

    2013-09-01

    In this study, 99 Gram-negative rod bacteria were isolated from cooling tower water, and biofilm samples were examined for cell-to-cell signaling systems, N-acyl homoserine lactone (AHL) signal molecule types, and biofilm formation capacity. Four of 39 (10 %) strains isolated from water samples and 14 of 60 (23 %) strains isolated from biofilm samples were found to be producing a variety of AHL signal molecules. It was determined that the AHL signal molecule production ability and the biofilm formation capacity of sessile bacteria is higher than planktonic bacteria, and there was a statistically significant difference between the AHL signal molecule production of these two groups (p < 0.05). In addition, it was found that bacteria belonging to the same species isolated from cooling tower water and biofilm samples produced different types of AHL signal molecules and that there were different types of AHL signal molecules in an AHL extract of bacteria. In the present study, it was observed that different isolates of the same strains did not produce the same AHLs or did not produce AHL molecules, and bacteria known as AHL producers did not produce AHL. These findings suggest that detection of signal molecules in bacteria isolated from cooling towers may contribute to prevention of biofilm formation, elimination of communication among bacteria in water systems, and blockage of quorum-sensing controlled virulence of these bacteria. PMID:23250628

  18. Development of a new real-time PCR system for simultaneous detection of bacteria and fungi in pathological samples.

    PubMed

    Fukumoto, Hitomi; Sato, Yuko; Hasegawa, Hideki; Saeki, Hidehisa; Katano, Harutaka

    2015-01-01

    A novel system for simultaneous detection of pathogenic bacteria and fungi in pathological samples was developed using a real-time polymerase chain reaction (PCR) system. This system, designated the "multi-microbial real-time PCR", has the potential to simultaneously detect 68 bacterial and 9 fungal species in a 96-well plate format. All probe-primer sets were designed to produce amplicons smaller than 210 bp using formalin-fixed paraffin-embedded samples as input. The specificity and sensitivity of each probe-primer set were tested against DNA extracted from pure cultures of specific pathogens. The multi-microbial real-time PCR system revealed profiles of microorganism infection in lung samples collected at autopsy from 10 patients with acquired immunodeficiency syndrome. Staphylococcus aureus was the most common microbe detected (n=8), but with low copy numbers. High copy numbers of Pseudomonas aeruginosa were detected in the lung samples with abscess (n=6). Enterococcus faecium (n=6), Elizabethkingia meningoseptica (n=4), and Candida albicans (n=4) were also frequently detected. In addition, a latent infection of Mycobacterium tuberculosis was detected in one case of pneumonia. In conclusion, this multi-microbial real-time PCR system can be useful for detecting bacteria and fungi in pathological specimens from patients with uncertain diagnoses.

  19. Development of a new real-time PCR system for simultaneous detection of bacteria and fungi in pathological samples

    PubMed Central

    Fukumoto, Hitomi; Sato, Yuko; Hasegawa, Hideki; Saeki, Hidehisa; Katano, Harutaka

    2015-01-01

    A novel system for simultaneous detection of pathogenic bacteria and fungi in pathological samples was developed using a real-time polymerase chain reaction (PCR) system. This system, designated the “multi-microbial real-time PCR”, has the potential to simultaneously detect 68 bacterial and 9 fungal species in a 96-well plate format. All probe-primer sets were designed to produce amplicons smaller than 210 bp using formalin-fixed paraffin-embedded samples as input. The specificity and sensitivity of each probe-primer set were tested against DNA extracted from pure cultures of specific pathogens. The multi-microbial real-time PCR system revealed profiles of microorganism infection in lung samples collected at autopsy from 10 patients with acquired immunodeficiency syndrome. Staphylococcus aureus was the most common microbe detected (n=8), but with low copy numbers. High copy numbers of Pseudomonas aeruginosa were detected in the lung samples with abscess (n=6). Enterococcus faecium (n=6), Elizabethkingia meningoseptica (n=4), and Candida albicans (n=4) were also frequently detected. In addition, a latent infection of Mycobacterium tuberculosis was detected in one case of pneumonia. In conclusion, this multi-microbial real-time PCR system can be useful for detecting bacteria and fungi in pathological specimens from patients with uncertain diagnoses. PMID:26823918

  20. Adaptive Sampling approach to environmental site characterization at Joliet Army Ammunition Plant: Phase 2 demonstration

    SciTech Connect

    Bujewski, G.E.; Johnson, R.L.

    1996-04-01

    Adaptive sampling programs provide real opportunities to save considerable time and money when characterizing hazardous waste sites. This Strategic Environmental Research and Development Program (SERDP) project demonstrated two decision-support technologies, SitePlanner{trademark} and Plume{trademark}, that can facilitate the design and deployment of an adaptive sampling program. A demonstration took place at Joliet Army Ammunition Plant (JAAP), and was unique in that it was tightly coupled with ongoing Army characterization work at the facility, with close scrutiny by both state and federal regulators. The demonstration was conducted in partnership with the Army Environmental Center`s (AEC) Installation Restoration Program and AEC`s Technology Development Program. AEC supported researchers from Tufts University who demonstrated innovative field analytical techniques for the analysis of TNT and DNT. SitePlanner{trademark} is an object-oriented database specifically designed for site characterization that provides an effective way to compile, integrate, manage and display site characterization data as it is being generated. Plume{trademark} uses a combination of Bayesian analysis and geostatistics to provide technical staff with the ability to quantitatively merge soft and hard information for an estimate of the extent of contamination. Plume{trademark} provides an estimate of contamination extent, measures the uncertainty associated with the estimate, determines the value of additional sampling, and locates additional samples so that their value is maximized.

  1. Biomarkers of sulfate reducing bacteria from a variety of different aged samples including a modern microbial mat

    NASA Astrophysics Data System (ADS)

    Pages, A.; Grice, K.; Lockhart, R.; Holman, A.; Melendez, I.; Van Kranendonk, M.; Jaraula, C.

    2011-12-01

    Most biomarkers present in sediments occur in only trace concentrations, trapped in kerogen or may be highly functionalised especially in recent sedimentary deposits making them difficult to chromatographically resolve, thus presenting considerable analytical challenges, especially for isotope studies. Innovative hydro (Hy) pyrolysis (Py) techniques are able to target or convert many of these compounds into free hydrocarbons more amenable to gas chromatography mass-spectrometry (GC-MS) and compound-specific isotope analysis (CSIA). HyPy has been applied to a modern layered smooth mat from Shark Bay, Western Australia. Saturate and aromatic fractions from different layers of the mat have been analysed by GC-MS and CSIA. After HyPy, an even-odd distribution of n-alkanes has been revealed as well as very long-chain n-alkanes up to n-C38. Stable carbon isotopic values of the n-alkanes indicated the presence of at least two bacterial communities. The short-chain n-alkanes were likely to be representative of a cyanobacteria community (δ13C, C15-C23, - 18 to -25 %VPDB) while the carbon isotopic values of the long-chain n-alkanes supported the presence of sulfate reducing bacteria (δ13C, C25-C33, - 30 to - 34 %VPDB). Long-chain fatty acids have been previously reported in sulfate reducing bacteria. It is hypothesised that this distribution and isotopic character representing sulfate reducing bacteria consortia may be preserved in the rock record. This hypothesis has been tested in Australian rocks: a Devonian carbonaceous concretion containing an exceptionally well preserved fossil invertebrate from the Canning Basin, Western Australia, a Paleoproterozoic sample (1.6 billion years old) from a lead-zinc ore deposit from the McArthur Basin, Northern Territories and a Paleoproterozoic chert (2.3 billion years old) from the Pilbara, Western Australia. Biomarkers of these samples showed a strong predominance of long-chain n-alkanes, up to n-C38 with an even-odd distribution

  2. Associations with rhizosphere bacteria can confer an adaptive advantage to plants

    PubMed Central

    Haney, Cara H.; Samuel, Buck S.; Bush, Jenifer; Ausubel, Frederick M.

    2016-01-01

    Host-associated microbiomes influence host health. However, it is unclear whether genotypic variations in host organisms influence the microbiome in ways that have adaptive consequences for the host. Here, we show that wild accessions of Arabidopsis thaliana differ in their ability to associate with the root-associated bacterium Pseudomonas fluorescens, with consequences for plant fitness. In a screen of 196 naturally occurring Arabidopsis accessions we identified lines that actively suppress Pseudomonas growth under gnotobiotic conditions. We planted accessions that support disparate levels of fluorescent Pseudomonads in natural soils; 16S ribosomal RNA sequencing revealed that accession-specific differences in the microbial communities were largely limited to a subset of Pseudomonadaceae species. These accession-specific differences in Pseudomonas growth resulted in enhanced or impaired fitness that depended on the host’s ability to support Pseudomonas growth, the specific Pseudomonas strains present in the soil and the nature of the stress. We suggest that small host-mediated changes in a microbiome can have large effects on host health. PMID:27019743

  3. Detecting Organic Compounds Released from Iron Oxidizing Bacteria using Sample Analysis at Mars (SAM) Like Instrument Protocols

    NASA Technical Reports Server (NTRS)

    Glavin, D. P.; Popa, R.; Martin, M. G.; Freissinet, C.; Fisk, M. R.; Dworkin, J. P.; Mahaffy, P. R.

    2012-01-01

    Mars is a planet of great interest for Astrobiology since its past environmental conditions are thought to have been favourable for the emergence life. At present, the Red Planet is extremely cold and dry and the surface is exposed to intense UV and ionizing radiation, conditions generally considered to be incompatible with life as we know it on Earth. It was proposed that the shallow subsurface of Mars, where temperatures can be above freezing and liquid water can exist on rock surfaces, could harbor chemolithoautotrophic bacteria such as the iron oxidizing microorganism Pseudomonas sp. HerB. The Mars Science Laboratory (MSL) mission will provide the next opportunity to carry out in situ measurements for organic compounds of possible biological origin on Mars. One instrument onboard MSL, called the Sample Analysis at Mars (SAM) instrument suite, will carry out a broad and sensitive search for organic compounds in surface samples using either high temperature pyrolysis or chemical extraction followed by gas chromatography mass spectrometry. We present gas chromatograph mass spectrometer (GC/MS) data on crushed olivine rock powders that have been inoculated with Pseudomonas sp. HerB at different concentrations ranging from approx 10(exp 2) to 10(exp 7) cells per gram. The inoculated olivine samples were heated under helium carrier gas flow at 500 C and the pyrolysis products concentrated using a SAM-like hydrocarbon trap set at -20 C followed by trap heating and analysis by GC/Ms. In addition, the samples were also extracted using a low temperature "one-pot" chemical extraction technique using N-methyl, N-(tert-butyldimethylsilyl) trifluoroacetamide (MTBSTFA) as the silylating agent prior to GC/MS analysis. We identified several aldehydes, thiols, and alkene nitriles after pyrolysis GC/MS analysis of the bacteria that were not found in the olivine control samples that had not been inoculated with bacteria. The distribution of pyrolysis products extracted from the

  4. The Portuguese adaptation of the Gudjonsson Suggestibility Scale (GSS1) in a sample of inmates.

    PubMed

    Pires, Rute; Silva, Danilo R; Ferreira, Ana Sousa

    2014-01-01

    This paper comprises two studies which address the validity of the Portuguese adaptation of the Gudjonsson Suggestibility Scale, GSS1. In study 1, the means and standard deviations for the suggestibility results of a sample of Portuguese inmates (N=40, Mage=37.5 years, SD=8.1) were compared to those of a sample of Icelandic inmates (Gudjonsson, 1997; Gudjonsson & Sigurdsson, 1996). Portuguese inmates' results were in line with the original results. In study 2, the means and standard deviations for the suggestibility results of the sample of Portuguese inmates were compared to those of a general Portuguese population sample (N=57, Mage=36.1 years, SD=12.7). The forensic sample obtained significantly higher scores in suggestibility measures than the general population sample. ANOVA confirmed that the increased suggestibility in the inmates sample was due to the limited memory capacity of this latter group. Given that the results of both studies 1 and 2 are in keeping with the author's original results (Gudjonsson, 1997), this may be regarded as a confirmation of the validity of the Portuguese GSS1.

  5. Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation

    NASA Astrophysics Data System (ADS)

    Venev, Sergey V.; Zeldovich, Konstantin B.

    2015-08-01

    Evolution of proteins in bacteria and archaea living in different conditions leads to significant correlations between amino acid usage and environmental temperature. The origins of these correlations are poorly understood, and an important question of protein theory, physics-based prediction of types of amino acids overrepresented in highly thermostable proteins, remains largely unsolved. Here, we extend the random energy model of protein folding by weighting the interaction energies of amino acids by their frequencies in protein sequences and predict the energy gap of proteins designed to fold well at elevated temperatures. To test the model, we present a novel scalable algorithm for simultaneous energy calculation for many sequences in many structures, targeting massively parallel computing architectures such as graphics processing unit. The energy calculation is performed by multiplying two matrices, one representing the complete set of sequences, and the other describing the contact maps of all structural templates. An implementation of the algorithm for the CUDA platform is available at http://www.github.com/kzeldovich/galeprot and calculates protein folding energies over 250 times faster than a single central processing unit. Analysis of amino acid usage in 64-mer cubic lattice proteins designed to fold well at different temperatures demonstrates an excellent agreement between theoretical and simulated values of energy gap. The theoretical predictions of temperature trends of amino acid frequencies are significantly correlated with bioinformatics data on 191 bacteria and archaea, and highlight protein folding constraints as a fundamental selection pressure during thermal adaptation in biological evolution.

  6. Adaptive millimeter-wave synthetic aperture imaging for compressive sampling of sparse scenes.

    PubMed

    Mrozack, Alex; Heimbeck, Martin; Marks, Daniel L; Richard, Jonathan; Everitt, Henry O; Brady, David J

    2014-06-01

    We apply adaptive sensing techniques to the problem of locating sparse metallic scatterers using high-resolution, frequency modulated continuous wave W-band RADAR. Using a single detector, a frequency stepped source, and a lateral translation stage, inverse synthetic aperture RADAR reconstruction techniques are used to search for one or two wire scatterers within a specified range, while an adaptive algorithm determined successive sampling locations. The two-dimensional location of each scatterer is thereby identified with sub-wavelength accuracy in as few as 1/4 the number of lateral steps required for a simple raster scan. The implications of applying this approach to more complex scattering geometries are explored in light of the various assumptions made.

  7. Application of a hollow-fiber, tangential-flow device for sampling suspended bacteria and particles from natural waters

    USGS Publications Warehouse

    Kuwabara, J.S.; Harvey, R.W.

    1990-01-01

    The design and application of a hollow-fiber tangential-flow filtration device has been used to concentrate bacteria and suspended particles from large volume surface water and groundwater samples (i.e., hundreds of liters). Filtrate tlux rates (4–8 L min−1) are equal to or faster than those of other devices that are based on continuous flow centrifugation and plate and frame filtration. Particle recovery efficiencies for inorganic particles (approximately 90%) were similar to other dewatering devices, but microbial cell recoveries (30–90%) were greatly improved by this technique relative to other currently available methods. Although requirements for operation and maintenance of the device are minimal, its size, as with other dewatering devices, limits its applicability at remote sample sites. Nevertheless, it has proven useful for sample collection in studies involving microbial transport and analysis of particle-associated trace inorganic solutes.

  8. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples.

    PubMed

    Wang, Rong-Fu; Beggs, Marjorie L; Robertson, Latriana H; Cerniglia, Carl E

    2002-08-01

    An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides. Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides fragilis, Bacteroides distasonis, Clostridium clostridiiforme, Clostridium leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus albus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium infantis, Eubacterium biforme, Eubacterium aerofaciens, Lactobacillus acidophilus, Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples.

  9. High-resolution in-depth imaging of optically cleared thick samples using an adaptive SPIM

    PubMed Central

    Masson, Aurore; Escande, Paul; Frongia, Céline; Clouvel, Grégory; Ducommun, Bernard; Lorenzo, Corinne

    2015-01-01

    Today, Light Sheet Fluorescence Microscopy (LSFM) makes it possible to image fluorescent samples through depths of several hundreds of microns. However, LSFM also suffers from scattering, absorption and optical aberrations. Spatial variations in the refractive index inside the samples cause major changes to the light path resulting in loss of signal and contrast in the deepest regions, thus impairing in-depth imaging capability. These effects are particularly marked when inhomogeneous, complex biological samples are under study. Recently, chemical treatments have been developed to render a sample transparent by homogenizing its refractive index (RI), consequently enabling a reduction of scattering phenomena and a simplification of optical aberration patterns. One drawback of these methods is that the resulting RI of cleared samples does not match the working RI medium generally used for LSFM lenses. This RI mismatch leads to the presence of low-order aberrations and therefore to a significant degradation of image quality. In this paper, we introduce an original optical-chemical combined method based on an adaptive SPIM and a water-based clearing protocol enabling compensation for aberrations arising from RI mismatches induced by optical clearing methods and acquisition of high-resolution in-depth images of optically cleared complex thick samples such as Multi-Cellular Tumour Spheroids. PMID:26576666

  10. High-resolution in-depth imaging of optically cleared thick samples using an adaptive SPIM

    NASA Astrophysics Data System (ADS)

    Masson, Aurore; Escande, Paul; Frongia, Céline; Clouvel, Grégory; Ducommun, Bernard; Lorenzo, Corinne

    2015-11-01

    Today, Light Sheet Fluorescence Microscopy (LSFM) makes it possible to image fluorescent samples through depths of several hundreds of microns. However, LSFM also suffers from scattering, absorption and optical aberrations. Spatial variations in the refractive index inside the samples cause major changes to the light path resulting in loss of signal and contrast in the deepest regions, thus impairing in-depth imaging capability. These effects are particularly marked when inhomogeneous, complex biological samples are under study. Recently, chemical treatments have been developed to render a sample transparent by homogenizing its refractive index (RI), consequently enabling a reduction of scattering phenomena and a simplification of optical aberration patterns. One drawback of these methods is that the resulting RI of cleared samples does not match the working RI medium generally used for LSFM lenses. This RI mismatch leads to the presence of low-order aberrations and therefore to a significant degradation of image quality. In this paper, we introduce an original optical-chemical combined method based on an adaptive SPIM and a water-based clearing protocol enabling compensation for aberrations arising from RI mismatches induced by optical clearing methods and acquisition of high-resolution in-depth images of optically cleared complex thick samples such as Multi-Cellular Tumour Spheroids.

  11. Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples.

    PubMed

    Budding, Andries E; Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M J E; Savelkoul, Paul H M

    2016-04-01

    Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice.

  12. Detecting Organic Compounds Released from Iron Oxidizing Bacteria using Sample Analysis at Mars (SAM)-like Instrument Protocols

    NASA Astrophysics Data System (ADS)

    Glavin, D. P.; Popa, R.; Martin, M. G.; Freissinet, C.; Fisk, M. R.; Dworkin, J. P.; Mahaffy, P. R.

    2012-12-01

    Mars is a planet of great interest for Astrobiology since its past environmental conditions are thought to have been favourable for the emergence life. At present, the Red Planet is extremely cold and dry and the surface is exposed to intense UV and ionizing radiation, conditions generally considered to be incompatible with life as we know it on Earth. It was proposed that the shallow subsurface of Mars, where temperatures can be above freezing and liquid water can exist on rock surfaces, could harbor chemolithoautotrophic bacteria such as the iron oxidizing microorganism Pseudomonas sp. HerB [Popa et al. 2012]. The Mars Science Laboratory (MSL) mission will provide the next opportunity to carry out in situ measurements for organic compounds of possible biological origin on Mars. One instrument onboard MSL, called the Sample Analysis at Mars (SAM) instrument suite, will carry out a broad and sensitive search for organic compounds in surface samples using either high temperature pyrolysis or chemical extraction followed by gas chromatography mass spectrometry [Mahaffy et al. 2012]. We present gas chromatograph mass spectrometer (GC/MS) data on crushed olivine rock powders that have been inoculated with Pseudomonas sp. HerB at different concentrations ranging from ~102 to 107 cells per gram. The inoculated olivine samples were heated under helium carrier gas flow at 500°C and the pyrolysis products concentrated using a SAM-like hydrocarbon trap set at -20°C followed by trap heating and analysis by GC/MS. In addition, the samples were also extracted using a low temperature "one-pot" chemical extraction technique using N-methyl, N-(tert-butyldimethylsilyl) trifluoroacetamide (MTBSTFA) as the silylating agent prior to GC/MS analysis [Stalport et al. 2012]. We identified several aldehydes, thiols, and alkene nitriles after pyrolysis GC/MS analysis of the bacteria that were not found in the olivine control samples that had not been inoculated with bacteria. The

  13. Organ sample generator for expected treatment dose construction and adaptive inverse planning optimization

    SciTech Connect

    Nie Xiaobo; Liang Jian; Yan Di

    2012-12-15

    Purpose: To create an organ sample generator (OSG) for expected treatment dose construction and adaptive inverse planning optimization. The OSG generates random samples of organs of interest from a distribution obeying the patient specific organ variation probability density function (PDF) during the course of adaptive radiotherapy. Methods: Principle component analysis (PCA) and a time-varying least-squares regression (LSR) method were used on patient specific geometric variations of organs of interest manifested on multiple daily volumetric images obtained during the treatment course. The construction of the OSG includes the determination of eigenvectors of the organ variation using PCA, and the determination of the corresponding coefficients using time-varying LSR. The coefficients can be either random variables or random functions of the elapsed treatment days depending on the characteristics of organ variation as a stationary or a nonstationary random process. The LSR method with time-varying weighting parameters was applied to the precollected daily volumetric images to determine the function form of the coefficients. Eleven h and n cancer patients with 30 daily cone beam CT images each were included in the evaluation of the OSG. The evaluation was performed using a total of 18 organs of interest, including 15 organs at risk and 3 targets. Results: Geometric variations of organs of interest during h and n cancer radiotherapy can be represented using the first 3 {approx} 4 eigenvectors. These eigenvectors were variable during treatment, and need to be updated using new daily images obtained during the treatment course. The OSG generates random samples of organs of interest from the estimated organ variation PDF of the individual. The accuracy of the estimated PDF can be improved recursively using extra daily image feedback during the treatment course. The average deviations in the estimation of the mean and standard deviation of the organ variation PDF for h

  14. Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaofeng; Badea, Cristian T.; Hood, Greg; Wetzel, Arthur W.; Stiles, Joel R.; Johnson, G. Allan

    2010-02-01

    Image reconstruction is one of the main challenges for fluorescence tomography. For in vivo experiments on small animals, in particular, the inhomogeneous optical properties and irregular surface of the animal make free-space image reconstruction challenging because of the difficulties in accurately modeling the forward problem and the finite dynamic range of the photodetector. These two factors are fundamentally limited by the currently available forward models and photonic technologies. Nonetheless, both limitations can be significantly eased using a signal processing approach. We have recently constructed a free-space panoramic fluorescence diffuse optical tomography system to take advantage of co-registered microCT data acquired from the same animal. In this article, we present a data processing strategy that adaptively selects the optical sampling points in the raw 2-D fluorescent CCD images. Specifically, the general sampling area and sampling density are initially specified to create a set of potential sampling points sufficient to cover the region of interest. Based on 3-D anatomical information from the microCT and the fluorescent CCD images, data points are excluded from the set when they are located in an area where either the forward model is known to be problematic (e.g., large wrinkles on the skin) or where the signal is unreliable (e.g., saturated or low signal-to-noise ratio). Parallel Monte Carlo software was implemented to compute the sensitivity function for image reconstruction. Animal experiments were conducted on a mouse cadaver with an artificial fluorescent inclusion. Compared to our previous results using a finite element method, the newly developed parallel Monte Carlo software and the adaptive sampling strategy produced favorable reconstruction results.

  15. Flow cytometric quantification of bacteria in vaginal swab samples self-collected by adolescents attending a gynecology clinic.

    PubMed

    Schellenberg, John; Blake Ball, T; Lane, Margo; Cheang, Mary; Plummer, Frank

    2008-06-01

    Bacterial vaginosis (BV) is an important risk factor in reproductive health outcomes, such as pre-term birth and sexually transmitted infections including HIV. However, its etiology, diagnosis and treatment remain poorly defined. We evaluated flow cytometry as a tool to quantify total bacterial cells in vaginal specimens self-collected longitudinally by adolescents. BV was diagnosed by Gram-stain (criteria of Hay and Ison). Average flow cytometric counts of bacterial cell-units (BCU) was log(10) 8.04 per gram sample and was found to correlate with sample weight (p<0.0001). BV was frequently observed in this group, with 22 of 32 participants (69%) diagnosed with BV for at least one timepoint. Surprisingly, increased BCU was associated with normal Hay-Ison score (p=0.0003), even when adjusting for sample weight (p=0.02). Since presence and quantity of Lactobacillus defines normal vaginal microbiology (ie. absence of BV), this result indicates a possible bias towards dominance of Lactobacillus cells in measurements of "total" BCU. Increased BCU per gram was associated in multivariate analysis with longer self-reported time since last menstruation (p=0.004) and last sexual intercourse (p=0.007). Sperm was detected in 3 samples provided by those reporting sexual intercourse in the previous 24 h. Light-scattering profiles of bacteria and vaginal cells in samples collected over time from an individual were often identical and distinct from other individuals. To our knowledge, this is the first description of flow cytometry for analysis of commensal bacteria in vaginal specimens. Further development may help to illuminate the complex dynamics of vaginal microbial communities underlying BV. PMID:18423913

  16. Distribution of epiphytic bacteria on olive leaves and the influence of leaf age and sampling time.

    PubMed

    Ercolani, G L

    1991-12-01

    Mesophilic heterotrophic, aerobic or facultatively anaerobic bacteria that grow on yeast tryptone glucose extract agar were isolated from the surface of olive leaves of 3 or 4 different ages in January, April, July, and October from 1984 to 1989. Unweighted average linkage cluster analysis on either the Jaccard coefficient or the simple matching coefficient recovered 1,701 representative strains in 32 phena defined at the 70% and 80% similarity level, respectively. Of these, 25 were identified to genus or lower level. From the identity of the representative strains, the frequency of occurrence among the phylloplane bacteria over the 6-year period was estimated at 51% forPseudomonas syringae, followed byXanthomonas campestris (6.7%),Erwinia herbicola (6%),Acetobacter aceti (4.7%),Gluconobacter oxydans (4.3%),Pseudomonas fluorescens (3.9%),Bacillus megaterium (3.8%),Leuconostoc mesenteroides subsp.dextranicum (3.1%),Lactobacillus plantarum (2.8%),Curtobacterium plantarum (2.2%),Micrococcus luteus (2.2%),Arthrobacter globiformis (1.4%),Klebsiella planticola (1.2%),Streptococcus faecium (1.2%),Clavibacter sp. (0.98%),Micrococcus sp. (0.82%),Serratia marcescens (0.81%),Bacillus subtilis (0.57%),Cellulomonas flavigena (0.4%),Erwinia sp. (0.37%),Zymomonas mobilis (0.3%),Bacillus sp. (0.29%),Alcaligenes faecalis (0.27%),Erwinia carotovora (0.08%), andPseudomonas aeruginosa (0.04%). Bacterial communities on leaves of a given age at a given time during any one year displayed a very similar structure but differed significantly from those on the leaves of the same age at a different time or on the leaves of a different age at any time during any one year. Communities on the leaves of a given age at a given time of the year were invariably dominated by one or another of only 9 taxa, which accounted for 22 to 98.5% of the isolates from those leaves. The communities on 10- and 13-month-old leaves were invariably made up of fewer taxa than those on younger leaves at the same time

  17. Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

    SciTech Connect

    Vrugt, Jasper A; Hyman, James M; Robinson, Bruce A; Higdon, Dave; Ter Braak, Cajo J F; Diks, Cees G H

    2008-01-01

    Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

  18. Influences of sample interference and interference controls on quantification of enterococci fecal indicator bacteria in surface water samples by the qPCR method.

    PubMed

    Haugland, Richard A; Siefring, Shawn; Lavender, Jennifer; Varma, Manju

    2012-11-15

    A quantitative polymerase chain reaction (qPCR) method for the detection of enterococci fecal indicator bacteria has been shown to be generally applicable for the analysis of temperate fresh (Great Lakes) and marine coastal waters and for providing risk-based determinations of water quality at recreational beaches. In this study we further examined the applicability of the method for analyses of diverse inland waters as well as tropical marine waters from Puerto Rico based on the frequencies of samples showing presumptive PCR interference. Interference was assessed by salmon DNA sample processing control (SPC) and internal amplification control (IAC) assay analysis results and pre-established acceptance criteria of <3.0 and <1.5 cycle threshold (Ct) offsets from control samples, respectively. SPC assay results were accepted in analyses of 93% of the inland water samples whereas the criterion was met at frequencies of 60% and 97% in analyses of samples from Puerto Rico in two different years of sampling. The functionality of the control assays and their acceptance criteria was assessed on the basis of relative recovery estimates of spiked enterococci target organisms extracted in the presence of water sample filters and sample-free control filters and was supported by observations that recovery estimates from the water sample and control filters were substantially different for samples that failed these criteria. Through the combined use of the SPC and IAC assays, two presumptive types of interference were identified. One type, observed in the tropical marine water samples, appeared to primarily affect the availability of the DNA templates for detection. The second type, observed in river water samples, appeared to primarily affect PCR amplification efficiency. In the presence of DNA template interference, adjustments from SPC assay results by the ΔΔCt comparative Ct calculation method decreased the variability of spiked enterococci recovery estimates and

  19. Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

    PubMed Central

    Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

    2016-01-01

    Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice. PMID:26763956

  20. Detection of diverse new Francisella-like bacteria in environmental samples.

    PubMed

    Barns, Susan M; Grow, Christy C; Okinaka, Richard T; Keim, Paul; Kuske, Cheryl R

    2005-09-01

    Following detection of putative Francisella species in aerosol samples from Houston, Texas, we surveyed soil and water samples from the area for the agent of tularemia, Francisella tularensis, and related species. The initial survey used 16S rRNA gene primers to detect Francisella species and related organisms by PCR amplification of DNA extracts from environmental samples. This analysis indicated that sequences related to Francisella were present in one water and seven soil samples. This is the first report of the detection of Francisella-related species in soil samples by DNA-based methods. Cloning and sequencing of PCR products indicated the presence of a wide variety of Francisella-related species. Sequences from two soil samples were 99.9% similar to previously reported sequences from F. tularensis isolates and may represent new subspecies. Additional analyses with primer sets developed for detection and differentiation of F. tularensis subspecies support the finding of very close relatives to known F. tularensis strains in some samples. While the pathogenicity of these organisms is unknown, they have the potential to be detected in F. tularensis-specific assays. Similarly, a potential new subspecies of Francisella philomiragia was identified. The majority of sequences obtained, while more similar to those of Francisella than to any other genus, were phylogenetically distinct from known species and formed several new clades potentially representing new species or genera. The results of this study revise our understanding of the diversity and distribution of Francisella and have implications for tularemia epidemiology and our ability to detect bioterrorist activities. PMID:16151142

  1. Identification and phylogenetic analysis of new sulfate-reducing bacteria isolated from oilfield samples.

    PubMed

    Chen, Wu; Xiang, Fu; Fu, Jie; Wang, Qiang; Wang, Wenjun; Zeng, Qingfu; Yu, Longjiang

    2009-01-01

    Microbiologically influenced corrosion (MIC) caused by sulfate-reducing bacteria (SRB) has been investigated in an oilfield injection water system. Strain CW-01 was isolated from an oilfield and strain CW-04 was isolated from biofilm dirt of pipeline walls. The strains were facultative anaerobes, non-motile, Gram-positive, pole flagellum, and spore-forming curved rods. The growth was observed over the temperature range 20-70 degrees C. Strain CW-01 grew optimally at 37 degrees C. The pH range for growth was 3.0-11, optimal at pH 6.0. Strain CW-04 grew optimally at 48 degrees C. The pH range for growth was 3.0-10, optimal at pH 7.2. The strains grew at a very broad range of salt concentrations. Optimal growth was observed with 1.5 g/L NaCl for strain CW-01 and 0.7 g/L NaCl for strain CW-04. The strains showed most similarity in physiological characteristics, except for acetone and saccharose. Analysis of the 16S rDNA sequences allowed strains CW-01 and CW-04 to be classified into the genus Desulfotomaculum. The corrosion speciality of the strains had been comparatively investigated. Especially SRB's growth curve, bearable oxygen capability, drug fastness and corrosion rate had been analyzed. The results showed that it is difficult to prevent bacterial corrosion caused by these two strains.

  2. A Surrogate-based Adaptive Sampling Approach for History Matching and Uncertainty Quantification

    SciTech Connect

    Li, Weixuan; Zhang, Dongxiao; Lin, Guang

    2015-02-25

    A critical procedure in reservoir simulations is history matching (or data assimilation in a broader sense), which calibrates model parameters such that the simulation results are consistent with field measurements, and hence improves the credibility of the predictions given by the simulations. Often there exist non-unique combinations of parameter values that all yield the simulation results matching the measurements. For such ill-posed history matching problems, Bayesian theorem provides a theoretical foundation to represent different solutions and to quantify the uncertainty with the posterior PDF. Lacking an analytical solution in most situations, the posterior PDF may be characterized with a sample of realizations, each representing a possible scenario. A novel sampling algorithm is presented here for the Bayesian solutions to history matching problems. We aim to deal with two commonly encountered issues: 1) as a result of the nonlinear input-output relationship in a reservoir model, the posterior distribution could be in a complex form, such as multimodal, which violates the Gaussian assumption required by most of the commonly used data assimilation approaches; 2) a typical sampling method requires intensive model evaluations and hence may cause unaffordable computational cost. In the developed algorithm, we use a Gaussian mixture model as the proposal distribution in the sampling process, which is simple but also flexible to approximate non-Gaussian distributions and is particularly efficient when the posterior is multimodal. Also, a Gaussian process is utilized as a surrogate model to speed up the sampling process. Furthermore, an iterative scheme of adaptive surrogate refinement and re-sampling ensures sampling accuracy while keeping the computational cost at a minimum level. The developed approach is demonstrated with an illustrative example and shows its capability in handling the above-mentioned issues. Multimodal posterior of the history matching

  3. Adaptive pulse width control and sampling for low power pulse oximetry.

    PubMed

    Gubbi, Sagar Venkatesh; Amrutur, Bharadwaj

    2015-04-01

    Remote sensing of physiological parameters could be a cost effective approach to improving health care, and low-power sensors are essential for remote sensing because these sensors are often energy constrained. This paper presents a power optimized photoplethysmographic sensor interface to sense arterial oxygen saturation, a technique to dynamically trade off SNR for power during sensor operation, and a simple algorithm to choose when to acquire samples in photoplethysmography. A prototype of the proposed pulse oximeter built using commercial-off-the-shelf (COTS) components is tested on 10 adults. The dynamic adaptation techniques described reduce power consumption considerably compared to our reference implementation, and our approach is competitive to state-of-the-art implementations. The techniques presented in this paper may be applied to low-power sensor interface designs where acquiring samples is expensive in terms of power as epitomized by pulse oximetry. PMID:25014964

  4. Adaptive sampling in two-phase designs: a biomarker study for progression in arthritis

    PubMed Central

    McIsaac, Michael A; Cook, Richard J

    2015-01-01

    Response-dependent two-phase designs are used increasingly often in epidemiological studies to ensure sampling strategies offer good statistical efficiency while working within resource constraints. Optimal response-dependent two-phase designs are difficult to implement, however, as they require specification of unknown parameters. We propose adaptive two-phase designs that exploit information from an internal pilot study to approximate the optimal sampling scheme for an analysis based on mean score estimating equations. The frequency properties of estimators arising from this design are assessed through simulation, and they are shown to be similar to those from optimal designs. The design procedure is then illustrated through application to a motivating biomarker study in an ongoing rheumatology research program. Copyright © 2015 © 2015 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd. PMID:25951124

  5. Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples.

    PubMed

    Guillén-Navarro, Karina; Herrera-López, David; López-Chávez, Mariana Y; Cancino-Gómez, Máximo; Reyes-Reyes, Ana L

    2015-11-01

    DNA extraction from environmental samples is a critical step for metagenomic analysis to study microbial communities, including those considered uncultivable. Nevertheless, obtaining good quality DNA in sufficient quantities for downstream methodologies is not always possible, and it depends on the complexity and stability of each ecosystem, which could be more problematic for samples from tropical regions because those ecosystems are less stable and more complex. Three laboratory methods for the extraction of nucleic acids from samples representing unstable (decaying coffee pulp and mangrove sediments) and relatively stable (compost and soil) environments were tested. The results were compared with those obtained using two commercial DNA extraction kits. The quality of the extracted DNA was evaluated by PCR amplification to verify the recovery of bacterial, archaeal, and fungal genetic material. The laboratory method that gave the best results used a lysis procedure combining physical, chemical, and enzymatic steps.

  6. Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples.

    PubMed

    Guillén-Navarro, Karina; Herrera-López, David; López-Chávez, Mariana Y; Cancino-Gómez, Máximo; Reyes-Reyes, Ana L

    2015-11-01

    DNA extraction from environmental samples is a critical step for metagenomic analysis to study microbial communities, including those considered uncultivable. Nevertheless, obtaining good quality DNA in sufficient quantities for downstream methodologies is not always possible, and it depends on the complexity and stability of each ecosystem, which could be more problematic for samples from tropical regions because those ecosystems are less stable and more complex. Three laboratory methods for the extraction of nucleic acids from samples representing unstable (decaying coffee pulp and mangrove sediments) and relatively stable (compost and soil) environments were tested. The results were compared with those obtained using two commercial DNA extraction kits. The quality of the extracted DNA was evaluated by PCR amplification to verify the recovery of bacterial, archaeal, and fungal genetic material. The laboratory method that gave the best results used a lysis procedure combining physical, chemical, and enzymatic steps. PMID:26014885

  7. An Energy Aware Adaptive Sampling Algorithm for Energy Harvesting WSN with Energy Hungry Sensors.

    PubMed

    Srbinovski, Bruno; Magno, Michele; Edwards-Murphy, Fiona; Pakrashi, Vikram; Popovici, Emanuel

    2016-03-28

    Wireless sensor nodes have a limited power budget, though they are often expected to be functional in the field once deployed for extended periods of time. Therefore, minimization of energy consumption and energy harvesting technology in Wireless Sensor Networks (WSN) are key tools for maximizing network lifetime, and achieving self-sustainability. This paper proposes an energy aware Adaptive Sampling Algorithm (ASA) for WSN with power hungry sensors and harvesting capabilities, an energy management technique that can be implemented on any WSN platform with enough processing power to execute the proposed algorithm. An existing state-of-the-art ASA developed for wireless sensor networks with power hungry sensors is optimized and enhanced to adapt the sampling frequency according to the available energy of the node. The proposed algorithm is evaluated using two in-field testbeds that are supplied by two different energy harvesting sources (solar and wind). Simulation and comparison between the state-of-the-art ASA and the proposed energy aware ASA (EASA) in terms of energy durability are carried out using in-field measured harvested energy (using both wind and solar sources) and power hungry sensors (ultrasonic wind sensor and gas sensors). The simulation results demonstrate that using ASA in combination with an energy aware function on the nodes can drastically increase the lifetime of a WSN node and enable self-sustainability. In fact, the proposed EASA in conjunction with energy harvesting capability can lead towards perpetual WSN operation and significantly outperform the state-of-the-art ASA.

  8. Adaptive sampling dual terahertz comb spectroscopy using dual free-running femtosecond lasers

    PubMed Central

    Yasui, Takeshi; Ichikawa, Ryuji; Hsieh, Yi-Da; Hayashi, Kenta; Cahyadi, Harsono; Hindle, Francis; Sakaguchi, Yoshiyuki; Iwata, Tetsuo; Mizutani, Yasuhiro; Yamamoto, Hirotsugu; Minoshima, Kaoru; Inaba, Hajime

    2015-01-01

    Terahertz (THz) dual comb spectroscopy (DCS) is a promising method for high-accuracy, high-resolution, broadband THz spectroscopy because the mode-resolved THz comb spectrum includes both broadband THz radiation and narrow-line CW-THz radiation characteristics. In addition, all frequency modes of a THz comb can be phase-locked to a microwave frequency standard, providing excellent traceability. However, the need for stabilization of dual femtosecond lasers has often hindered its wide use. To overcome this limitation, here we have demonstrated adaptive-sampling THz-DCS, allowing the use of free-running femtosecond lasers. To correct the fluctuation of the time and frequency scales caused by the laser timing jitter, an adaptive sampling clock is generated by dual THz-comb-referenced spectrum analysers and is used for a timing clock signal in a data acquisition board. The results not only indicated the successful implementation of THz-DCS with free-running lasers but also showed that this configuration outperforms standard THz-DCS with stabilized lasers due to the slight jitter remained in the stabilized lasers. PMID:26035687

  9. Motion-adapted pulse sequences for oriented sample (OS) solid-state NMR of biopolymers.

    PubMed

    Lu, George J; Opella, Stanley J

    2013-08-28

    One of the main applications of solid-state NMR is to study the structure and dynamics of biopolymers, such as membrane proteins, under physiological conditions where the polypeptides undergo global motions as they do in biological membranes. The effects of NMR radiofrequency irradiations on nuclear spins are strongly influenced by these motions. For example, we previously showed that the MSHOT-Pi4 pulse sequence yields spectra with resonance line widths about half of those observed using the conventional pulse sequence when applied to membrane proteins undergoing rapid uniaxial rotational diffusion in phospholipid bilayers. In contrast, the line widths were not changed in microcrystalline samples where the molecules did not undergo global motions. Here, we demonstrate experimentally and describe analytically how some Hamiltonian terms are susceptible to sample motions, and it is their removal through the critical π/2 Z-rotational symmetry that confers the "motion adapted" property to the MSHOT-Pi4 pulse sequence. This leads to the design of separated local field pulse sequence "Motion-adapted SAMPI4" and is generalized to an approach for the design of decoupling sequences whose performance is superior in the presence of molecular motions. It works by cancelling the spin interaction by explicitly averaging the reduced Wigner matrix to zero, rather than utilizing the 2π nutation to average spin interactions. This approach is applicable to both stationary and magic angle spinning solid-state NMR experiments.

  10. A comparison of two 16S rRNA gene-based PCR primer sets in unraveling anammox bacteria from different environmental samples.

    PubMed

    Han, Ping; Huang, Yu-Tzu; Lin, Jih-Gaw; Gu, Ji-Dong

    2013-12-01

    Two 16S rRNA gene-based PCR primer sets (Brod541F/Amx820R and A438f/A684r) for detecting anammox bacteria were compared using sediments from Mai Po wetlands (MP), the South China Sea (SCS), a freshwater reservoir (R2), and sludge granules from a wastewater treatment plant (A2). By comparing their ability in profiling anammox bacteria, the recovered diversity, community structure, and abundance of anammox bacteria among all these diverse samples indicated that A438f/A684r performed better than Brod541F/Amx820R in retrieving anammox bacteria from these different environmental samples. Five Scalindua subclusters (zhenghei-I, SCS-I, SCS-III, arabica, and brodae) dominated in SCS whereas two Scalindua subclusters (zhenghei-II and wagneri) and one cluster of Kuenenia dominated in MP. R2 showed a higher diversity of anammox bacteria with two new retrieved clusters (R2-New-1 and R2-New-2), which deserves further detailed study. The dominance of Brocadia in sample A2 was supported by both of the primer sets used. Results collectively indicate strongly niche-specific community structures of anammox bacteria in different environments, and A438f/A684r is highly recommended for screening anammox bacteria from various environments when dealing with a collection of samples with diverse physiochemical characteristics.

  11. Adaption of G-TAG Software for Validating Touch and Go Asteroid Sample Return Design Methodology

    NASA Technical Reports Server (NTRS)

    Blackmore, Lars James C.; Acikmese, Behcet; Mandic, Milan

    2012-01-01

    A software tool is used to demonstrate the feasibility of Touch and Go (TAG) sampling for Asteroid Sample Return missions. TAG is a concept whereby a spacecraft is in contact with the surface of a small body, such as a comet or asteroid, for a few seconds or less before ascending to a safe location away from the small body. Previous work at JPL developed the G-TAG simulation tool, which provides a software environment for fast, multi-body simulations of the TAG event. G-TAG is described in Multibody Simulation Software Testbed for Small-Body Exploration and Sampling, (NPO-47196) NASA Tech Briefs, Vol. 35, No. 11 (November 2011), p.54. This current innovation adapts this tool to a mission that intends to return a sample from the surface of an asteroid. In order to demonstrate the feasibility of the TAG concept, the new software tool was used to generate extensive simulations that demonstrate the designed spacecraft meets key requirements. These requirements state that contact force and duration must be sufficient to ensure that enough material from the surface is collected in the brushwheel sampler (BWS), and that the spacecraft must survive the contact and must be able to recover and ascend to a safe position, and maintain velocity and orientation after the contact.

  12. Isolation and partial characterization of phosphate solubilizing bacteria isolated from soil and marine samples.

    PubMed

    Mujahid, Talat Yasmeen; Siddiqui, Khaizran; Ahmed, Rifat; Kazmi, Shahana U; Ahmed, Nuzhat

    2014-09-01

    In the present study the potential of indigenous bacterial isolates from soil rhizosphere and marine environment to promote plant growth was determined. Eight bacterial strains isolated from soil and marine samples were characterized for the phosphate solubilizing activity. Qualitative and quantitative estimation of phosphate solubilization is done. MIC of antibiotic and heavy metals were checked for these strains. Strains show a diverse pattern of antibiotic and heavy metals resistance.

  13. Multi-species attributes as the condition for adaptive sampling of rare species using two-stage sequential sampling with an auxiliary variable

    USGS Publications Warehouse

    Panahbehagh, B.; Smith, D.R.; Salehi, M.M.; Hornbach, D.J.; Brown, D.J.; Chan, F.; Marinova, D.; Anderssen, R.S.

    2011-01-01

    Assessing populations of rare species is challenging because of the large effort required to locate patches of occupied habitat and achieve precise estimates of density and abundance. The presence of a rare species has been shown to be correlated with presence or abundance of more common species. Thus, ecological community richness or abundance can be used to inform sampling of rare species. Adaptive sampling designs have been developed specifically for rare and clustered populations and have been applied to a wide range of rare species. However, adaptive sampling can be logistically challenging, in part, because variation in final sample size introduces uncertainty in survey planning. Two-stage sequential sampling (TSS), a recently developed design, allows for adaptive sampling, but avoids edge units and has an upper bound on final sample size. In this paper we present an extension of two-stage sequential sampling that incorporates an auxiliary variable (TSSAV), such as community attributes, as the condition for adaptive sampling. We develop a set of simulations to approximate sampling of endangered freshwater mussels to evaluate the performance of the TSSAV design. The performance measures that we are interested in are efficiency and probability of sampling a unit occupied by the rare species. Efficiency measures the precision of population estimate from the TSSAV design relative to a standard design, such as simple random sampling (SRS). The simulations indicate that the density and distribution of the auxiliary population is the most important determinant of the performance of the TSSAV design. Of the design factors, such as sample size, the fraction of the primary units sampled was most important. For the best scenarios, the odds of sampling the rare species was approximately 1.5 times higher for TSSAV compared to SRS and efficiency was as high as 2 (i.e., variance from TSSAV was half that of SRS). We have found that design performance, especially for adaptive

  14. Bioluminescence-based identification of nisin producers - a rapid and simple screening method for nisinogenic bacteria in food samples.

    PubMed

    Virolainen, Nina; Guglielmetti, Simone; Arioli, Stefania; Karp, Matti

    2012-08-17

    We present a simple and rapid method for screening nisin producers that directly identifies nisinogenic bacteria by induction of bioluminescence within the Lactococcus lactis NZ9800lux biosensor strain (Immonen and Karp, 2007, Biosensors and Bioelectronics 22, 1982-7). An overlay of putative nisinogenic colonies with the biosensor strain gives identification results within 1h. Functionality and specificity of the method were verified by screening nisin producers among 144 raw milk colonies and a panel of 91 lactococcal strains. Studies performed on strains and colonies that did not induce bioluminescence but inhibited growth of the biosensor demonstrated that only nisinogenic bacteria can cause induction. Bacteria known to produce bacteriocins other than nisin failed to induce bioluminescence, further verifying the specificity of the assay. We discovered a non-inducing but inhibitory lactococcal strain harboring a modified nisin Z gene, and demonstrated that the source of the inhibitory action is not a non-inducing variant of nisin, but a bacteriocin of lower molecular weight. The concentration of nisin producers in a raw milk sample was 1.3 × 10(2)CFU/ml. We identified from raw milk a total of seven nisin Z producing L. lactis subsp. lactis colonies, which were shown by genetic fingerprinting to belong to three different groups. Among the panel of 91 lactococci, four strains were nisin A producers, and one strain harbored the modified nisin Z gene. The method presented here is robust, cost-effective and simple to perform, and avoids the pitfalls of traditional screening methods by directly specifying the identity of the inhibitory substance.

  15. Lab-on-a-chip modules for detection of highly pathogenic bacteria: from sample preparation to detection

    NASA Astrophysics Data System (ADS)

    Julich, S.; Kopinč, R.; Hlawatsch, N.; Moche, C.; Lapanje, A.; Gärtner, C.; Tomaso, H.

    2014-05-01

    Lab-on-a-chip systems are innovative tools for the detection and identification of microbial pathogens in human and veterinary medicine. The major advantages are small sample volume and a compact design. Several fluidic modules have been developed to transform analytical procedures into miniaturized scale including sampling, sample preparation, target enrichment, and detection procedures. We present evaluation data for single modules that will be integrated in a chip system for the detection of pathogens. A microfluidic chip for purification of nucleic acids was established for cell lysis using magnetic beads. This assay was evaluated with spiked environmental aerosol and swab samples. Bacillus thuringiensis was used as simulant for Bacillus anthracis, which is closely related but non-pathogenic for humans. Stationary PCR and a flow-through PCR chip module were investigated for specific detection of six highly pathogenic bacteria. The conventional PCR assays could be transferred into miniaturized scale using the same temperature/time profile. We could demonstrate that the microfluidic chip modules are suitable for the respective purposes and are promising tools for the detection of bacterial pathogens. Future developments will focus on the integration of these separate modules to an entire lab-on-a-chip system.

  16. Detection of Campylobacter Bacteria in Air Samples for Continuous Real-Time Monitoring of Campylobacter Colonization in Broiler Flocks▿

    PubMed Central

    Olsen, Katja N.; Lund, Marianne; Skov, Julia; Christensen, Laurids S.; Hoorfar, Jeffrey

    2009-01-01

    Improved monitoring tools are important for the control of Campylobacter bacteria in broiler production. In this study, we compare the sensitivities of detection of Campylobacter by PCR with feces, dust, and air samples during the lifetimes of broilers in two poultry houses and conclude that the sensitivity of detection of Campylobacter in air is comparable to that in other sample materials. Profiling of airborne particles in six poultry houses revealed that the aerodynamic conditions were dependent on the age of the chickens and very comparable among different poultry houses, with low proportions of particles in the 0.5- to 2-μm-diameter range and high proportions in the 2- to 5-μm-diameter range. Campylobacter could also be detected by PCR in air samples collected at the hanging stage during the slaughter process but not at the other stages tested at the slaughterhouse. The exploitation of airborne dust in poultry houses as a sample material for the detection of Campylobacter and other pathogens provides an intriguing possibility, in conjunction with new detection technologies, for allowing continuous or semicontinuous monitoring of colonization status. PMID:19201953

  17. Detection of Campylobacter bacteria in air samples for continuous real-time monitoring of Campylobacter colonization in broiler flocks.

    PubMed

    Olsen, Katja N; Lund, Marianne; Skov, Julia; Christensen, Laurids S; Hoorfar, Jeffrey

    2009-04-01

    Improved monitoring tools are important for the control of Campylobacter bacteria in broiler production. In this study, we compare the sensitivities of detection of Campylobacter by PCR with feces, dust, and air samples during the lifetimes of broilers in two poultry houses and conclude that the sensitivity of detection of Campylobacter in air is comparable to that in other sample materials. Profiling of airborne particles in six poultry houses revealed that the aerodynamic conditions were dependent on the age of the chickens and very comparable among different poultry houses, with low proportions of particles in the 0.5- to 2-microm-diameter range and high proportions in the 2- to 5-microm-diameter range. Campylobacter could also be detected by PCR in air samples collected at the hanging stage during the slaughter process but not at the other stages tested at the slaughterhouse. The exploitation of airborne dust in poultry houses as a sample material for the detection of Campylobacter and other pathogens provides an intriguing possibility, in conjunction with new detection technologies, for allowing continuous or semicontinuous monitoring of colonization status.

  18. Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

    PubMed

    Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

    2015-12-01

    The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction.

  19. Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

    PubMed

    Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

    2015-12-01

    The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction. PMID:26370071

  20. Scanning electron microscopy coupled with energy-dispersive X-ray spectrometry for quick detection of sulfur-oxidizing bacteria in environmental water samples

    NASA Astrophysics Data System (ADS)

    Sun, Chengjun; Jiang, Fenghua; Gao, Wei; Li, Xiaoyun; Yu, Yanzhen; Yin, Xiaofei; Wang, Yong; Ding, Haibing

    2016-03-01

    Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry (EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time (within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.

  1. Differentially Private Histogram Publication For Dynamic Datasets: An Adaptive Sampling Approach

    PubMed Central

    Li, Haoran; Jiang, Xiaoqian; Xiong, Li; Liu, Jinfei

    2016-01-01

    Differential privacy has recently become a de facto standard for private statistical data release. Many algorithms have been proposed to generate differentially private histograms or synthetic data. However, most of them focus on “one-time” release of a static dataset and do not adequately address the increasing need of releasing series of dynamic datasets in real time. A straightforward application of existing histogram methods on each snapshot of such dynamic datasets will incur high accumulated error due to the composibility of differential privacy and correlations or overlapping users between the snapshots. In this paper, we address the problem of releasing series of dynamic datasets in real time with differential privacy, using a novel adaptive distance-based sampling approach. Our first method, DSFT, uses a fixed distance threshold and releases a differentially private histogram only when the current snapshot is sufficiently different from the previous one, i.e., with a distance greater than a predefined threshold. Our second method, DSAT, further improves DSFT and uses a dynamic threshold adaptively adjusted by a feedback control mechanism to capture the data dynamics. Extensive experiments on real and synthetic datasets demonstrate that our approach achieves better utility than baseline methods and existing state-of-the-art methods. PMID:26973795

  2. Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature Sets

    SciTech Connect

    Vogel, Thomas; Perez, Danny

    2015-08-28

    We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. The method is particularly useful for the fast and reliable estimation of the microcanonical temperature T (U) or, equivalently, of the density of states g(U) over a wide range of energies.

  3. Accelerating the Convergence of Replica Exchange Simulations Using Gibbs Sampling and Adaptive Temperature Sets

    DOE PAGES

    Vogel, Thomas; Perez, Danny

    2015-08-28

    We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. The methodmore » is particularly useful for the fast and reliable estimation of the microcanonical temperature T (U) or, equivalently, of the density of states g(U) over a wide range of energies.« less

  4. Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential

    NASA Astrophysics Data System (ADS)

    Babin, Volodymyr; Karpusenka, Vadzim; Moradi, Mahmoud; Roland, Christopher; Sagui, Celeste

    We discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β-turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community.

  5. Identification of Chromium Resistant Bacteria from Dry Fly Ash Sample of Mejia MTPS Thermal Power Plant, West Bengal, India.

    PubMed

    Roychowdhury, Roopali; Mukherjee, Pritam; Roy, Madhumita

    2016-02-01

    Eight chromium resistant bacteria were isolated from a dry fly ash sample of DVC-MTPS thermal power plant located in Bankura, West Bengal, India. These isolates displayed different degrees of chromate reduction under aerobic conditions. According to 16S rDNA gene analysis, five of them were Staphylococcus, two were Bacillus and one was Micrococcus. The minimum inhibitory concentration towards chromium and the ability to reduce hexavalent chromium to trivalent chromium was highest in Staphylococcus haemolyticus strain HMR17. All the strains were resistant to multiple heavy metals (As, Cu, Cd, Co, Zn, Mn, Pb and Fe) and reduced toxic hexavalent chromium to relatively non toxic trivalent chromium even in the presence of these multiple heavy metals. All of them showed resistance to different antibiotics. In a soil microcosm study, S. haemolyticus strain HMR17 completely reduced 4 mM hexavalent chromium within 7 days of incubation.

  6. Application of a pathogen microarray for the analysis of viruses and bacteria in clinical diagnostic samples from pigs.

    PubMed

    Jaing, Crystal J; Thissen, James B; Gardner, Shea N; McLoughlin, Kevin S; Hullinger, Pam J; Monday, Nicholas A; Niederwerder, Megan C; Rowland, Raymond R R

    2015-05-01

    Many of the disease syndromes challenging the commercial swine industry involve the analysis of complex problems caused by polymicrobial, emerging or reemerging, and transboundary pathogens. This study investigated the utility of the Lawrence Livermore Microbial Detection Array (Lawrence Livermore National Laboratory, Livermore, California), designed to detect 8,101 species of microbes, in the evaluation of known and unknown microbes in serum, oral fluid, and tonsil from pigs experimentally coinfected with Porcine reproductive and respiratory syndrome virus (PRRSV) and Porcine circovirus-2 (PCV-2). The array easily identified PRRSV and PCV-2, but at decreased sensitivities compared to standard polymerase chain reaction detection methods. The oral fluid sample was the most informative, possessing additional signatures for several swine-associated bacteria, including Streptococcus sp., Clostridium sp., and Staphylococcus sp.

  7. Identification of Chromium Resistant Bacteria from Dry Fly Ash Sample of Mejia MTPS Thermal Power Plant, West Bengal, India.

    PubMed

    Roychowdhury, Roopali; Mukherjee, Pritam; Roy, Madhumita

    2016-02-01

    Eight chromium resistant bacteria were isolated from a dry fly ash sample of DVC-MTPS thermal power plant located in Bankura, West Bengal, India. These isolates displayed different degrees of chromate reduction under aerobic conditions. According to 16S rDNA gene analysis, five of them were Staphylococcus, two were Bacillus and one was Micrococcus. The minimum inhibitory concentration towards chromium and the ability to reduce hexavalent chromium to trivalent chromium was highest in Staphylococcus haemolyticus strain HMR17. All the strains were resistant to multiple heavy metals (As, Cu, Cd, Co, Zn, Mn, Pb and Fe) and reduced toxic hexavalent chromium to relatively non toxic trivalent chromium even in the presence of these multiple heavy metals. All of them showed resistance to different antibiotics. In a soil microcosm study, S. haemolyticus strain HMR17 completely reduced 4 mM hexavalent chromium within 7 days of incubation. PMID:26602566

  8. An Energy Aware Adaptive Sampling Algorithm for Energy Harvesting WSN with Energy Hungry Sensors.

    PubMed

    Srbinovski, Bruno; Magno, Michele; Edwards-Murphy, Fiona; Pakrashi, Vikram; Popovici, Emanuel

    2016-01-01

    Wireless sensor nodes have a limited power budget, though they are often expected to be functional in the field once deployed for extended periods of time. Therefore, minimization of energy consumption and energy harvesting technology in Wireless Sensor Networks (WSN) are key tools for maximizing network lifetime, and achieving self-sustainability. This paper proposes an energy aware Adaptive Sampling Algorithm (ASA) for WSN with power hungry sensors and harvesting capabilities, an energy management technique that can be implemented on any WSN platform with enough processing power to execute the proposed algorithm. An existing state-of-the-art ASA developed for wireless sensor networks with power hungry sensors is optimized and enhanced to adapt the sampling frequency according to the available energy of the node. The proposed algorithm is evaluated using two in-field testbeds that are supplied by two different energy harvesting sources (solar and wind). Simulation and comparison between the state-of-the-art ASA and the proposed energy aware ASA (EASA) in terms of energy durability are carried out using in-field measured harvested energy (using both wind and solar sources) and power hungry sensors (ultrasonic wind sensor and gas sensors). The simulation results demonstrate that using ASA in combination with an energy aware function on the nodes can drastically increase the lifetime of a WSN node and enable self-sustainability. In fact, the proposed EASA in conjunction with energy harvesting capability can lead towards perpetual WSN operation and significantly outperform the state-of-the-art ASA. PMID:27043559

  9. An Energy Aware Adaptive Sampling Algorithm for Energy Harvesting WSN with Energy Hungry Sensors

    PubMed Central

    Srbinovski, Bruno; Magno, Michele; Edwards-Murphy, Fiona; Pakrashi, Vikram; Popovici, Emanuel

    2016-01-01

    Wireless sensor nodes have a limited power budget, though they are often expected to be functional in the field once deployed for extended periods of time. Therefore, minimization of energy consumption and energy harvesting technology in Wireless Sensor Networks (WSN) are key tools for maximizing network lifetime, and achieving self-sustainability. This paper proposes an energy aware Adaptive Sampling Algorithm (ASA) for WSN with power hungry sensors and harvesting capabilities, an energy management technique that can be implemented on any WSN platform with enough processing power to execute the proposed algorithm. An existing state-of-the-art ASA developed for wireless sensor networks with power hungry sensors is optimized and enhanced to adapt the sampling frequency according to the available energy of the node. The proposed algorithm is evaluated using two in-field testbeds that are supplied by two different energy harvesting sources (solar and wind). Simulation and comparison between the state-of-the-art ASA and the proposed energy aware ASA (EASA) in terms of energy durability are carried out using in-field measured harvested energy (using both wind and solar sources) and power hungry sensors (ultrasonic wind sensor and gas sensors). The simulation results demonstrate that using ASA in combination with an energy aware function on the nodes can drastically increase the lifetime of a WSN node and enable self-sustainability. In fact, the proposed EASA in conjunction with energy harvesting capability can lead towards perpetual WSN operation and significantly outperform the state-of-the-art ASA. PMID:27043559

  10. Real-time nutrient monitoring in rivers: adaptive sampling strategies, technological challenges and future directions

    NASA Astrophysics Data System (ADS)

    Blaen, Phillip; Khamis, Kieran; Lloyd, Charlotte; Bradley, Chris

    2016-04-01

    Excessive nutrient concentrations in river waters threaten aquatic ecosystem functioning and can pose substantial risks to human health. Robust monitoring strategies are therefore required to generate reliable estimates of river nutrient loads and to improve understanding of the catchment processes that drive spatiotemporal patterns in nutrient fluxes. Furthermore, these data are vital for prediction of future trends under changing environmental conditions and thus the development of appropriate mitigation measures. In recent years, technological developments have led to an increase in the use of continuous in-situ nutrient analysers, which enable measurements at far higher temporal resolutions than can be achieved with discrete sampling and subsequent laboratory analysis. However, such instruments can be costly to run and difficult to maintain (e.g. due to high power consumption and memory requirements), leading to trade-offs between temporal and spatial monitoring resolutions. Here, we highlight how adaptive monitoring strategies, comprising a mixture of temporal sample frequencies controlled by one or more 'trigger variables' (e.g. river stage, turbidity, or nutrient concentration), can advance our understanding of catchment nutrient dynamics while simultaneously overcoming many of the practical and economic challenges encountered in typical in-situ river nutrient monitoring applications. We present examples of short-term variability in river nutrient dynamics, driven by complex catchment behaviour, which support our case for the development of monitoring systems that can adapt in real-time to rapid environmental changes. In addition, we discuss the advantages and disadvantages of current nutrient monitoring techniques, and suggest new research directions based on emerging technologies and highlight how these might improve: 1) monitoring strategies, and 2) understanding of linkages between catchment processes and river nutrient fluxes.

  11. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

    USGS Publications Warehouse

    Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

    2008-01-01

    Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of

  12. Selective detection of live bacteria combining propidium monoazide sample treatment with microarray technology.

    PubMed

    Nocker, Andreas; Mazza, Alberto; Masson, Luke; Camper, Anne K; Brousseau, Roland

    2009-03-01

    The use of DNA-based molecular detection tools for bacterial diagnostics is hampered by the inability to distinguish signals originating from live and dead cells. The detection of live cells is typically most relevant in molecular diagnostics. DNA-intercalating dyes like ethidium monoazide and propidium monoazide (PMA) offer a possibility to selectively remove cells with compromised cell membranes from the analysis. Once these dyes enter a cell, they bind to DNA and can be covalently crosslinked to it by light exposure. PCR amplification of such modified DNA is strongly inhibited. In this study we evaluated the suitability of propidium monoazide treatment to exclude isopropanol-killed cells from detection in defined mixtures using diagnostic microarray technology. The organisms comprised Pseudomonas aeruginosa, Listeria monocytogenes, Salmonella typhimurium, Serratia marcescens, and Escherichia coli O157:H7. PCR products obtained from amplification of chaperonin 60 genes (cpn60; coding for GroEL) were hybridized to a custom-designed microarray containing strain-specific cpn60-based 35-mer oligonucleotide probes. Results were compared with data from quantitative PCR, which confirmed that PMA could successfully inhibit amplification of DNA from killed cells in the mixtures. Although microarray data based on analysis of end-point PCR amplicons is not quantitative, results showed a significant signal reduction when targeting killed cells and consistently agreed with qPCR results. Treatment of samples with PMA in combination with diagnostic microarray detection can therefore be considered beneficial when analyzing mixtures of intact and membrane-compromised cells. Minimization of detection signals deriving from dead cells will render data more relevant in studies including pathogen risk assessment.

  13. Diversity of bacteria producing pigmented colonies in aerosol, snow and soil samples from remote glacial areas (Antarctica, Alps and Andes)

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

  14. Design of Field Experiments for Adaptive Sampling of the Ocean with Autonomous Vehicles

    NASA Astrophysics Data System (ADS)

    Zheng, H.; Ooi, B. H.; Cho, W.; Dao, M. H.; Tkalich, P.; Patrikalakis, N. M.

    2010-05-01

    Due to the highly non-linear and dynamical nature of oceanic phenomena, the predictive capability of various ocean models depends on the availability of operational data. A practical method to improve the accuracy of the ocean forecast is to use a data assimilation methodology to combine in-situ measured and remotely acquired data with numerical forecast models of the physical environment. Autonomous surface and underwater vehicles with various sensors are economic and efficient tools for exploring and sampling the ocean for data assimilation; however there is an energy limitation to such vehicles, and thus effective resource allocation for adaptive sampling is required to optimize the efficiency of exploration. In this paper, we use physical oceanography forecasts of the coastal zone of Singapore for the design of a set of field experiments to acquire useful data for model calibration and data assimilation. The design process of our experiments relied on the oceanography forecast including the current speed, its gradient, and vorticity in a given region of interest for which permits for field experiments could be obtained and for time intervals that correspond to strong tidal currents. Based on these maps, resources available to our experimental team, including Autonomous Surface Craft (ASC) are allocated so as to capture the oceanic features that result from jets and vortices behind bluff bodies (e.g., islands) in the tidal current. Results are summarized from this resource allocation process and field experiments conducted in January 2009.

  15. Iterative Monte Carlo with bead-adapted sampling for complex-time correlation functions.

    PubMed

    Jadhao, Vikram; Makri, Nancy

    2010-03-14

    In a recent communication [V. Jadhao and N. Makri, J. Chem. Phys. 129, 161102 (2008)], we introduced an iterative Monte Carlo (IMC) path integral methodology for calculating complex-time correlation functions. This method constitutes a stepwise evaluation of the path integral on a grid selected by a Monte Carlo procedure, circumventing the exponential growth of statistical error with increasing propagation time, while realizing the advantageous scaling of importance sampling in the grid selection and integral evaluation. In the present paper, we present an improved formulation of IMC, which is based on a bead-adapted sampling procedure; thus leading to grid point distributions that closely resemble the absolute value of the integrand at each iteration. We show that the statistical error of IMC does not grow upon repeated iteration, in sharp contrast to the performance of the conventional path integral approach which leads to exponential increase in statistical uncertainty. Numerical results on systems with up to 13 degrees of freedom and propagation up to 30 times the "thermal" time variant Planck's over 2pibeta/2 illustrate these features.

  16. Iterative Monte Carlo with bead-adapted sampling for complex-time correlation functions

    NASA Astrophysics Data System (ADS)

    Jadhao, Vikram; Makri, Nancy

    2010-03-01

    In a recent communication [V. Jadhao and N. Makri, J. Chem. Phys. 129, 161102 (2008)], we introduced an iterative Monte Carlo (IMC) path integral methodology for calculating complex-time correlation functions. This method constitutes a stepwise evaluation of the path integral on a grid selected by a Monte Carlo procedure, circumventing the exponential growth of statistical error with increasing propagation time, while realizing the advantageous scaling of importance sampling in the grid selection and integral evaluation. In the present paper, we present an improved formulation of IMC, which is based on a bead-adapted sampling procedure; thus leading to grid point distributions that closely resemble the absolute value of the integrand at each iteration. We show that the statistical error of IMC does not grow upon repeated iteration, in sharp contrast to the performance of the conventional path integral approach which leads to exponential increase in statistical uncertainty. Numerical results on systems with up to 13 degrees of freedom and propagation up to 30 times the "thermal" time ℏβ /2 illustrate these features.

  17. Motion-adapted pulse sequences for oriented sample (OS) solid-state NMR of biopolymers

    PubMed Central

    Lu, George J.; Opella, Stanley J.

    2013-01-01

    One of the main applications of solid-state NMR is to study the structure and dynamics of biopolymers, such as membrane proteins, under physiological conditions where the polypeptides undergo global motions as they do in biological membranes. The effects of NMR radiofrequency irradiations on nuclear spins are strongly influenced by these motions. For example, we previously showed that the MSHOT-Pi4 pulse sequence yields spectra with resonance line widths about half of those observed using the conventional pulse sequence when applied to membrane proteins undergoing rapid uniaxial rotational diffusion in phospholipid bilayers. In contrast, the line widths were not changed in microcrystalline samples where the molecules did not undergo global motions. Here, we demonstrate experimentally and describe analytically how some Hamiltonian terms are susceptible to sample motions, and it is their removal through the critical π/2 Z-rotational symmetry that confers the “motion adapted” property to the MSHOT-Pi4 pulse sequence. This leads to the design of separated local field pulse sequence “Motion-adapted SAMPI4” and is generalized to an approach for the design of decoupling sequences whose performance is superior in the presence of molecular motions. It works by cancelling the spin interaction by explicitly averaging the reduced Wigner matrix to zero, rather than utilizing the 2π nutation to average spin interactions. This approach is applicable to both stationary and magic angle spinning solid-state NMR experiments. PMID:24006989

  18. Occurrence of bacteria producing broad-spectrum beta-lactamases and qnr genes in hospital and urban wastewater samples.

    PubMed

    Röderová, Magdaléna; Sedláková, Miroslava Htoutou; Pudová, Vendula; Hricová, Kristýna; Silová, Romana; Imwensi, Peter Eghonghon Odion; Bardoň, Jan; Kolář, Milan

    2016-04-01

    The aims were to investigate the level of antibiotic-resistant bacteria in hospital and urban wastewater and to determine the similarity of isolates obtained from wastewater and hospitalized patients. Wastewater samples were collected in September 2013 and 2014. After identification using MALDI-TOF MS, beta-lactamase production was determined by relevant phenotypic tests. Genes responsible for the production of single beta-lactamase groups and Qnr proteins were established. The epidemiological relationship of the isolates from wastewater and hospitalized patients was determined by PFGE. A total of 51 isolates of enterobacteria were obtained. Overall, 45.1% of them produced broad-spectrum beta-lactamases. Genes encoding TEM, SHV, CTX-M, CIT, DHA and EBC types of enzymes and Qnr proteins were detected. No broad-spectrum beta-lactamase production was confirmed in the urban wastewater treatment plant. The most important finding was the detection of two identical isolates of K. pneumoniae in 2013, one from a patient's urinary catheter and the other from a wastewater sample. PMID:27196551

  19. Occurrence of bacteria producing broad-spectrum beta-lactamases and qnr genes in hospital and urban wastewater samples.

    PubMed

    Röderová, Magdaléna; Sedláková, Miroslava Htoutou; Pudová, Vendula; Hricová, Kristýna; Silová, Romana; Imwensi, Peter Eghonghon Odion; Bardoň, Jan; Kolář, Milan

    2016-04-01

    The aims were to investigate the level of antibiotic-resistant bacteria in hospital and urban wastewater and to determine the similarity of isolates obtained from wastewater and hospitalized patients. Wastewater samples were collected in September 2013 and 2014. After identification using MALDI-TOF MS, beta-lactamase production was determined by relevant phenotypic tests. Genes responsible for the production of single beta-lactamase groups and Qnr proteins were established. The epidemiological relationship of the isolates from wastewater and hospitalized patients was determined by PFGE. A total of 51 isolates of enterobacteria were obtained. Overall, 45.1% of them produced broad-spectrum beta-lactamases. Genes encoding TEM, SHV, CTX-M, CIT, DHA and EBC types of enzymes and Qnr proteins were detected. No broad-spectrum beta-lactamase production was confirmed in the urban wastewater treatment plant. The most important finding was the detection of two identical isolates of K. pneumoniae in 2013, one from a patient's urinary catheter and the other from a wastewater sample.

  20. Comparison of DOT-ELISA and Standard-ELISA for Detection of the Vibrio cholerae Toxin in Culture Supernatants of Bacteria Isolated from Human and Environmental Samples.

    PubMed

    Meza-Lucas, Antonio; Pérez-Villagómez, María-Fernanda; Martínez-López, José-Patricio; García-Rodea, Ricardo; Martínez-Castelán, María-Guadalupe; Escobar-Gutiérrez, Alejandro; de-la-Rosa-Arana, Jorge-Luis; Villanueva-Zamudio, Altagracia

    2016-09-01

    A comparison of DOT-ELISA and Standard-ELISA was made for detection of Vibrio cholerae toxin in culture supernatants of bacteria isolated from human and environmental samples. A total of 293 supernatants were tested in a double blind assay. A correlation of 100 % was obtained between both techniques. The cholera toxin was found in 20 Inaba and 3 Ogawa strains. Positive samples were from seafood (17 samples), potable water (1 sample) and sewage (5 samples). The DOT-ELISA was useful as the standard-ELISA to confirm the presence of cholera toxin in the environmental samples.

  1. Comparison of DOT-ELISA and Standard-ELISA for Detection of the Vibrio cholerae Toxin in Culture Supernatants of Bacteria Isolated from Human and Environmental Samples.

    PubMed

    Meza-Lucas, Antonio; Pérez-Villagómez, María-Fernanda; Martínez-López, José-Patricio; García-Rodea, Ricardo; Martínez-Castelán, María-Guadalupe; Escobar-Gutiérrez, Alejandro; de-la-Rosa-Arana, Jorge-Luis; Villanueva-Zamudio, Altagracia

    2016-09-01

    A comparison of DOT-ELISA and Standard-ELISA was made for detection of Vibrio cholerae toxin in culture supernatants of bacteria isolated from human and environmental samples. A total of 293 supernatants were tested in a double blind assay. A correlation of 100 % was obtained between both techniques. The cholera toxin was found in 20 Inaba and 3 Ogawa strains. Positive samples were from seafood (17 samples), potable water (1 sample) and sewage (5 samples). The DOT-ELISA was useful as the standard-ELISA to confirm the presence of cholera toxin in the environmental samples. PMID:27407304

  2. 120nm resolution in thick samples with structured illumination and adaptive optics

    NASA Astrophysics Data System (ADS)

    Thomas, Benjamin; Sloan, Megan; Wolstenholme, Adrian J.; Kner, Peter

    2014-03-01

    μLinear Structured Illumination Microscopy (SIM) provides a two-fold increase over the diffraction limited resolution. SIM produces excellent images with 120nm resolution in tissue culture cells in two and three dimensions. For SIM to work correctly, the point spread function (PSF) and optical transfer function (OTF) must be known, and, ideally, should be unaberrated. When imaging through thick samples, aberrations will be introduced into the optical system which will reduce the peak intensity and increase the width of the PSF. This will lead to reduced resolution and artifacts in SIM images. Adaptive optics can be used to correct the optical wavefront restoring the PSF to its unaberrated state, and AO has been used in several types of fluorescence microscopy. We demonstrate that AO can be used with SIM to achieve 120nm resolution through 25m of tissue by imaging through the full thickness of an adult C. elegans roundworm. The aberrations can be corrected over a 25μm × 45μm field of view with one wavefront correction setting, demonstrating that AO can be used effectively with widefield superresolution techniques.

  3. A new spectral variable selection pattern using competitive adaptive reweighted sampling combined with successive projections algorithm.

    PubMed

    Tang, Guo; Huang, Yue; Tian, Kuangda; Song, Xiangzhong; Yan, Hong; Hu, Jing; Xiong, Yanmei; Min, Shungeng

    2014-10-01

    The competitive adaptive reweighted sampling-successive projections algorithm (CARS-SPA) method was proposed as a novel variable selection approach to process multivariate calibration. The CARS was first used to select informative variables, and then SPA to refine the variables with minimum redundant information. The proposed method was applied to near-infrared (NIR) reflectance data of nicotine in tobacco lamina and NIR transmission data of active ingredient in pesticide formulation. As a result, fewer but more informative variables were selected by CARS-SPA than by direct CARS. In the system of pesticide formulation, a multiple linear regression (MLR) model using variables selected by CARS-SPA provided a better prediction than the full-range partial least-squares (PLS) model, successive projections algorithm (SPA) model and uninformative variables elimination-successive projections algorithm (UVE-SPA) processed model. The variable subsets selected by CARS-SPA included the spectral ranges with sufficient chemical information, whereas the uninformative variables were hardly selected.

  4. Quantification of Uncultured Ruminococcus obeum-Like Bacteria in Human Fecal Samples by Fluorescent In Situ Hybridization and Flow Cytometry Using 16S rRNA-Targeted Probes

    PubMed Central

    Zoetendal, Erwin G.; Ben-Amor, Kaouther; Harmsen, Hermie J. M.; Schut, Frits; Akkermans, Antoon D. L.; de Vos, Willem M.

    2002-01-01

    A 16S rRNA-targeted probe was designed and validated in order to quantify the number of uncultured Ruminococcus obeum-like bacteria by fluorescent in situ hybridization (FISH). These bacteria have frequently been found in 16S ribosomal DNA clone libraries prepared from bacterial communities in the human intestine. Thirty-two reference strains from the human intestine, including a phylogenetically related strain and strains of some other Ruminococcus species, were used as negative controls and did not hybridize with the new probe. Microscopic and flow cytometric analyses revealed that a group of morphologically similar bacteria in feces did hybridize with this probe. Moreover, it was found that all hybridizing cells also hybridized with a probe specific for the Clostridium coccoides-Eubacterium rectale group, a group that includes the uncultured R. obeum-like bacteria. Quantification of the uncultured R. obeum-like bacteria and the C. coccoides-E. rectale group by flow cytometry and microscopy revealed that these groups comprised approximately 2.5 and 16% of the total community in fecal samples, respectively. The uncultured R. obeum-like bacteria comprise about 16% of the C. coccoides-E. rectale group. These results indicate that the uncultured R. obeum-like bacteria are numerically important in human feces. Statistical analysis revealed no significant difference between the microscopic and flow cytometric counts and the different feces sampling times, while a significant host-specific effect on the counts was observed. Our data demonstrate that the combination of FISH and flow cytometry is a useful approach for studying the ecology of uncultured bacteria in the human gastrointestinal tract. PMID:12200269

  5. Adapt

    NASA Astrophysics Data System (ADS)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  6. Identification of Opportunistic Pathogenic Bacteria in Drinking Water Samples of Different Rural Health Centers and Their Clinical Impacts on Humans

    PubMed Central

    Pindi, Pavan Kumar; Raghuveer Yadav, P.; Shiva Shanker, A.

    2013-01-01

    International drinking water quality monitoring programs have been established in order to prevent or to reduce the risk of contracting water-related infections. A survey was performed on groundwater-derived drinking water from 13 different hospitals in the Mahabubnagar District. A total of 55 bacterial strains were isolated which belonged to both gram-positive and gram-negative bacteria. All the taxa were identified based on the 16S rRNA gene sequence analysis based on which they are phylogenetically close to 27 different taxa. Many of the strains are closely related to their phylogenetic neighbors and exhibit from 98.4 to 100% sequence similarity at the 16S rRNA gene sequence level. The most common group was similar to Acinetobacter junii (21.8%) and Acinetobacter calcoaceticus (10.9%) which were shared by 7 and 5 water samples, respectively. Out of 55 isolates, only 3 isolates belonged to coliform group which are Citrobacter freundii and Pantoea anthophila. More than half (52.7%, 29 strains) of the phylogenetic neighbors which belonged to 12 groups were reported to be pathogenic and isolated from clinical specimens. Out of 27 representative taxa are affiliated have eight representative genera in drinking water except for those affiliated with the genera Exiguobacterium, Delftia, Kocuria, and Lysinibacillus. PMID:23862144

  7. Bacteria detection based on the evolution of enzyme-generated volatile organic compounds: determination of Listeria monocytogenes in milk samples.

    PubMed

    Tait, Emma; Perry, John D; Stanforth, Stephen P; Dean, John R

    2014-10-27

    The rapid detection of Listeria monocytogenes contamination in food is essential to prevent food-borne illness in humans. The aim of this study was to differentiate non-contaminated milk from milk contaminated with L. monocytogenes using enzyme substrates coupled with the analysis of volatile organic compounds (VOCs). The method is based on the activity of β-glucosidase and hippuricase enzymes and the detection of a specific VOC i.e. 2-nitrophenol and 3-fluoroaniline, respectively. VOCs were extracted, separated and detected by headspace-solid phase microextraction coupled to gas chromatography-mass spectrometry (HS-SPME GC-MS). This approach required the inclusion of the selective agent's cycloheximide, nalidixic acid and acriflavine HCl in the growth medium to inhibit interfering bacteria. The VOCs were liberated by L. monocytogenes provided that samples contained at least 1-1.5×10(2) CFU ml(-1) of milk prior to overnight incubation. This approach shows potential for future development as a rapid method for the detection of L. monocytogenes contaminated milk.

  8. Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria.

    PubMed

    Levin, Bruce R

    2010-10-28

    Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR) abound in the genomes of almost all archaebacteria and nearly half the eubacteria sequenced. Through a genetic interference mechanism, bacteria with CRISPR regions carrying copies of the DNA of previously encountered phage and plasmids abort the replication of phage and plasmids with these sequences. Thus it would seem that protection against infecting phage and plasmids is the selection pressure responsible for establishing and maintaining CRISPR in bacterial populations. But is it? To address this question and provide a framework and hypotheses for the experimental study of the ecology and evolution of CRISPR, I use mathematical models of the population dynamics of CRISPR-encoding bacteria with lytic phage and conjugative plasmids. The results of the numerical (computer simulation) analysis of the properties of these models with parameters in the ranges estimated for Escherichia coli and its phage and conjugative plasmids indicate: (1) In the presence of lytic phage there are broad conditions where bacteria with CRISPR-mediated immunity will have an advantage in competition with non-CRISPR bacteria with otherwise higher Malthusian fitness. (2) These conditions for the existence of CRISPR are narrower when there is envelope resistance to the phage. (3) While there are situations where CRISPR-mediated immunity can provide bacteria an advantage in competition with higher Malthusian fitness bacteria bearing deleterious conjugative plasmids, the conditions for this to obtain are relatively narrow and the intensity of selection favoring CRISPR weak. The parameters of these models can be independently estimated, the assumption behind their construction validated, and the hypotheses generated from the analysis of their properties tested in experimental populations of bacteria with lytic phage and conjugative plasmids. I suggest protocols for estimating these parameters and outline the design of

  9. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

    PubMed Central

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  10. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer. PMID:27499762

  11. An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.

    PubMed

    Zandi, Kasra; Butler, Gregory; Kharma, Nawwaf

    2016-01-01

    Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer.

  12. Some Features of the Sampling Distribution of the Ability Estimate in Computerized Adaptive Testing According to Two Stopping Rules.

    ERIC Educational Resources Information Center

    Blais, Jean-Guy; Raiche, Gilles

    This paper examines some characteristics of the statistics associated with the sampling distribution of the proficiency level estimate when the Rasch model is used. These characteristics allow the judgment of the meaning to be given to the proficiency level estimate obtained in adaptive testing, and as a consequence, they can illustrate the…

  13. The Parent Version of the Preschool Social Skills Rating System: Psychometric Analysis and Adaptation with a German Preschool Sample

    ERIC Educational Resources Information Center

    Hess, Markus; Scheithauer, Herbert; Kleiber, Dieter; Wille, Nora; Erhart, Michael; Ravens-Sieberer, Ulrike

    2014-01-01

    The Social Skills Rating System (SSRS) developed by Gresham and Elliott (1990) is a multirater, norm-referenced instrument measuring social skills and adaptive behavior in preschool children. The aims of the present study were (a) to test the factorial structure of the Parent Form of the SSRS for the first time with a German preschool sample (391…

  14. Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity.

    PubMed

    Liu, Yuanhua; Zhang, Chenhong; Zhao, Liping; Nardini, Christine

    2010-12-01

    With the expanding availability of sequencing technologies, research previously centered on the human genome can now afford to include the study of humans' internal ecosystem (human microbiome). Given the scale of the data involved in this metagenomic research (two orders of magnitude larger than the human genome) and their importance in relation to human health, it is crucial to guarantee (along with the appropriate data collection and taxonomy) proper tools for data analysis. We propose to adapt the approaches defined for the analysis of gene-expression microarray in order to infer information in metagenomics. In particular, we applied SAM, a broadly used tool for the identification of differentially expressed genes among different samples classes, to a reported dataset on a research model with mice of two genotypes (a high density lipoprotein knockout mouse and its wild-type counterpart). The data contain two different diets (high-fat or normal-chow) to ensure the onset of obesity, prodrome of metabolic syndromes (MS). By using 16S rRNA gene as a genomic diversity marker, we illustrate how this approach can identify bacterial populations differentially enriched among different genetic and dietary conditions of the host. This approach faithfully reproduces highly-relevant results from phylogenetic and standard statistical analyses, used to explain the role of the gut microbiome in relation to obesity. This represents a promising proof-of-principle for using functional genomic approaches in the fast growing area of metagenomics, and warrants the availability of a large body of thoroughly tested and theoretically sound methodologies to this exciting new field.

  15. Dynamics of Nitrification and Denitrification in Root-Oxygenated Sediments and Adaptation of Ammonia-Oxidizing Bacteria to Low-Oxygen or Anoxic Habitats

    PubMed Central

    Bodelier, P.; Libochant, J. A.; Blom, C.; Laanbroek, H. J.

    1996-01-01

    Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria. The oxygen-releasing, aerenchymatous emergent macrophyte Glyceria maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and early summer. The stimulation of the aerobic nitrifying bacteria in the freshwater sediment, ascribed to oxygen release by the roots of G. maxima, disappeared in late summer. Numbers and activities of the nitrifying bacteria were positively correlated, and a positive relationship with denitrification activities also was found. To assess possible adaptations of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats, a comparison was made between the freshwater lake sediment and three soils differing in oxicity profiles. Oxygen kinetics and tolerance to anoxia of the ammonia-oxidizing communities from these habitats were determined. The apparent K(infm) values for oxygen of the ammonia-oxidizing community in the lake sediment were in the range of 5 to 15 (mu)M, which was substantially lower than the range of K(infm) values for oxygen of the ammonia-oxidizing community from a permanently oxic dune location. Upon anoxic incubation, the ammonia-oxidizing communities of dune, chalk grassland, and calcareous grassland soils lost 99, 95, and 92% of their initial nitrifying capacity, respectively. In contrast, the ammonia-oxidizing community in the lake sediment started to nitrify within 1 h upon exposure to oxygen at the level of the initial capacity. It is argued that the conservation of the nitrifying capacity during anoxic periods and the ability to react instantaneously to the presence of oxygen are important traits of nitrifiers in fluctuating oxic-anoxic environments such as the root zone of aerenchymatous plant species. PMID:16535441

  16. A comparison of adaptive sampling designs and binary spatial models: A simulation study using a census of Bromus inermis

    USGS Publications Warehouse

    Irvine, Kathryn M.; Thornton, Jamie; Backus, Vickie M.; Hohmann, Matthew G.; Lehnhoff, Erik A.; Maxwell, Bruce D.; Michels, Kurt; Rew, Lisa

    2013-01-01

    Commonly in environmental and ecological studies, species distribution data are recorded as presence or absence throughout a spatial domain of interest. Field based studies typically collect observations by sampling a subset of the spatial domain. We consider the effects of six different adaptive and two non-adaptive sampling designs and choice of three binary models on both predictions to unsampled locations and parameter estimation of the regression coefficients (species–environment relationships). Our simulation study is unique compared to others to date in that we virtually sample a true known spatial distribution of a nonindigenous plant species, Bromus inermis. The census of B. inermis provides a good example of a species distribution that is both sparsely (1.9 % prevalence) and patchily distributed. We find that modeling the spatial correlation using a random effect with an intrinsic Gaussian conditionally autoregressive prior distribution was equivalent or superior to Bayesian autologistic regression in terms of predicting to un-sampled areas when strip adaptive cluster sampling was used to survey B. inermis. However, inferences about the relationships between B. inermis presence and environmental predictors differed between the two spatial binary models. The strip adaptive cluster designs we investigate provided a significant advantage in terms of Markov chain Monte Carlo chain convergence when trying to model a sparsely distributed species across a large area. In general, there was little difference in the choice of neighborhood, although the adaptive king was preferred when transects were randomly placed throughout the spatial domain.

  17. Adaptation of G-TAG Software for Validating Touch-and-Go Comet Surface Sampling Design Methodology

    NASA Technical Reports Server (NTRS)

    Mandic, Milan; Acikmese, Behcet; Blackmore, Lars

    2011-01-01

    The G-TAG software tool was developed under the R&TD on Integrated Autonomous Guidance, Navigation, and Control for Comet Sample Return, and represents a novel, multi-body dynamics simulation software tool for studying TAG sampling. The G-TAG multi-body simulation tool provides a simulation environment in which a Touch-and-Go (TAG) sampling event can be extensively tested. TAG sampling requires the spacecraft to descend to the surface, contact the surface with a sampling collection device, and then to ascend to a safe altitude. The TAG event lasts only a few seconds but is mission-critical with potentially high risk. Consequently, there is a need for the TAG event to be well characterized and studied by simulation and analysis in order for the proposal teams to converge on a reliable spacecraft design. This adaptation of the G-TAG tool was developed to support the Comet Odyssey proposal effort, and is specifically focused to address comet sample return missions. In this application, the spacecraft descends to and samples from the surface of a comet. Performance of the spacecraft during TAG is assessed based on survivability and sample collection performance. For the adaptation of the G-TAG simulation tool to comet scenarios, models are developed that accurately describe the properties of the spacecraft, approach trajectories, and descent velocities, as well as the models of the external forces and torques acting on the spacecraft. The adapted models of the spacecraft, descent profiles, and external sampling forces/torques were more sophisticated and customized for comets than those available in the basic G-TAG simulation tool. Scenarios implemented include the study of variations in requirements, spacecraft design (size, locations, etc. of the spacecraft components), and the environment (surface properties, slope, disturbances, etc.). The simulations, along with their visual representations using G-View, contributed to the Comet Odyssey New Frontiers proposal

  18. Optimization of the β LACTA test for the detection of extended-spectrum-β-lactamase-producing bacteria directly in urine samples.

    PubMed

    Amzalag, Jonas; Mizrahi, Assaf; Naouri, Diane; Nguyen, Jean Claude; Ganansia, Olivier; Le Monnier, Alban

    2016-09-01

    The β LACTA™ test (BLT) is a chromogenic test detecting resistance to third-generation cephalosporins on bacterial colonies. Some studies have shown that this test can be used directly in urine samples. The aim of this study was to determine the optimal conditions of use of this test in order to detect the ESBL-producing bacteria directly in urine samples. During a 4-months period, a total of 365 consecutive urine samples were tested with the BLT using the recommendation of the manufacturer. We isolated 56 ESBL-producing bacteria and 17 AmpC-overproducing bacteria. ESBL- and/or AmpC β-lactamase-producing bacteria isolates were systematically characterized by disc diffusion antibiotic susceptibility testing interpreted according to the guidelines of EUCAST. The sensitivity and the specificity for 3GC-resistance detection, regardless the mechanism of resistance, were, respectively, 60.3% and 100%, whereas for ESBL detection, it was, respectively, 75.4% and 99.7%. We applied then modification of the initial protocol considering urines with a bacteriuria >1000/μL, a reading time at 30 min and considering any change of the initial colour as positive. The overall sensitivity was 81% and the sensitivity for ESBL-detection raised to 95.7%.

  19. Effect of rumen bacteria from sheep adapted to a tanninferous diet on in vitro fermentation parameters of pistachio hulls using bovine inoculum

    PubMed Central

    Babaei, Y; Rouzbehan, Y; Alipour, D

    2015-01-01

    Sheep adapted to consume tannins rich feeds such as oak leaf (OL) appear to develop defensive mechanisms by their ruminal bacteria against these polyphenols. The capabilities of ruminal isolated tannins resistant bacteria from these animals to ferment a tanniniferous feed (i.e., pistachio hulls, (PH) which were incubated with rumen fluid from Holstein dairy cows was assessed. Six g positive cocci were isolated from the rumen of sheep and the 16s rRNA gene sequences showed them to be closely related to Streptococcus gallolyticus. In three runs of in vitro gas production (GP), the effect of two of the isolates incubated with buffered-ruminal fluid of Holstein cow and PH was evaluated. The GP was recorded from 1 to 96 h of incubation. Incubating either of the isolates with PH caused a significantly higher in vitro gas production, estimated parameters, in vitro organic matter disappearance, metabolisable energy and volatile fatty acids than those without any isolate. The improvement in the ruminal parameters when either of the isolates was used suggested the possible presence of isolated tannins-resistant bacteria (Streptococcus gallolyticus sp.), however, in vivo studies must be conducted to confirm the in vitro results. PMID:27175203

  20. Effect of rumen bacteria from sheep adapted to a tanninferous diet on in vitro fermentation parameters of pistachio hulls using bovine inoculum.

    PubMed

    Babaei, Y; Rouzbehan, Y; Alipour, D

    2015-01-01

    Sheep adapted to consume tannins rich feeds such as oak leaf (OL) appear to develop defensive mechanisms by their ruminal bacteria against these polyphenols. The capabilities of ruminal isolated tannins resistant bacteria from these animals to ferment a tanniniferous feed (i.e., pistachio hulls, (PH) which were incubated with rumen fluid from Holstein dairy cows was assessed. Six g positive cocci were isolated from the rumen of sheep and the 16s rRNA gene sequences showed them to be closely related to Streptococcus gallolyticus. In three runs of in vitro gas production (GP), the effect of two of the isolates incubated with buffered-ruminal fluid of Holstein cow and PH was evaluated. The GP was recorded from 1 to 96 h of incubation. Incubating either of the isolates with PH caused a significantly higher in vitro gas production, estimated parameters, in vitro organic matter disappearance, metabolisable energy and volatile fatty acids than those without any isolate. The improvement in the ruminal parameters when either of the isolates was used suggested the possible presence of isolated tannins-resistant bacteria (Streptococcus gallolyticus sp.), however, in vivo studies must be conducted to confirm the in vitro results. PMID:27175203

  1. Effects of Holding Time, Storage, and the Preservation of Samples on Sample Integrity for the Detection of Fecal Indicator Bacteria by Quantitative Polymerase Chain Reaction (qPCR)-based assays.

    EPA Science Inventory

    The purpose of this project was to answer questions related to storage of samples to be analyzed by the quantitative polymerase chain reaction (qPCR)-based assays for fecal indicator bacteria. The project was divided into two parts. The first part was to determine if filters th...

  2. Fatty acid and hydroxy acid adaptation in three gram-negative hydrocarbon-degrading bacteria in relation to carbon source.

    PubMed

    Soltani, Mohamed; Metzger, Pierre; Largeau, Claude

    2005-12-01

    The lipids of three gram-negative bacteria, Acinetobacter calcoaceticus, Marinobacter aquaeolei, and Pseudomonas oleovorans grown on mineral media supplemented with ammonium acetate or hydrocarbons, were isolated, purified, and their structures determined. Three pools of lipids were isolated according to a sequential procedure: unbound lipids extracted with organic solvents, comprising metabolic lipids and the main part of membrane lipids, OH--labile lipids (mainly ester-bound in the lipopolysaccharides, LPS) and H+-labile lipids (mainly amide-bound in the LPS). Unsaturated FA composition gave evidence for an aerobic desaturation pathway for the synthesis of these acids in A. calcoaceticus and M. aquaeolei, a nonclassic route in gram-negative bacteria. Surprisingly, both aerobic and anaerobic pathways are operating in the studied strain of P. oleovorans. The increase of the proportion of saturated FA observed for the strain of P. oleovorans grown on light hydrocarbons would increase the temperature transition of the lipids for maintaining the inner membrane fluidity. An opposite phenomenon occurs in A. calcoaceticus and M. aquaeolei grown on solid or highly viscous C19 hydrocarbons. The increases of FA < C18 when the bacteria were grown on n-nonadecane, or of iso-FA in cultures on isononadecane would decrease the transition temperature of the lipids, to maintain the fluidity of the inner membranes. Moreover, P. oleovorans grown on hydrocarbons greatly decreases the proportion of P-hydroxy acids of LPS, thus likely maintaining the physical properties of the outer membrane. By contrast, no dramatic change in hydroxy acid composition occurred in the other two bacteria. PMID:16477811

  3. Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.

    PubMed

    Ngugi, David Kamanda; Blom, Jochen; Stepanauskas, Ramunas; Stingl, Ulrich

    2016-06-01

    Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine-seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.

  4. Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines

    PubMed Central

    Ngugi, David Kamanda; Blom, Jochen; Stepanauskas, Ramunas; Stingl, Ulrich

    2016-01-01

    Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine–seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean. PMID:26657763

  5. Influences of sample interference and interference controls on quantification of enterococci fecal indicator bacteria in surface water samples by the qPCR method

    EPA Science Inventory

    A quantitative polymerase chain reaction (qPCR) method for the detection of entercocci fecal indicator bacteria has been shown to be generally applicable for the analysis of temperate fresh (Great Lakes) and marine coastal waters and for providing risk-based determinations of wat...

  6. Immune tolerance to an intestine-adapted bacteria, Chryseobacterium sp., injected into the hemocoel of Protaetia brevitarsis seulensis.

    PubMed

    Lee, Jiae; Hwang, Sejung; Cho, Saeyoull

    2016-01-01

    To explore the interaction of gut microbes and the host immune system, bacteria were isolated from the gut of Protaetia brevitarsis seulensis larvae. Chryseobacterium sp., Bacillus subtilis, Arthrobacter arilaitensis, Bacillus amyloliquefaciens, Bacillus megaterium, and Lysinibacillus xylanilyticus were cultured in vitro, identified, and injected in the hemocoel of P. brevitarsis seulensis larvae, respectively. There were no significant changes in phagocytosis-associated lysosomal formation or pathogen-related autophagosome in immune cells (granulocytes) from Chryseobacterium sp.-challenged larvae. Next, we examined changes in the transcription of innate immune genes such as peptidoglycan recognition proteins and antimicrobial peptides following infection with Chryseobacterium sp. PGRP-1 and -2 transcripts, which may be associated with melanization generated by prophenoloxidase (PPO), were either highly or moderately expressed at 24 h post-infection with Chryseobacterium sp. However, PGRP-SC2 transcripts, which code for bactericidal amidases, were expressed at low levels. With respect to antimicrobial peptides, only coleoptericin was moderately expressed in Chryseobacterium sp.-challenged larvae, suggesting maintenance of an optimum number of Chryseobacterium sp. All examined genes were expressed at significantly higher levels in larvae challenged with a pathogenic bacterium. Our data demonstrated that gut-inhabiting bacteria, the Chryseobacterium sp., induced a weaker immune response than other pathogenic bacteria, E. coli K12. PMID:27530146

  7. Immune tolerance to an intestine-adapted bacteria, Chryseobacterium sp., injected into the hemocoel of Protaetia brevitarsis seulensis

    PubMed Central

    Lee, Jiae; Hwang, Sejung; Cho, Saeyoull

    2016-01-01

    To explore the interaction of gut microbes and the host immune system, bacteria were isolated from the gut of Protaetia brevitarsis seulensis larvae. Chryseobacterium sp., Bacillus subtilis, Arthrobacter arilaitensis, Bacillus amyloliquefaciens, Bacillus megaterium, and Lysinibacillus xylanilyticus were cultured in vitro, identified, and injected in the hemocoel of P. brevitarsis seulensis larvae, respectively. There were no significant changes in phagocytosis-associated lysosomal formation or pathogen-related autophagosome in immune cells (granulocytes) from Chryseobacterium sp.-challenged larvae. Next, we examined changes in the transcription of innate immune genes such as peptidoglycan recognition proteins and antimicrobial peptides following infection with Chryseobacterium sp. PGRP-1 and -2 transcripts, which may be associated with melanization generated by prophenoloxidase (PPO), were either highly or moderately expressed at 24 h post-infection with Chryseobacterium sp. However, PGRP-SC2 transcripts, which code for bactericidal amidases, were expressed at low levels. With respect to antimicrobial peptides, only coleoptericin was moderately expressed in Chryseobacterium sp.-challenged larvae, suggesting maintenance of an optimum number of Chryseobacterium sp. All examined genes were expressed at significantly higher levels in larvae challenged with a pathogenic bacterium. Our data demonstrated that gut-inhabiting bacteria, the Chryseobacterium sp., induced a weaker immune response than other pathogenic bacteria, E. coli K12. PMID:27530146

  8. Sample preparation and biomass determination of SRF model mixture using cryogenic milling and the adapted balance method

    SciTech Connect

    Schnöller, Johannes Aschenbrenner, Philipp; Hahn, Manuel; Fellner, Johann; Rechberger, Helmut

    2014-11-15

    Highlights: • An alternative sample comminution procedure for SRF is tested. • Proof of principle is shown on a SRF model mixture. • The biogenic content of the SRF is analyzed with the adapted balance method. • The novel method combines combustion analysis and a data reconciliation algorithm. • Factors for the variance of the analysis results are statistically quantified. - Abstract: The biogenic fraction of a simple solid recovered fuel (SRF) mixture (80 wt% printer paper/20 wt% high density polyethylene) is analyzed with the in-house developed adapted balance method (aBM). This fairly new approach is a combination of combustion elemental analysis (CHNS) and a data reconciliation algorithm based on successive linearisation for evaluation of the analysis results. This method shows a great potential as an alternative way to determine the biomass content in SRF. However, the employed analytical technique (CHNS elemental analysis) restricts the probed sample mass to low amounts in the range of a few hundred milligrams. This requires sample comminution to small grain sizes (<200 μm) to generate representative SRF specimen. This is not easily accomplished for certain material mixtures (e.g. SRF with rubber content) by conventional means of sample size reduction. This paper presents a proof of principle investigation of the sample preparation and analysis of an SRF model mixture with the use of cryogenic impact milling (final sample comminution) and the adapted balance method (determination of biomass content). The so derived sample preparation methodology (cutting mills and cryogenic impact milling) shows a better performance in accuracy and precision for the determination of the biomass content than one solely based on cutting mills. The results for the determination of the biogenic fraction are within 1–5% of the data obtained by the reference methods, selective dissolution method (SDM) and {sup 14}C-method ({sup 14}C-M)

  9. Psychometric Properties of the Schedule for Nonadaptive and Adaptive Personality in a PTSD Sample

    ERIC Educational Resources Information Center

    Wolf, Erika J.; Harrington, Kelly M.; Miller, Mark W.

    2011-01-01

    This study evaluated the psychometric characteristics of the Schedule for Nonadaptive and Adaptive Personality (SNAP; Clark, 1996) in 280 individuals who screened positive for posttraumatic stress disorder (PTSD). The SNAP validity, trait, temperament, and personality disorder (PD) scales were compared with scales on the Brief Form of the…

  10. Adaption of egg and larvae sampling techniques for lake sturgeon and broadcast spawning fishes in a deep river

    USGS Publications Warehouse

    Roseman, Edward F.; Kennedy, Gregory W.; Craig, Jaquelyn; Boase, James; Soper, Karen

    2011-01-01

    In this report we describe how we adapted two techniques for sampling lake sturgeon (Acipenser fulvescens) and other fish early life history stages to meet our research needs in the Detroit River, a deep, flowing Great Lakes connecting channel. First, we developed a buoy-less method for sampling fish eggs and spawning activity using egg mats deployed on the river bottom. The buoy-less method allowed us to fish gear in areas frequented by boaters and recreational anglers, thus eliminating surface obstructions that interfered with recreational and boating activities. The buoy-less method also reduced gear loss due to drift when masses of floating aquatic vegetation would accumulate on buoys and lines, increasing the drag on the gear and pulling it downstream. Second, we adapted a D-frame drift net system formerly employed in shallow streams to assess larval lake sturgeon dispersal for use in the deeper (>8 m) Detroit River using an anchor and buoy system.

  11. Evaluation of endoscopically obtained duodenal biopsy samples from cats and dogs in an adapter-modified Ussing chamber

    PubMed Central

    DeBiasio, John V.; Suchodolski, Jan S.; Newman, Shelley; Musch, Mark W.; Steiner, Jörg M.

    2014-01-01

    This study was conducted to evaluate an adapter-modified Ussing chamber for assessment of transport physiology in endoscopically obtained duodenal biopsies from healthy cats and dogs, as well as dogs with chronic enteropathies. 17 duodenal biopsies from five cats and 51 duodenal biopsies from 13 dogs were obtained. Samples were transferred into an adapter-modified Ussing chamber and sequentially exposed to various absorbagogues and secretagogues. Overall, 78.6% of duodenal samples obtained from cats responded to at least one compound. In duodenal biopsies obtained from dogs, the rate of overall response ranged from 87.5% (healthy individuals; n = 8), to 63.6% (animals exhibiting clinical signs of gastrointestinal disease and histopathological unremarkable duodenum; n = 15), and 32.1% (animals exhibiting clinical signs of gastrointestinal diseases and moderate to severe histopathological lesions; n = 28). Detailed information regarding the magnitude and duration of the response are provided. The adapter-modified Ussing chamber enables investigation of the absorptive and secretory capacity of endoscopically obtained duodenal biopsies from cats and dogs and has the potential to become a valuable research tool. The response of samples was correlated with histopathological findings. PMID:24378587

  12. Multifunctional Nutrient-Binding Proteins Adapt Human Symbiotic Bacteria for Glycan Competition in the Gut by Separately Promoting Enhanced Sensing and Catalysis

    PubMed Central

    Cameron, Elizabeth A.; Kwiatkowski, Kurt J.; Lee, Byung-Hoo; Hamaker, Bruce R.; Koropatkin, Nicole M.

    2014-01-01

    ABSTRACT To compete for the dynamic stream of nutrients flowing into their ecosystem, colonic bacteria must respond rapidly to new resources and then catabolize them efficiently once they are detected. The Bacteroides thetaiotaomicron starch utilization system (Sus) is a model for nutrient acquisition by symbiotic gut bacteria, which harbor thousands of related Sus-like systems. Structural investigation of the four Sus outer membrane proteins (SusD, -E, -F, and -G) revealed that they contain a total of eight starch-binding sites that we demonstrated, using genetic and biochemical approaches, to play distinct roles in starch metabolism in vitro and in vivo in gnotobiotic mice. SusD, whose homologs are abundant in the human microbiome, is critical for the initial sensing of available starch, allowing sus transcriptional activation at much lower concentrations than without this function. In contrast, seven additional binding sites across SusE, -F, and -G are dispensable for sus activation. However, they optimize the rate of growth on starch in a manner dependent on the expression of the bacterial polysaccharide capsule, suggesting that they have evolved to offset the diffusion barrier created by this structure. These findings demonstrate how proteins with similar biochemical behavior can serve orthogonal functions during different stages of cellular adaptation to nutrients. Finally, we demonstrated in gnotobiotic mice fed a starch-rich diet that the Sus binding sites confer a competitive advantage to B. thetaiotaomicron in vivo in a manner that is dependent on other colonizing microbes. This study reveals how numerically dominant families of carbohydrate-binding proteins in the human microbiome fulfill separate and sometimes cooperative roles to optimize gut commensal bacteria for nutrient acquisition. PMID:25205092

  13. Direct detection of viable bacteria, molds, and yeasts by reverse transcriptase PCR in contaminated milk samples after heat treatment.

    PubMed

    Vaitilingom, M; Gendre, F; Brignon, P

    1998-03-01

    A fast, sensitive, and target contaminant-modulable method was developed to detect viable bacteria, molds, and yeasts after heat treatment. By reverse transcriptase PCR with elongation factor gene (EF-Tu or EF-1 alpha)-specific primers, the detection level was 10 cells ml of milk-1. The simplicity and rapidity (4 h) of the procedure suggests that this method may be easily transposable to other foods and other contaminants. PMID:9501455

  14. Autochthonous bioaugmentation with environmental samples rich in hydrocarbonoclastic bacteria for bench-scale bioremediation of oily seawater and desert soil.

    PubMed

    Ali, Nedaa; Dashti, Narjes; Salamah, Samar; Al-Awadhi, Husain; Sorkhoh, Naser; Radwan, Samir

    2016-05-01

    Oil-contaminated seawater and desert soil batches were bioaugmented with suspensions of pea (Pisum sativum) rhizosphere and soil with long history of oil pollution. Oil consumption was measured by gas-liquid chromatography. Hydrocarbonoclastic bacteria in the bioremediation batches were counted using a mineral medium with oil vapor as a sole carbon source and characterized by their 16S ribosomal RNA (rRNA)-gene sequences. Most of the oil was consumed during the first 2-4 months, and the oil-removal rate decreased or ceased thereafter due to nutrient and oxygen depletion. Supplying the batches with NaNO3 (nitrogen fertilization) at a late phase of bioremediation resulted in reenhanced oil consumption and bacterial growth. In the seawater batches bioaugmented with rhizospheric suspension, the autochthonous rhizospheric bacterial species Microbacterium oxidans and Rhodococcus spp. were established and contributed to oil-removal. The rhizosphere-bioaugmented soil batches selectively favored Arthrobacter nitroguajacolicus, Caulobacter segnis, and Ensifer adherens. In seawater batches bioaugmented with long-contaminated soil, the predominant oil-removing bacterium was the marine species Marinobacter hydrocarbonoclasticus. In soil batches on the other hand, the autochthonous inhabitants of the long-contaminated soil, Pseudomonas and Massilia species were established and contributed to oil removal. It was concluded that the use of rhizospheric bacteria for inoculating seawater and desert soil and of bacteria in long-contaminated soil for inoculating desert soil follows the concept of "autochthonous bioaugmentation." Inoculating seawater with bacteria in long-contaminated soil, on the other hand, merits the designation "allochthonous bioaugmentation."

  15. Direct Detection of Viable Bacteria, Molds, and Yeasts by Reverse Transcriptase PCR in Contaminated Milk Samples after Heat Treatment

    PubMed Central

    Vaitilingom, Marc; Gendre, Francois; Brignon, Pierre

    1998-01-01

    A fast, sensitive, and target contaminant-modulable method was developed to detect viable bacteria, molds, and yeasts after heat treatment. By reverse transcriptase PCR with elongation factor gene (EF-Tu or EF-1α)-specific primers, the detection level was 10 cells ml of milk−1. The simplicity and rapidity (4 h) of the procedure suggests that this method may be easily transposable to other foods and other contaminants. PMID:9501455

  16. Small sample properties of an adaptive filter with application to low volume statistical process control

    SciTech Connect

    Crowder, S.V.; Eshleman, L.

    1998-08-01

    In many manufacturing environments such as the nuclear weapons complex, emphasis has shifted from the regular production and delivery of large orders to infrequent small orders. However, the challenge to maintain the same high quality and reliability standards white building much smaller lot sizes remains. To meet this challenge, specific areas need more attention, including fast and on-target process start-up, low volume statistical process control, process characterization with small experiments, and estimating reliability given few actual performance tests of the product. In this paper the authors address the issue of low volume statistical process control. They investigate an adaptive filtering approach to process monitoring with a relatively short time series of autocorrelated data. The emphasis is on estimation and minimization of mean squared error rather than the traditional hypothesis testing and run length analyses associated with process control charting. The authors develop an adaptive filtering technique that assumes initial process parameters are unknown, and updates the parameters as more data become available. Using simulation techniques, they study the data requirements (the length of a time series of autocorrelated data) necessary to adequately estimate process parameters. They show that far fewer data values are needed than is typically recommended for process control applications. And they demonstrate the techniques with a case study from the nuclear weapons manufacturing complex.

  17. Small Sample Properties of an Adaptive Filter with Application to Low Volume Statistical Process Control

    SciTech Connect

    CROWDER, STEPHEN V.

    1999-09-01

    In many manufacturing environments such as the nuclear weapons complex, emphasis has shifted from the regular production and delivery of large orders to infrequent small orders. However, the challenge to maintain the same high quality and reliability standards while building much smaller lot sizes remains. To meet this challenge, specific areas need more attention, including fast and on-target process start-up, low volume statistical process control, process characterization with small experiments, and estimating reliability given few actual performance tests of the product. In this paper we address the issue of low volume statistical process control. We investigate an adaptive filtering approach to process monitoring with a relatively short time series of autocorrelated data. The emphasis is on estimation and minimization of mean squared error rather than the traditional hypothesis testing and run length analyses associated with process control charting. We develop an adaptive filtering technique that assumes initial process parameters are unknown, and updates the parameters as more data become available. Using simulation techniques, we study the data requirements (the length of a time series of autocorrelated data) necessary to adequately estimate process parameters. We show that far fewer data values are needed than is typically recommended for process control applications. We also demonstrate the techniques with a case study from the nuclear weapons manufacturing complex.

  18. Preliminary survey of antibiotic-resistant fecal indicator bacteria and pathogenic Escherichia coli from river-water samples collected in Oakland County, Michigan, 2003

    USGS Publications Warehouse

    Fogarty, Lisa R.; Duris, Joseph W.; Aichele, Stephen S.

    2005-01-01

    A preliminary study was done in Oakland County, Michigan, to determine the concentration of fecal indicator bacteria (fecal coliform bacteria and enterococci), antibiotic resistance patterns of these two groups, and the presence of potentially pathogenic Escherichia coli (E. coli). For selected sites, specific members of these groups [E. coli, Enterococcus faecium (E. faecium) and Enterococcus faecalis (E. faecalis)] were isolated and tested for levels of resistance to specific antibiotics used to treat human infections by pathogens in these groups and for their potential to transfer these resistances. In addition, water samples from all sites were tested for indicators of potentially pathogenic E. coli by three assays: a growth-based assay for sorbitol-negative E. coli, an immunological assay for E. coli O157, and a molecular assay for three virulence and two serotype genes. Samples were also collected from two non-urbanized sites outside of Oakland County. Results from the urbanized Oakland County area were compared to those from these two non-urbanized sites. Fecal indicator bacteria concentrations exceeded State of Michigan recreational water-quality standards and (or) recommended U.S. Environmental Protection Agency (USEPA) standards in samples from all but two Oakland County sites. Multiple-antibiotic-resistant fecal coliform bacteria were found at all sites, including two reference sites from outside the county. Two sites (Stony Creek and Paint Creek) yielded fecal coliform isolates resistant to all tested antibiotics. Patterns indicative of extended-spectrum-β-lactamase (ESBL)- producing fecal coliform bacteria were found at eight sites in Oakland County and E. coli resistant to clinically significant antibiotics were recovered from the River Rouge, Clinton River, and Paint Creek. Vancomycin-resistant presumptive enterococci were found at six sites in Oakland County and were not found at the reference sites. Evidence of acquired antibiotic resistances was

  19. A tortoise-hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria.

    PubMed

    Nahum, Joshua R; Godfrey-Smith, Peter; Harding, Brittany N; Marcus, Joseph H; Carlson-Stevermer, Jared; Kerr, Benjamin

    2015-06-16

    In the context of Wright's adaptive landscape, genetic epistasis can yield a multipeaked or "rugged" topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to fix rapidly on one, which may not be the highest peak. In a spatially structured population, on the other hand, beneficial mutations take longer to spread. This slowdown allows distant parts of the population to explore the landscape semiindependently. Such a population can simultaneously discover multiple peaks, and the genotype at the highest discovered peak is expected to dominate eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the fable of the tortoise and the hare, the structured population (tortoise) starts relatively slow but eventually surpasses the unstructured population (hare) in average fitness. In contrast, on single-peak landscapes that lack epistasis, all uphill paths converge. Given such "smooth" topography, breadth of search is devalued and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the tortoise-hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we explore average fitness in metapopulations of Escherichia coli. Consistent with a rugged landscape topography, we find a tortoise-hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright's shifting balance process.

  20. The influence of incubation time, sample preparation and exposure to oxygen on the quality of the MALDI-TOF MS spectrum of anaerobic bacteria.

    PubMed

    Veloo, A C M; Elgersma, P E; Friedrich, A W; Nagy, E; van Winkelhoff, A J

    2014-12-01

    With matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), bacteria can be identified quickly and reliably. This accounts especially for anaerobic bacteria. Because growth rate and oxygen sensitivity differ among anaerobic bacteria, we aimed to study the influence of incubation time, exposure to oxygen and sample preparation on the quality of the spectrum using the Bruker system. Also, reproducibility and inter-examiner variability were determined. Twenty-six anaerobic species, representing 17 genera, were selected based on gram-stain characteristics, growth rate and colony morphology. Inter-examiner variation showed that experience in the preparation of the targets can be a significant variable. The influence of incubation time was determined between 24 and 96 h of incubation. Reliable species identification was obtained after 48 h of incubation for gram-negative anaerobes and after 72 h for gram-positive anaerobes. Exposure of the cultures to oxygen did not influence the results of the MALDI-TOF MS identifications of all tested gram-positive species. Fusobacterium necrophorum and Prevotella intermedia could not be identified after >24 h and 48 h of exposure to oxygen, respectively. Other tested gram-negative bacteria could be identified after 48 h of exposure to oxygen. Most of the tested species could be identified using the direct spotting method. Bifidobacterium longum and Finegoldia magna needed on-target extraction with 70% formic acid in order to obtain reliable species identification and Peptoniphilus ivorii a full extraction. Spectrum quality was influenced by the amount of bacteria spotted on the target, the homogeneity of the smear and the experience of the examiner.

  1. Formation of histamine and biogenic amines in cold-smoked tuna: an investigation of psychrotolerant bacteria from samples implicated in cases of histamine fish poisoning.

    PubMed

    Emborg, Jette; Dalgaard, Paw

    2006-04-01

    Two outbreaks and a single case of histamine fish poisoning associated with cold-smoked tuna (CST) were reported in Denmark during 2004. The bacteria most likely responsible for histamine formation in CST implicated in histamine fish poisoning was identified for the first time in this study. Product characteristics and profiles of biogenic amines in the implicated products were also recorded. In the single poisoning case, psychrotolerant Morganella morganii-like bacteria most likely was responsible for the histamine production in CST with 2.2% +/- 0.6% NaCl in the water phase (WPS). In outbreak 1, Photobacterium phosphoreum most likely formed the histamine in CST with 1.3% +/- 0.1% WPS. In outbreak 2, which involved 10 persons, the bacteria responsible for histamine formation could not be determined. The measured concentrations of WPS were very low compared with those of randomly collected commercial samples of CST and cold-smoked blue marlin (4.1 to 12.7% WPS). Challenge tests at 5 degrees C with psychrotolerant M. morganii and P. phosphoreum in CST with 4.4% WPS revealed growth and toxic histamine formation by the psychrotolerant M. morganii-like bacteria but not by P. phosphoreum. In a storage trial with naturally contaminated CST containing 6.9% WPS, lactic acid bacteria dominated the microbiota, and no significant histamine formation was observed during the shelf life of about 40 days at 5 degrees C and of about 16 days at 10 degrees C. To prevent toxic histamine formation, CST should be produced with >5% WPS and distributed with a declared 5 degrees C shelf life of 3 to 4 weeks or less.

  2. Ribosomal PCR and DNA sequencing for detection and identification of bacteria: experience from 6 years of routine analyses of patient samples.

    PubMed

    Jensen, Kristine Helander; Dargis, Rimtas; Christensen, Jens Jørgen; Kemp, Michael

    2014-03-01

    The use of broad range PCR and DNA sequencing of bacterial 16S ribosomal RNA genes for routine diagnostics of bacterial infections was evaluated. Here, the results from more than 2600 analyses during a 6-year period (2003-2009) are presented. Almost half of the samples were from joints and bones, and the second most frequent origin of samples was from the central nervous system. Overall, 26% of all samples were positive for bacterial DNA and bacterial identification was obtained in 80% of the PCR-positive samples by subsequent DNA sequencing. Ambiguous species identification was noticed among non-haemolytic streptococci, especially within the mitis group. The data show that ribosomal PCR with subsequent DNA sequencing of the PCR product is a most valuable supplement to culture for identifying bacterial agents of both acute and prolonged infections. However, some bacteria, including non-haemolytic streptococci, may not be precisely identified.

  3. Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria.

    PubMed

    Gelderman, Grant; Sivakumar, Anusha; Lipp, Sarah; Contreras, Lydia

    2015-02-01

    sRNAs play a significant role in controlling and regulating cellular metabolism. One of the more interesting aspects of certain sRNAs is their ability to make global changes in the cell by interacting with regulatory proteins. In this work, we demonstrate the use of an in vivo Tri-molecular Fluorescence Complementation assay to detect and visualize the central regulatory sRNA-protein interaction of the Carbon Storage Regulatory system in E. coli. The Carbon Storage Regulator consists primarily of an RNA binding protein, CsrA, that alters the activity of mRNA targets and of an sRNA, CsrB, that modulates the activity of CsrA. We describe the construction of a fluorescence complementation system that detects the interactions between CsrB and CsrA. Additionally, we demonstrate that the intensity of the fluorescence of this system is able to detect changes in the affinity of the CsrB-CsrA interaction, as caused by mutations in the protein sequence of CsrA. While previous methods have adopted this technique to study mRNA or RNA localization, this is the first attempt to use this technique to study the sRNA-protein interaction directly in bacteria. This method presents a potentially powerful tool to study complex bacterial RNA protein interactions in vivo.

  4. A tortoise–hare pattern seen in adapting structured and unstructured populations suggests a rugged fitness landscape in bacteria

    PubMed Central

    Nahum, Joshua R.; Godfrey-Smith, Peter; Harding, Brittany N.; Marcus, Joseph H.; Carlson-Stevermer, Jared; Kerr, Benjamin

    2015-01-01

    In the context of Wright’s adaptive landscape, genetic epistasis can yield a multipeaked or “rugged” topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to fix rapidly on one, which may not be the highest peak. In a spatially structured population, on the other hand, beneficial mutations take longer to spread. This slowdown allows distant parts of the population to explore the landscape semiindependently. Such a population can simultaneously discover multiple peaks, and the genotype at the highest discovered peak is expected to dominate eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the fable of the tortoise and the hare, the structured population (tortoise) starts relatively slow but eventually surpasses the unstructured population (hare) in average fitness. In contrast, on single-peak landscapes that lack epistasis, all uphill paths converge. Given such “smooth” topography, breadth of search is devalued and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the tortoise–hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we explore average fitness in metapopulations of Escherichia coli. Consistent with a rugged landscape topography, we find a tortoise–hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright’s shifting balance process. PMID:25964348

  5. Adaptation of Cryo-Sectioning for IEM Labeling of Asymmetric Samples: A Study Using Caenorhabditis elegans.

    PubMed

    Nicolle, Ophélie; Burel, Agnès; Griffiths, Gareth; Michaux, Grégoire; Kolotuev, Irina

    2015-08-01

    Cryo-sectioning procedures, initially developed by Tokuyasu, have been successfully improved for tissues and cultured cells, enabling efficient protein localization on the ultrastructural level. Without a standard procedure applicable to any sample, currently existing protocols must be individually modified for each model organism or asymmetric sample. Here, we describe our method that enables reproducible cryo-sectioning of Caenorhabditis elegans larvae/adults and embryos. We have established a chemical-fixation procedure in which flat embedding considerably simplifies manipulation and lateral orientation of larvae or adults. To bypass the limitations of chemical fixation, we have improved the hybrid cryo-immobilization-rehydration technique and reduced the overall time required to complete this procedure. Using our procedures, precise cryo-sectioning orientation can be combined with good ultrastructural preservation and efficient immuno-electron microscopy protein localization. Also, GFP fluorescence can be efficiently preserved, permitting a direct correlation of the fluorescent signal and its subcellular localization. Although developed for C. elegans samples, our method addresses the challenge of working with small asymmetric samples in general, and thus could be used to improve the efficiency of immuno-electron localization in other model organisms.

  6. Reliability and Validity of the Spanish Adaptation of EOSS, Comparing Normal and Clinical Samples

    ERIC Educational Resources Information Center

    Valero-Aguayo, Luis; Ferro-Garcia, Rafael; Lopez-Bermudez, Miguel Angel; de Huralde, Ma. Angeles Selva-Lopez

    2012-01-01

    The Experiencing of Self Scale (EOSS) was created for the evaluation of Functional Analytic Psychotherapy (Kohlenberg & Tsai, 1991, 2001, 2008) in relation to the concept of the experience of personal self as socially and verbally constructed. This paper presents a reliability and validity study of the EOSS with a Spanish sample (582 participants,…

  7. Thriving while engaging in risk? Examining trajectories of adaptive functioning, delinquency, and substance use in a nationally representative sample of U.S. adolescents.

    PubMed

    Warren, Michael T; Wray-Lake, Laura; Rote, Wendy M; Shubert, Jennifer

    2016-02-01

    Recent advances in positive youth development theory and research explicate complex associations between adaptive functioning and risk behavior, acknowledging that high levels of both co-occur in the lives of some adolescents. However, evidence on nuanced overlapping developmental trajectories of adaptive functioning and risk has been limited to 1 sample of youth and a single conceptualization of adaptive functioning. We build on prior work by utilizing a nationally representative sample of U.S. adolescents (N = 1,665) followed from 7th grade until after high school and using a measure of adaptive functioning that was validated in a secondary sample of older adolescents (N = 93). In using dual trajectory growth mixture modeling to investigate links between developmental trajectories of adaptive functioning and delinquency and substance use, respectively, results provided evidence of heterogeneity in the overlap between adaptive functioning and risk trajectories. Males were more likely to be in the highest adaptive functioning group as well as the most at-risk delinquency class. The magnitude of negative associations between adaptive functioning and both risk behaviors decreased at Wave 3, indicating a decoupling of adaptive functioning and risk as youth aged. These findings converge in underscoring the need to generate a cohesive theory that specifies factors that promote adaptive functioning and risk in concert.

  8. Acquiring Peak Samples from Phytoplankton Thin Layers and Intermediate Nepheloid Layers by an Autonomous Underwater Vehicle with Adaptive Triggering

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; McEwen, R.; Ryan, J. P.; Bellingham, J. G.; Harvey, J.; Vrijenhoek, R.

    2010-12-01

    Phytoplankton thin layers (PTLs) affect many fundamental aspects of coastal ocean ecology including primary productivity, development of harmful algal blooms (HABs) and the survival and growth of zooplankton and fish larvae. Intermediate nepheloid layers (INLs) that contain suspended particulate matter transported from the bottom boundary layer of continental shelves and slopes also affect biogeochemistry and ecology of ocean margins. To better understand the impacts of these types of layers, we have developed an adaptive sampling method for an autonomous underwater vehicle (AUV) to detect a layer (adjusting detection parameters in situ), acquire water samples from peaks in the layer, and acquire control samples outside the layer. We have used the method in a number of field experiments with the AUV Dorado, which is equipped with ten water samplers (called "gulpers"). In real time, the algorithm tracks background levels of fluorescence and optical backscatter and the peaks' baseline to ensure that detection is tuned to the ambient conditions. The algorithm cross-checks fluorescence and backscatter signals to differentiate PTLs from INLs. To capture peak water samples with minimal delay, the algorithm exploits the AUV's sawtooth (i.e., yo-yo) trajectory: the vehicle crosses the detected layer twice in one yo-yo cycle. At the first crossing, it detects the layer's peak and saves its signal height. Sampling is triggered at the second crossing when the signal reaches the saved peak height plus meeting additional timing and depth conditions. The algorithm is also capable of triggering gulpers to acquire control samples outside the layer for comparison with ambient water. The sequence of peak and control samples can be set based on need. In recent AUV Dorado missions, the algorithm triggered the gulpers to acquire peak and control samples from INLs and PTLs in Monterey Bay. Zooplankton analysis of some peak samples showed very high concentrations of mussel and barnacle

  9. Exploration and characterization of agriculturally and industrially important haloalkaliphilic bacteria from environmental samples of hypersaline Sambhar lake, India.

    PubMed

    Sahay, Harmesh; Mahfooz, Sahil; Singh, Atul K; Singh, Surendra; Kaushik, Rajeev; Saxena, Anil K; Arora, Dilip K

    2012-11-01

    Screening of bacteria from Sambhar lake, an extreme hypersaline environment of India, led to the isolation of 93 haloalkaliphilic bacteria growing optimally in media with 2-25 % salt and 6-12 pH. Based on 16S rRNA gene sequences, 93 isolates were further categorized into 32 groups, with each group representing a different taxa belonging to 3 phyla (Firmicutes, Proteobacteria and Actinobacteria). Majority of the isolates (53.12 %) showed similarity with phylum Firmicutes which was followed by Proteobacteria (40.63 %) and Actinobacteria (6.25 %). The isolates belonging to 32 representative groups were further evaluated for the production of extracellular enzymes viz. amylase, cellulase, protease and xylanase, plant growth promoting attributes and BIOLOG™ substrate usage. Among all the isolates, xylanase producing isolates were in maximum (68 %) as compared to protease (56 %), cellulase (40 %), and amylase (37 %) producing strains. Similarly, among plant growth promoting activities, ammonia producing isolates were highest (56 %) when compared to those producing ACC deaminase (53 %), IAA (50 %), hydrogen cyanide (28 %), siderophore (21 %) and solubilizing P (34 %). Isolates showing enzymatic and PGP activities could be further utilized for promoting plant growth in saline affected area. PMID:22828794

  10. Social Daydreaming and Adjustment: An Experience-Sampling Study of Socio-Emotional Adaptation During a Life Transition.

    PubMed

    Poerio, Giulia L; Totterdell, Peter; Emerson, Lisa-Marie; Miles, Eleanor

    2016-01-01

    Estimates suggest that up to half of waking life is spent daydreaming; that is, engaged in thought that is independent of, and unrelated to, one's current task. Emerging research indicates that daydreams are predominately social suggesting that daydreams may serve socio-emotional functions. Here we explore the functional role of social daydreaming for socio-emotional adjustment during an important and stressful life transition (the transition to university) using experience-sampling with 103 participants over 28 days. Over time, social daydreams increased in their positive characteristics and positive emotional outcomes; specifically, participants reported that their daydreams made them feel more socially connected and less lonely, and that the content of their daydreams became less fanciful and involved higher quality relationships. These characteristics then predicted less loneliness at the end of the study, which, in turn was associated with greater social adaptation to university. Feelings of connection resulting from social daydreams were also associated with less emotional inertia in participants who reported being less socially adapted to university. Findings indicate that social daydreaming is functional for promoting socio-emotional adjustment to an important life event. We highlight the need to consider the social content of stimulus-independent cognitions, their characteristics, and patterns of change, to specify how social thoughts enable socio-emotional adaptation.

  11. Social Daydreaming and Adjustment: An Experience-Sampling Study of Socio-Emotional Adaptation During a Life Transition

    PubMed Central

    Poerio, Giulia L.; Totterdell, Peter; Emerson, Lisa-Marie; Miles, Eleanor

    2016-01-01

    Estimates suggest that up to half of waking life is spent daydreaming; that is, engaged in thought that is independent of, and unrelated to, one’s current task. Emerging research indicates that daydreams are predominately social suggesting that daydreams may serve socio-emotional functions. Here we explore the functional role of social daydreaming for socio-emotional adjustment during an important and stressful life transition (the transition to university) using experience-sampling with 103 participants over 28 days. Over time, social daydreams increased in their positive characteristics and positive emotional outcomes; specifically, participants reported that their daydreams made them feel more socially connected and less lonely, and that the content of their daydreams became less fanciful and involved higher quality relationships. These characteristics then predicted less loneliness at the end of the study, which, in turn was associated with greater social adaptation to university. Feelings of connection resulting from social daydreams were also associated with less emotional inertia in participants who reported being less socially adapted to university. Findings indicate that social daydreaming is functional for promoting socio-emotional adjustment to an important life event. We highlight the need to consider the social content of stimulus-independent cognitions, their characteristics, and patterns of change, to specify how social thoughts enable socio-emotional adaptation. PMID:26834685

  12. Differential sampling for fast frequency acquisition via adaptive extended least squares algorithm

    NASA Technical Reports Server (NTRS)

    Kumar, Rajendra

    1987-01-01

    This paper presents a differential signal model along with appropriate sampling techinques for least squares estimation of the frequency and frequency derivatives and possibly the phase and amplitude of a sinusoid received in the presence of noise. The proposed algorithm is recursive in mesurements and thus the computational requirement increases only linearly with the number of measurements. The dimension of the state vector in the proposed algorithm does not depend upon the number of measurements and is quite small, typically around four. This is an advantage when compared to previous algorithms wherein the dimension of the state vector increases monotonically with the product of the frequency uncertainty and the observation period. Such a computational simplification may possibly result in some loss of optimality. However, by applying the sampling techniques of the paper such a possible loss in optimality can made small.

  13. The Application of Adaptive Sampling and Analysis Program (ASAP) Techniques to NORM Sites

    SciTech Connect

    Johnson, Robert; Smith, Karen P.; Quinn, John

    1999-10-29

    The results from the Michigan demonstration establish that this type of approach can be very effective for NORM sites. The advantages include (1) greatly reduced per sample analytical costs; (2) a reduced reliance on soil sampling and ex situ gamma spectroscopy analyses; (3) the ability to combine characterization with remediation activities in one fieldwork cycle; (4) improved documentation; and (5) ultimately better remediation, as measured by greater precision in delineating soils that are not in compliance with requirements from soils that are in compliance. In addition, the demonstration showed that the use of real-time technologies, such as the RadInSoil, can facilitate the implementation of a Multi-Agency Radiation Survey and Site Investigation Manual (MARSSIM)-based final status survey program

  14. Intracellular Bacteria in Protozoa

    NASA Astrophysics Data System (ADS)

    Görtz, Hans-Dieter; Brigge, Theo

    Intracellular bacteria in humans are typically detrimental, and such infections are regarded by the patients as accidental and abnormal. In protozoa it seems obvious that many bacteria have coevolved with their hosts and are well adapted to the intracellular way of life. Manifold interactions between hosts and intracellular bacteria are found, and examples of antibacterial resistance of unknown mechanisms are observed. The wide diversity of intracellular bacteria in protozoa has become particularly obvious since they have begun to be classified by molecular techniques. Some of the bacteria are closely related to pathogens; others are responsible for the production of toxins.

  15. Genetic adaptation to elevated carbon dioxide atmospheres by Pseudomonas-like bacteria isolated from rock cod (Sebastes spp. )

    SciTech Connect

    Johnson, A.R.; Ogrydziak, D.M.

    1984-09-01

    The microorganisms on rock cod fillets stored in a modified atmosphere (MA; 80% CO/sub 2/ - 20% air) at 4/sup 0/C for 21 days were isolated. Only Lactobacillus sp. (71 to 87%) and tan-colored Pseudomonas sp.-like isolates (TAN isolates) were found. The TAN isolates grew more slowly in MA than in air at 8/sup 0/C. When TAN isolates were grown in air at 8/sup 0/C, there was an initial decline in viable counts for 10 to 30 h followed by exponential growth. During this exponential growth phase in MA, the growth rates of the TAN isolates from MA-stored fish were significantly greater than those of the TAN isolates from fresh fish. When a TAN isolate from fresh fish was grown under MA for 21 days, it then grew as rapidly under MA as isolates from MA-stored fish. These results suggest that the TAN isolates genetically adapt to high levels of CO/sub 2/. 17 references, 3 figures, 1 table.

  16. The effect of incubation temperature and site of sampling on assessment of the numbers of bacteria on red meat carcasses at commercial abattoirs.

    PubMed

    Roberts, T A; MacFie, H J; Hudson, W R

    1980-12-01

    Several sites on commercial beef, pork and lamb carcasses were sampled at the end of the slaughterline. Total viable counts (TVC) of bacteria were assessed by incubation at 37, 20 and 1 degree C in addition to presumptive coliforms (PC), Enterobacteriaceae (ENT) and faecal streptococci (FS). Statistical analyses showed consistently dirty sites within an abattoir but these sites varied from one abattoir to another. Inter-site differences were unaffected by the incubation temperature of the TVC. Numbers of PC, ENT and FS did not mimic TVC. Empirical sampling plans are proposed to detect the highest count on a carcass by bulking samples from known dirty sites. At the end of the slaughterline TVC 37 degrees C is the most useful bacteriological index. PMID:7462589

  17. Avoidance and activation as keys to depression: adaptation of the Behavioral Activation for Depression Scale in a Spanish sample.

    PubMed

    Barraca, Jorge; Pérez-Alvarez, Marino; Lozano Bleda, José Héctor

    2011-11-01

    In this paper we present the adaptation of the Behavioral Activation for Depression Scale (BADS), developed by Kanter, Mulick, Busch, Berlin, and Martell (2007), in a Spanish sample. The psychometric properties were tested in a sample of 263 participants (124 clinical and 139 non-clinical). The results show that, just as in the original English version, the Spanish BADS is a valid and internally consistent scale. Construct validity was examined by correlation with the BDI-II, AAQ, ATQ, MCQ-30, STAI and EROS. Factor analysis justified the four-dimensions of the original instrument (Activation, Avoidance/Rumination, Work/School Impairment and Social Impairment), although with some differences in the factor loadings of the items. Further considerations about the usefulness of the BADS in the clinical treatment of depressed patients are also suggested.

  18. Adaption of egg and larvae sampling techniques for lake sturgeon and broadcast spawning fishes in a deep river

    USGS Publications Warehouse

    Roseman, E.F.; Boase, J.; Kennedy, G.; Craig, J.; Soper, K.

    2011-01-01

    In this report we describe how we adapted two techniques for sampling lake sturgeon (Acipenser fulvescens) and other fish early life history stages to meet our research needs in the Detroit River, a deep, flowing Great Lakes connecting channel. First, we developed a buoy-less method for sampling fish eggs and spawning activity using egg mats deployed on the river bottom. The buoy-less method allowed us to fish gear in areas frequented by boaters and recreational anglers, thus eliminating surface obstructions that interfered with recreational and boating activities. The buoy-less method also reduced gear loss due to drift when masses of floating aquatic vegetation would accumulate on buoys and lines, increasing the drag on the gear and pulling it downstream. Second, we adapted a D-frame drift net system formerly employed in shallow streams to assess larval lake sturgeon dispersal for use in the deeper (>8m) Detroit River using an anchor and buoy system. ?? 2011 Blackwell Verlag, Berlin.

  19. Assessment of Different Sampling Methods for Measuring and Representing Macular Cone Density Using Flood-Illuminated Adaptive Optics

    PubMed Central

    Feng, Shu; Gale, Michael J.; Fay, Jonathan D.; Faridi, Ambar; Titus, Hope E.; Garg, Anupam K.; Michaels, Keith V.; Erker, Laura R.; Peters, Dawn; Smith, Travis B.; Pennesi, Mark E.

    2015-01-01

    Purpose To describe a standardized flood-illuminated adaptive optics (AO) imaging protocol suitable for the clinical setting and to assess sampling methods for measuring cone density. Methods Cone density was calculated following three measurement protocols: 50 × 50-μm sampling window values every 0.5° along the horizontal and vertical meridians (fixed-interval method), the mean density of expanding 0.5°-wide arcuate areas in the nasal, temporal, superior, and inferior quadrants (arcuate mean method), and the peak cone density of a 50 × 50-μm sampling window within expanding arcuate areas near the meridian (peak density method). Repeated imaging was performed in nine subjects to determine intersession repeatability of cone density. Results Cone density montages could be created for 67 of the 74 subjects. Image quality was determined to be adequate for automated cone counting for 35 (52%) of the 67 subjects. We found that cone density varied with different sampling methods and regions tested. In the nasal and temporal quadrants, peak density most closely resembled histological data, whereas the arcuate mean and fixed-interval methods tended to underestimate the density compared with histological data. However, in the inferior and superior quadrants, arcuate mean and fixed-interval methods most closely matched histological data, whereas the peak density method overestimated cone density compared with histological data. Intersession repeatability testing showed that repeatability was greatest when sampling by arcuate mean and lowest when sampling by fixed interval. Conclusions We show that different methods of sampling can significantly affect cone density measurements. Therefore, care must be taken when interpreting cone density results, even in a normal population. PMID:26325414

  20. Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples.

    PubMed Central

    Siering, P L; Ghiorse, W C

    1997-01-01

    Comparative sequence analysis of the 16S rRNA genes from several Leptothrix and Sphaerotilus strains led to the design of an oligonucleotide probe (PS-1) based on a sequence within the hypervariable region 1 specific for four Leptothrix strains and for one of the four Sphaerotilus natans strains examined. Another probe (PSP-6) was based on a sequence within the hypervariable region 2. PSP-6 was specific for one of the two evolutionary lineages previously described for Leptothrix spp. (P. L. Siering and W. C. Ghiorse, Int. J. Syst. Bacteriol. 46:173-182, 1996). Fluorescein-labeled oligonucleotide probes were synthesized, and their specificity for fluorescence in situ hybridization identification was confirmed by a laser scanning microscopy technique (W. C. Ghiorse, D. N. Miller, R. L. Sandoli, and P. L. Siering, Microsc. Res. Tech. 33:73-86, 1996) to compare whole-cell hybridizations of closely related bacteria. Probe specificity was also tested in dot blot against total RNA isolated from four Leptothrix strains, four Sphaerotilus strains, and 15 other members of the class Proteobacteria. When the probes were tested on samples from the Sapsucker Woods wetland habitat where Leptothrix spp. are thought to play a role in manganese and iron oxidation, positive signals were obtained from several sheathed filamentous bacteria including some that were morphologically similar to previously isolated strains of "Leptothrix discophora." Other unknown filamentous sheathed bacteria also gave strong positive signals. This work provides a foundation for future studies correlating the presence of members of the Leptothrix-Sphaerotilus group of sheathed bacteria with manganese and iron oxidation activity in habitats where biological iron and manganese oxidation are important environmental processes. PMID:9023942

  1. Development and application of 16S rRNA-targeted probes for detection of iron- and manganese-oxidizing sheathed bacteria in environmental samples.

    PubMed

    Siering, P L; Ghiorse, W C

    1997-02-01

    Comparative sequence analysis of the 16S rRNA genes from several Leptothrix and Sphaerotilus strains led to the design of an oligonucleotide probe (PS-1) based on a sequence within the hypervariable region 1 specific for four Leptothrix strains and for one of the four Sphaerotilus natans strains examined. Another probe (PSP-6) was based on a sequence within the hypervariable region 2. PSP-6 was specific for one of the two evolutionary lineages previously described for Leptothrix spp. (P. L. Siering and W. C. Ghiorse, Int. J. Syst. Bacteriol. 46:173-182, 1996). Fluorescein-labeled oligonucleotide probes were synthesized, and their specificity for fluorescence in situ hybridization identification was confirmed by a laser scanning microscopy technique (W. C. Ghiorse, D. N. Miller, R. L. Sandoli, and P. L. Siering, Microsc. Res. Tech. 33:73-86, 1996) to compare whole-cell hybridizations of closely related bacteria. Probe specificity was also tested in dot blot against total RNA isolated from four Leptothrix strains, four Sphaerotilus strains, and 15 other members of the class Proteobacteria. When the probes were tested on samples from the Sapsucker Woods wetland habitat where Leptothrix spp. are thought to play a role in manganese and iron oxidation, positive signals were obtained from several sheathed filamentous bacteria including some that were morphologically similar to previously isolated strains of "Leptothrix discophora." Other unknown filamentous sheathed bacteria also gave strong positive signals. This work provides a foundation for future studies correlating the presence of members of the Leptothrix-Sphaerotilus group of sheathed bacteria with manganese and iron oxidation activity in habitats where biological iron and manganese oxidation are important environmental processes. PMID:9023942

  2. Evaluation of single and two-stage adaptive sampling designs for estimation of density and abundance of freshwater mussels in a large river

    USGS Publications Warehouse

    Smith, D.R.; Rogala, J.T.; Gray, B.R.; Zigler, S.J.; Newton, T.J.

    2011-01-01

    Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non-adaptive versions of single and two-stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two-stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers.

  3. Adapting hydrological model structure to catchment characteristics: A large-sample experiment

    NASA Astrophysics Data System (ADS)

    Addor, Nans; Clark, Martyn P.; Nijssen, Bart

    2016-04-01

    Current hydrological modeling frameworks do not offer a clear way to systematically investigate the relationship between model complexity and model fidelity. The characterization of this relationship has so far relied on comparisons of different modules within the same model or comparisons of entirely different models. This lack of granularity in the differences between the model constructs makes it difficult to pinpoint model features that contribute to good simulations and means that the number of models or modeling hypotheses evaluated is usually small. Here we use flexible modeling frameworks to comprehensively and systematically compare modeling alternatives across the continuum of model complexity. A key goal is to explore which model structures are most adequate for catchments in different hydroclimatic conditions. Starting from conceptual models based on the Framework for Understanding Structural Errors (FUSE), we progressively increase model complexity by replacing conceptual formulations by physically explicit ones (process complexity) and by refining model spatial resolution (spatial complexity) using the newly developed Structure for Unifying Multiple Modeling Alternatives (SUMMA). To investigate how to best reflect catchment characteristics using model structure, we rely on a recently released data set of 671 catchments in the continuous United States. Instead of running hydrological simulations in every catchment, we use clustering techniques to define catchment clusters, run hydrological simulations for representative members of each cluster, develop hypotheses (e.g., when specific process representations have useful explanatory power) and test these hypotheses using other members of the cluster. We thus refine our catchment clustering based on insights into dominant hydrological processes gained from our modeling approach. With this large-sample experiment, we seek to uncover trade-offs between realism and practicality, and formulate general

  4. Behaviour of lactic acid bacteria populations in Pecorino di Carmasciano cheese samples submitted to environmental conditions prevailing in the gastrointestinal tract: evaluation by means of a polyphasic approach.

    PubMed

    Ricciardi, Annamaria; Blaiotta, Giuseppe; Di Cerbo, Alessandro; Succi, Mariantonietta; Aponte, Maria

    2014-06-01

    The survival of the autochthonous microflora, of samples collected during Pecorino di Carmasciano cheese manufacturing, was evaluated along the passage through a model mimicking the gastro-intestinal tract. The aim was the selection of lactic acid bacteria potentially able to arrive alive and metabolically active to the colon. The dynamics of lactic microbiota, throughout simulated digestion of cheese samples, were evaluated by means of an approach PCR-DGGE-based. Dominant species after cheese digestion could be related to the Lactobacillus plantarum and Lactobacillus casei groups. Sixty-three strains, which survived to simulated gastro-intestinal transit, were further evaluated for technological features and tolerance to human digestion in several experimental conditions, according to routinely used protocols. Bacterial survival appeared to be, more than strain-specific, strongly affected by experimental conditions, i.e. some strains showed an acceptable survival when resuspended in skim milk but not in ewe milk and vice versa. Nevertheless according to data, one gram of fresh Pecorino di Carmasciano cheese may convey to human colon about the same amount of viable LAB of a probiotic drink. Although it cannot be assumed that lactobacilli introduced with Pecorino have beneficial effects on the host, the healthy impact of autochthonous lactic acid bacteria of naturally fermented food has a broad consensus in the current literature. PMID:24742995

  5. [The short version of Critical Care Family Needs Inventory (CCFNI): adaptation and validation for a spanish sample].

    PubMed

    Gómez-Martíinez, S; Arnal, R Ballester; Juliá, B Gil

    2011-01-01

    Relatives play an important role in the disease process of patients admitted to Intensive Care Units (ICU). It is therefore important to know the needs of people close to the patient in order to try to improve their adaption to a situation as difficult as an ICU admission. The aim of this study was the adaptation and validation of the short version of the Critical Care Family Needs Inventory (CCFNI) for a Spanish sample. The inventory was applied to 55 relatives of patients admitted to the ICU of the Hospital General de Castellón. After the removal of three items for different reasons, we performed an Exploratory Factor Analysis with the 11 remaining items to determine the factor structure of the questionnaire. We also made a descriptive analysis of the items, and internal consistency and construct validity were calculated through Cronbach's α and Pearson correlation coefficient respectively. The results of the principal components factor analysis using varimax rotation indicated a four-factor solution. These four factors corresponded to: medical attention to the patient, personal attention to the relatives, communication between the family and the doctor, and perceived improvements in the Unit. The short version of CCFNI showed good internal consistency for both the total scale and factors. The results suggest that the CCFNI is a suitable measure for assessing the different needs presented by the relatives of patients admitted to an Intensive Care Unit, showing adequate psychometric properties.

  6. A New Sampling Strategy for the Detection of Fecal Bacteria Integrated with USEPA Method 1622/1623

    EPA Science Inventory

    USEPA Method 1622/1623 requires the concentration of Cryptosporidium and Giardia from 10 liters of water samples prior to detection. During this process the supernatant is discarded because it is assumed that most protozoa are retained in the filtration and centrifugation steps....

  7. Particle System Based Adaptive Sampling on Spherical Parameter Space to Improve the MDL Method for Construction of Statistical Shape Models

    PubMed Central

    Zhou, Xiangrong; Hirano, Yasushi; Tachibana, Rie; Hara, Takeshi; Kido, Shoji; Fujita, Hiroshi

    2013-01-01

    Minimum description length (MDL) based group-wise registration was a state-of-the-art method to determine the corresponding points of 3D shapes for the construction of statistical shape models (SSMs). However, it suffered from the problem that determined corresponding points did not uniformly spread on original shapes, since corresponding points were obtained by uniformly sampling the aligned shape on the parameterized space of unit sphere. We proposed a particle-system based method to obtain adaptive sampling positions on the unit sphere to resolve this problem. Here, a set of particles was placed on the unit sphere to construct a particle system whose energy was related to the distortions of parameterized meshes. By minimizing this energy, each particle was moved on the unit sphere. When the system became steady, particles were treated as vertices to build a spherical mesh, which was then relaxed to slightly adjust vertices to obtain optimal sampling-positions. We used 47 cases of (left and right) lungs and 50 cases of livers, (left and right) kidneys, and spleens for evaluations. Experiments showed that the proposed method was able to resolve the problem of the original MDL method, and the proposed method performed better in the generalization and specificity tests. PMID:23861721

  8. Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples.

    PubMed

    dos Santos Furtado, A L; Casper, P

    2000-08-01

    The efficiency of different treatments was tested to extract bacterial cells from freshwater sediment samples. The influence of sonication, density gradient centrifugation, fixation by formalin and centrifugation speed on bacterial recovery was investigated. The method developed by Smith and Azam [Mar. Microb. Food Webs 6 (1992) 107] to measure microbial activity on bacterioplankton (3H-leucine incorporation), was also evaluated in sediment samples. After 1 min of sonication bacterial abundance was reduced by about 47% in diluted sediments with tetrasodium pyrophosphate. With the addition of Percoll after sonication, bacterial counts were not significantly different (P<0.05). Fixation by formalin increased bacterial counts using sonication. However, higher bacterial abundance was estimated in non-sonicated samples. Bacterial abundance in samples centrifuged at 7000xg with and without Percoll was not significantly different (P<0.05). Highest bacterial abundance was obtained after centrifugation at low speed (750xg). Bacterial abundance decreased with higher centrifugation speed (750, 1500 and 3000xg), the difference, however, was not significant. Bacterial production ranged from 0.10 microg C cm(-3) d(-1) in autoclaved sediment to 0. 27 microg C cm(-3) d(-1) in untreated sediment. The radioactivity measured in controls of both untreated and autoclaved sediment was high (70 and 91%, respectively), indicating a high level of leucine adsorption in sediment particles. In contrast, radioactivity in control samples previously centrifuged was markedly lower (6%). Despite the high values of radioactivity in the controls, bacterial production in untreated sediment was significantly higher than in centrifuged sediment (P<0.05).

  9. Highly sensitive direct detection and quantification of Burkholderia pseudomallei bacteria in environmental soil samples by using real-time PCR.

    PubMed

    Trung, Trinh Thanh; Hetzer, Adrian; Göhler, André; Topfstedt, Eylin; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Peacock, Sharon J; Steinmetz, Ivo

    2011-09-01

    The soil bacterium and potential biothreat agent Burkholderia pseudomallei causes the infectious disease melioidosis, which is naturally acquired through environmental contact with the bacterium. Environmental detection of B. pseudomallei represents the basis for the development of a geographical risk map for humans and livestock. The aim of the present study was to develop a highly sensitive, culture-independent, DNA-based method that allows direct quantification of B. pseudomallei from soil. We established a protocol for B. pseudomallei soil DNA isolation, purification, and quantification by quantitative PCR (qPCR) targeting a type three secretion system 1 single-copy gene. This assay was validated using 40 soil samples from Northeast Thailand that underwent parallel bacteriological culture. All 26 samples that were B. pseudomallei positive by direct culture were B. pseudomallei qPCR positive, with a median of 1.84 × 10(4) genome equivalents (range, 3.65 × 10(2) to 7.85 × 10(5)) per gram of soil, assuming complete recovery of DNA. This was 10.6-fold (geometric mean; range, 1.1- to 151.3-fold) higher than the bacterial count defined by direct culture. Moreover, the qPCR detected B. pseudomallei in seven samples (median, 36.9 genome equivalents per g of soil; range, 9.4 to 47.3) which were negative by direct culture. These seven positive results were reproduced using a nested PCR targeting a second, independent B. pseudomallei-specific sequence. Two samples were direct culture and qPCR negative but nested PCR positive. Five samples were negative by both PCR methods and culture. In conclusion, our PCR-based system provides a highly specific and sensitive tool for the quantitative environmental surveillance of B. pseudomallei.

  10. Bacteria Counter

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Science Applications, Inc.'s ATP Photometer makes a rapid and accurate count of the bacteria in a body fluid sample. Instrument provides information on the presence and quantity of bacteria by measuring the amount of light emitted by the reaction between two substances. Substances are ATP adenosine triphosphate and luciferase. The reactants are applied to a human body sample and the ATP Photometer observes the intensity of the light emitted displaying its findings in a numerical output. Total time lapse is usually less than 10 minutes, which represents a significant time savings in comparison of other techniques. Other applications are measuring organisms in fresh and ocean waters, determining bacterial contamination of foodstuffs, biological process control in the beverage industry, and in assay of activated sewage sludge.

  11. Modular microfluidic system for biological sample preparation

    DOEpatents

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.

  12. Adaptation of a speciation sampling cartridge for measuring ammonia flux from cattle feedlots using relaxed eddy accumulation

    NASA Astrophysics Data System (ADS)

    Baum, K. A.; Ham, J. M.

    Improved measurements of ammonia losses from cattle feedlots are needed to quantify the national NH 3 emissions inventory and evaluate management techniques for reducing emissions. Speciation cartridges composed of glass honeycomb denuders and filter packs were adapted to measure gaseous NH 3 and aerosol NH 4+ fluxes using relaxed eddy accumulation (REA). Laboratory testing showed that a cartridge equipped with four honeycomb denuders had a total capture capacity of 1800 μg of NH 3. In the field, a pair of cartridges was deployed adjacent to a sonic anemometer and an open-path gas analyzer on a mobile tower. High-speed valves were attached to the inlets of the cartridges and controlled by a datalogger so that up- and down-moving eddies were independently sampled based on direction of the vertical wind speed and a user-defined deadband. Air flowed continuously through the cartridges even when not sampling by means of a recirculating air handling system. Eddy covariance measurement of CO 2 and H 2O, as measured by the sonic and open-path gas analyzer, were used to determine the relaxation factor needed to compute REA-based fluxes. The REA system was field tested at the Beef Research Unit at Kansas State University in the summer and fall of 2007. Daytime NH 3 emissions ranged between 68 and 127 μg m -2 s -1; fluxes tended to follow a diurnal pattern correlated with latent heat flux. Daily fluxes of NH 3 were between 2.5 and 4.7 g m -2 d -1 and on average represented 38% of fed nitrogen. Aerosol NH 4+ fluxes were negligible compared with NH 3 emissions. An REA system designed around the high-capacity speciation cartridges can be used to measure NH 3 fluxes from cattle feedlots and other strong sources. The system could be adapted to measure fluxes of other gases and aerosols.

  13. Electrochemical Genosensor To Detect Pathogenic Bacteria (Escherichia coli O157:H7) As Applied in Real Food Samples (Fresh Beef) To Improve Food Safety and Quality Control.

    PubMed

    Abdalhai, Mandour H; Fernandes, António Maximiano; Xia, Xiaofeng; Musa, Abubakr; Ji, Jian; Sun, Xiulan

    2015-05-27

    The electrochemical genosensor is one of the most promising methods for the rapid and reliable detection of pathogenic bacteria. In a previous work, we performed an efficient electrochemical genosensor detection of Staphylococcus aureus by using lead sulfide nanoparticles (PbSNPs). As a continuation of this study, in the present work, the electrochemical genosensor was used to detect Escherichia coli O157:H7. The primer and probes were designed using NCBI database and Sigma-Aldrich primer and probe software. The capture and signalizing probes were modified by thiol (SH) and amine (NH2), respectively. Then, the signalizing probe was connected using cadmium sulfide nanoparticles (CdSNPs), which showed well-defined peaks after electrochemical detection. The genosensor was prepared by immobilization of complementary DNA on the gold electrode surface, which hybridizes with a specific fragment gene from pathogenic to make a sandwich structure. The conductivity and sensitivity of the sensor were increased by using multiwalled carbon nanotubes (MWCNT) that had been modified using chitosan deposited as a thin layer on the glass carbon electrode (GCE) surface, followed by a deposit of bismuth. The peak currents of E. coli O157:H7 correlated in a linear fashion with the concentration of tDNA. The detection limit was 1.97 × 10(-14) M, and the correlation coefficient was 0.989. A poorly defined current response was observed as the negative control and baseline. Our results showed high sensitivity and selectivity of the electrochemical DNA biosensor to the pathogenic bacteria E. coli O157:H7. The biosensor was also used to evaluate the detection of pathogen in real beef samples contaminated artificially. Compared with other electrochemical DNA biosensors, we conclude that this genosensor provides for very efficient detection of pathogenic bacteria. Therefore, this method may have potential application in food safety and related fields.

  14. Electrochemical Genosensor To Detect Pathogenic Bacteria (Escherichia coli O157:H7) As Applied in Real Food Samples (Fresh Beef) To Improve Food Safety and Quality Control.

    PubMed

    Abdalhai, Mandour H; Fernandes, António Maximiano; Xia, Xiaofeng; Musa, Abubakr; Ji, Jian; Sun, Xiulan

    2015-05-27

    The electrochemical genosensor is one of the most promising methods for the rapid and reliable detection of pathogenic bacteria. In a previous work, we performed an efficient electrochemical genosensor detection of Staphylococcus aureus by using lead sulfide nanoparticles (PbSNPs). As a continuation of this study, in the present work, the electrochemical genosensor was used to detect Escherichia coli O157:H7. The primer and probes were designed using NCBI database and Sigma-Aldrich primer and probe software. The capture and signalizing probes were modified by thiol (SH) and amine (NH2), respectively. Then, the signalizing probe was connected using cadmium sulfide nanoparticles (CdSNPs), which showed well-defined peaks after electrochemical detection. The genosensor was prepared by immobilization of complementary DNA on the gold electrode surface, which hybridizes with a specific fragment gene from pathogenic to make a sandwich structure. The conductivity and sensitivity of the sensor were increased by using multiwalled carbon nanotubes (MWCNT) that had been modified using chitosan deposited as a thin layer on the glass carbon electrode (GCE) surface, followed by a deposit of bismuth. The peak currents of E. coli O157:H7 correlated in a linear fashion with the concentration of tDNA. The detection limit was 1.97 × 10(-14) M, and the correlation coefficient was 0.989. A poorly defined current response was observed as the negative control and baseline. Our results showed high sensitivity and selectivity of the electrochemical DNA biosensor to the pathogenic bacteria E. coli O157:H7. The biosensor was also used to evaluate the detection of pathogen in real beef samples contaminated artificially. Compared with other electrochemical DNA biosensors, we conclude that this genosensor provides for very efficient detection of pathogenic bacteria. Therefore, this method may have potential application in food safety and related fields. PMID:25965077

  15. Flowthrough Bacteria-Detection System

    NASA Technical Reports Server (NTRS)

    Grana, D. C.; Wilkins, J. R.

    1983-01-01

    Online system allows repetitive cycling of sample intake, bacteria counting and sterilization. System measures bacteria count by using sample/incubate/ measure cycle. Steps in cycle are on/off operations to cycle automated easily.

  16. A novel challenge test incorporating irradiation (60Co) of compost sub-samples to validate thermal lethality towards pathogenic bacteria.

    PubMed

    Moore, John E; Watabe, Miyuki; Stewart, Andrew; Cherie Millar, B; Rao, Juluri R

    2009-01-01

    Maturing compost heaps normally attaining temperatures ranging from 55 to 65 degrees C is generally regarded to conform to recommended biological risks and sanitation standards for composts stipulated by either EU or US-EPA. Composted products derived from animal sources are further required by EU biohazard safety regulatory legislation that such composts either attain 70 degrees C for over 3h during maturation or via treatment at 70 degrees C for 1h before being considered for dispensation on land. The setting of the upper limit of thermal lethality at 70 degrees C/1h for achieving biosecurity of the animal waste composted products (e.g. pelleted fertilizer formulations) is not properly substantiated by specific validation tests, comprising a 'wipe-out' step (usually via autoclaving) followed by inoculation of a prescribed bacterium, exposure to 70 degrees C/1h and the lethality determined. Pelleted formulations of composts are not amenable for wet methods (autoclaving) for wipe-out sterilization step as this is detrimental to the pellet and compromises sample integrity. This study describes a laboratory method involving the employment of ((60)Co) irradiation 'wipe-out' step to: (a) compost sub-samples drawn from compost formulation heaps and (b) pelleted products derived from composted animal products while determining the thermal lethality of a given time/temperature (70 degrees C/1h) treatment process and by challenging the irradiated sample (not just with one bacterium but), out with 10 potential food-poisoning organisms from the bacterial genera (Campylobacter, Escherichia, Listeria, Salmonella, Yersinia) frequently detected in pig and poultry farm wastes. This challenge test on compost sub-samples can be a useful intervention ploy for 'inspection and validation' technique for composters during the compost maturity process, whose attainment of temperatures of 55-65 degrees C is presumed sufficient for attainment of sanitation. Stringent measures are further

  17. Exploring equivalence domain in nonlinear inverse problems using Covariance Matrix Adaption Evolution Strategy (CMAES) and random sampling

    NASA Astrophysics Data System (ADS)

    Grayver, Alexander V.; Kuvshinov, Alexey V.

    2016-05-01

    This paper presents a methodology to sample equivalence domain (ED) in nonlinear partial differential equation (PDE)-constrained inverse problems. For this purpose, we first applied state-of-the-art stochastic optimization algorithm called Covariance Matrix Adaptation Evolution Strategy (CMAES) to identify low-misfit regions of the model space. These regions were then randomly sampled to create an ensemble of equivalent models and quantify uncertainty. CMAES is aimed at exploring model space globally and is robust on very ill-conditioned problems. We show that the number of iterations required to converge grows at a moderate rate with respect to number of unknowns and the algorithm is embarrassingly parallel. We formulated the problem by using the generalized Gaussian distribution. This enabled us to seamlessly use arbitrary norms for residual and regularization terms. We show that various regularization norms facilitate studying different classes of equivalent solutions. We further show how performance of the standard Metropolis-Hastings Markov chain Monte Carlo algorithm can be substantially improved by using information CMAES provides. This methodology was tested by using individual and joint inversions of magneotelluric, controlled-source electromagnetic (EM) and global EM induction data.

  18. Measurement of the Viscoelastic Properties of Damping Materials: Adaptation of the Wave Propagation Method to Test Samples of Short Length

    NASA Astrophysics Data System (ADS)

    LEMERLE, P.

    2002-02-01

    Wave propagation methods allow the deduction of the viscoelastic damping properties of materials from the waveform pattern of a transitory wave: the wave profile is recorded at two travel distances in a thin bar made of the medium studied. In the case of linear viscoelasticity, the characteristics of the material are deduced directly from the transfer function of the two pulses measured. From a theoretical point of view, these methods are of great interest as they bridge a gap between vibratory methods and ultrasonic methods, allowing results to be obtained in a frequency range covering one and a half to two decades in the audiometric range (20 Hz-20 kHz). However, they have not been used much in industrial applications due to the difficulty and cost involved in producing samples in the form of bars. This study shows how this type of method can be adapted to measuring the viscoelastic properties of damping materials using reduced size and common shaped samples such as end-stop buffers.

  19. ADAPTIVE ANNEALED IMPORTANCE SAMPLING FOR MULTIMODAL POSTERIOR EXPLORATION AND MODEL SELECTION WITH APPLICATION TO EXTRASOLAR PLANET DETECTION

    SciTech Connect

    Liu, Bin

    2014-07-01

    We describe an algorithm that can adaptively provide mixture summaries of multimodal posterior distributions. The parameter space of the involved posteriors ranges in size from a few dimensions to dozens of dimensions. This work was motivated by an astrophysical problem called extrasolar planet (exoplanet) detection, wherein the computation of stochastic integrals that are required for Bayesian model comparison is challenging. The difficulty comes from the highly nonlinear models that lead to multimodal posterior distributions. We resort to importance sampling (IS) to estimate the integrals, and thus translate the problem to be how to find a parametric approximation of the posterior. To capture the multimodal structure in the posterior, we initialize a mixture proposal distribution and then tailor its parameters elaborately to make it resemble the posterior to the greatest extent possible. We use the effective sample size (ESS) calculated based on the IS draws to measure the degree of approximation. The bigger the ESS is, the better the proposal resembles the posterior. A difficulty within this tailoring operation lies in the adjustment of the number of mixing components in the mixture proposal. Brute force methods just preset it as a large constant, which leads to an increase in the required computational resources. We provide an iterative delete/merge/add process, which works in tandem with an expectation-maximization step to tailor such a number online. The efficiency of our proposed method is tested via both simulation studies and real exoplanet data analysis.

  20. Adaptive Function in Preschoolers in Relation to Developmental Delay and Diagnosis of Autism Spectrum Disorders: Insights from a Clinical Sample

    ERIC Educational Resources Information Center

    Milne, Susan L.; McDonald, Jenny L.; Comino, Elizabeth J.

    2013-01-01

    This study aims to explore the relationship between developmental ability, autism and adaptive skills in preschoolers. Adaptive function was assessed in 152 preschoolers with autism, with and without developmental delay, and without autism, with and without developmental delay. Their overall adaptive function, measured by the general adaptive…

  1. An integrated direct loop-mediated isothermal amplification microdevice incorporated with an immunochromatographic strip for bacteria detection in human whole blood and milk without a sample preparation step.

    PubMed

    Lee, Dohwan; Kim, Yong Tae; Lee, Jee Won; Kim, Do Hyun; Seo, Tae Seok

    2016-05-15

    We have developed an integrated direct loop-mediated isothermal amplification (Direct LAMP) microdevice incorporated with an immunochromatographic strip (ICS) to identify bacteria contaminated in real samples. The Direct LAMP is a novel isothermal DNA amplification technique which does not require thermal cycling steps as well as any sample preparation steps such as cell lysis and DNA extraction for amplifying specific target genes. In addition, the resultant amplicons were colorimetrically detected on the ICS, thereby enabling the entire genetic analysis process to be simplified. The two functional units (Direct LAMP and ICS) were integrated on a single device without use of the tedious and complicated microvalve and tubing systems. The utilization of a slidable plate allows us to manipulate the fluidic control in the microchannels manually and the sequential operation of the Direct LAMP and ICS detection could be performed by switching the slidable plate to each functional unit. Thus, the combination of the direct isothermal amplification without any sample preparation and thermal cycling steps, the ICS based amplicon detection by naked eyes, and the slidable plate to eliminate the microvalves in the integrated microdevice would be an ideal platform for point-of-care DNA diaganotics. On the integrated Direct LAMP-ICS microdevice, we could analyze Staphylococcus aureus (S. aureus) and Escherichia coli O157:H7 (E. coli O157:H7) contaminated in human whole blood or milk at a single-cell level within 1h.

  2. A new calculation method adapted to the experimental conditions for determining samples γ-activities induced by 14 MeV neutrons

    NASA Astrophysics Data System (ADS)

    Rzama, A.; Erramli, H.; Misdaq, M. A.

    1994-09-01

    Induced gamma-activities of different disk shaped irradiated samples and standards with 14 MeV neutrons have been determined by using a Monte Carlo calculation method adapted to the experimental conditions. The self-absorption of the multienergetic emitted gamma rays has been taken into account in the final samples activities. The influence of the different activation parameters has been studied. Na, K, Cl and P contents in biological (red beet) samples have been determined.

  3. Modern Subsurface Bacteria in Pristine 2.7 Ga-Old Fossil Stromatolite Drillcore Samples from the Fortescue Group, Western Australia

    PubMed Central

    Gérard, Emmanuelle; Moreira, David; Philippot, Pascal; Van Kranendonk, Martin J.; López-García, Purificación

    2009-01-01

    Background Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible. Methodology/Principal Findings In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper “fresh” samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth. Conclusions/Significance The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life

  4. Pattern of multiresistant to antimicrobials and heavy metal tolerance in bacteria isolated from sewage sludge samples from a composting process at a recycling plant in southern Brazil.

    PubMed

    Heck, Karina; De Marco, Évilin Giordana; Duarte, Mariana Wanderlei; Salamoni, Sabrina Pinto; Van Der Sand, Sueli

    2015-06-01

    The composting process is a viable alternative for the recycling of household organic waste and sewage sludge generated during wastewater treatment. However, this technique can select microorganisms resistant to antimicrobials and heavy metals as a result of excess chemicals present in compost windrow. This study evaluates the antimicrobial multiresistant and tolerance to heavy metals in bacteria isolated from the composting process with sewage sludge. Fourteen antimicrobials were used in 344 strains for the resistance profile and four heavy metals (chromium, copper, zinc, and lead) for the minimum biocide concentration assay. The strains used were from the sewage sludge sample (beginning of the process) and the compost sample (end of the process). Strains with higher antimicrobial and heavy metal profile were identified by 16S rRNA gene sequencing. The results showed a multiresistant profile in 48 % of the strains, with the highest percentage of strains resistant to nitrofurantoin (65 %) and β-lactams (58 %). The strains isolated from the sewage sludge and the end of the composting process were more tolerant to copper, with a lethal dose of approximately 900 mg L(-1) for about 50 % of the strains. The genera that showed the highest multiresistant profile and increased tolerance to the metals tested were Pseudomonas and Ochrobactrum. The results of this study may contribute to future research and the revision and regulation of legislation on sewage sludge reuse in soils.

  5. The importance of correcting for variable probe-sample interactions in AFM-IR spectroscopy: AFM-IR of dried bacteria on a polyurethane film.

    PubMed

    Barlow, Daniel E; Biffinger, Justin C; Cockrell-Zugell, Allison L; Lo, Michael; Kjoller, Kevin; Cook, Debra; Lee, Woo Kyung; Pehrsson, Pehr E; Crookes-Goodson, Wendy J; Hung, Chia-Suei; Nadeau, Lloyd J; Russell, John N

    2016-08-01

    AFM-IR is a combined atomic force microscopy-infrared spectroscopy method that shows promise for nanoscale chemical characterization of biological-materials interactions. In an effort to apply this method to quantitatively probe mechanisms of microbiologically induced polyurethane degradation, we have investigated monolayer clusters of ∼200 nm thick Pseudomonas protegens Pf-5 bacteria (Pf) on a 300 nm thick polyether-polyurethane (PU) film. Here, the impact of the different biological and polymer mechanical properties on the thermomechanical AFM-IR detection mechanism was first assessed without the additional complication of polymer degradation. AFM-IR spectra of Pf and PU were compared with FTIR and showed good agreement. Local AFM-IR spectra of Pf on PU (Pf-PU) exhibited bands from both constituents, showing that AFM-IR is sensitive to chemical composition both at and below the surface. One distinct difference in local AFM-IR spectra on Pf-PU was an anomalous ∼4× increase in IR peak intensities for the probe in contact with Pf versus PU. This was attributed to differences in probe-sample interactions. In particular, significantly higher cantilever damping was observed for probe contact with PU, with a ∼10× smaller Q factor. AFM-IR chemical mapping at single wavelengths was also affected. We demonstrate ratioing of mapping data for chemical analysis as a simple method to cancel the extreme effects of the variable probe-sample interactions. PMID:27403761

  6. Pattern of multiresistant to antimicrobials and heavy metal tolerance in bacteria isolated from sewage sludge samples from a composting process at a recycling plant in southern Brazil.

    PubMed

    Heck, Karina; De Marco, Évilin Giordana; Duarte, Mariana Wanderlei; Salamoni, Sabrina Pinto; Van Der Sand, Sueli

    2015-06-01

    The composting process is a viable alternative for the recycling of household organic waste and sewage sludge generated during wastewater treatment. However, this technique can select microorganisms resistant to antimicrobials and heavy metals as a result of excess chemicals present in compost windrow. This study evaluates the antimicrobial multiresistant and tolerance to heavy metals in bacteria isolated from the composting process with sewage sludge. Fourteen antimicrobials were used in 344 strains for the resistance profile and four heavy metals (chromium, copper, zinc, and lead) for the minimum biocide concentration assay. The strains used were from the sewage sludge sample (beginning of the process) and the compost sample (end of the process). Strains with higher antimicrobial and heavy metal profile were identified by 16S rRNA gene sequencing. The results showed a multiresistant profile in 48 % of the strains, with the highest percentage of strains resistant to nitrofurantoin (65 %) and β-lactams (58 %). The strains isolated from the sewage sludge and the end of the composting process were more tolerant to copper, with a lethal dose of approximately 900 mg L(-1) for about 50 % of the strains. The genera that showed the highest multiresistant profile and increased tolerance to the metals tested were Pseudomonas and Ochrobactrum. The results of this study may contribute to future research and the revision and regulation of legislation on sewage sludge reuse in soils. PMID:25944755

  7. Anaerobic bacteria

    MedlinePlus

    Anaerobic bacteria are bacteria that do not live or grow when oxygen is present. In humans, these ... Goldstein EJ. Diseases caused by non-spore forming anaerobic bacteria. In: Goldman L, Schafer AI, eds. Goldman's ...

  8. Diagnosing Intellectual Disability in a Forensic Sample: Gender and Age Effects on the Relationship between Cognitive and Adaptive Functioning

    ERIC Educational Resources Information Center

    Hayes, Susan C.

    2005-01-01

    Background: The relationship between adaptive behaviour and cognitive functioning in offenders with intellectual disabilities is not well researched. This study aims to examine gender and age effects on the relationship between these two areas of functioning. Method: The "Vineland Adaptive Behavior Scales" (VABS) and the "Kaufman Brief…

  9. Developing an Instructional Material Using a Concept Cartoon Adapted to the 5E Model: A Sample of Teaching Erosion

    ERIC Educational Resources Information Center

    Birisci, Salih; Metin, Mustafa

    2010-01-01

    Using different instructional materials adapted within the constructivist learning theory will enhance students' conceptual understanding. From this point of view, an instructional instrument using a concept cartoon adapted with 5E model has developed and introduced in this study. The study has some deficiencies in investigating students'…

  10. Development of an Abbreviated Form of the Penn Line Orientation Test Using Large Samples and Computerized Adaptive Test Simulation

    PubMed Central

    Moore, Tyler M.; Scott, J. Cobb; Reise, Steven P.; Port, Allison M.; Jackson, Chad T.; Ruparel, Kosha; Savitt, Adam P.; Gur, Raquel E.; Gur, Ruben C.

    2015-01-01

    Visuospatial processing is a commonly assessed neurocognitive domain, with deficits linked to dysfunction in right posterior regions of the brain. With the growth of large-scale clinical research studies there is an increased need for efficient and scalable assessments of neurocognition, including visuospatial processing. The purpose of the current study was to use a novel method that combines item response theory (IRT) and computerized adaptive testing (CAT) approaches to create an abbreviated form of the computerized Penn Line Orientation Test (PLOT). The 24-item PLOT was administered to 8,498 youths (aged 8 to 21) as part of the Philadelphia Neurodevelopmental Cohort study and, by web-based data collection, in an independent sample of 4,593 adults from Great Britain as part of a television documentary. IRT-based CAT simulations were used to select the best PLOT items for an abbreviated form by performing separate simulations in each group and choosing only items that were selected as useful (i.e., high item discrimination and in the appropriate difficulty range) in at least one of the simulations. Fifteen items were chosen for the final, short form of the PLOT, indicating substantial agreement among the models in how they evaluated each item's usefulness. Moreover, this abbreviated version performed comparably to the full version in tests of sensitivity to age and sex effects. This abbreviated version of the PLOT cuts administration time by 50% without detectable loss of information, which points to its feasibility for large-scale clinical and genomic studies. PMID:25822834

  11. Mortality of fecal bacteria in seawater

    SciTech Connect

    Garcia-Lara, J.; Menon, P.; Servais, P.; Billen, G. )

    1991-03-01

    The authors propose a method for determining the mortality rate for allochthonous bacteria released in aquatic environments without interference due to the loss of culturability in specific culture media. This method consists of following the disappearance of radioactivity from the trichloracetic acid-insoluble fraction in water samples to which ({sup 3}H)thymidine-prelabeled allochthonous bacteria have been added. In coastal seawater, they found that the actual rate of disappearance of fecal bacteria was 1 order of magnitude lower than the rate of loss of culturability on specific media. Minor adaptation of the procedure may facilitate assessment of the effect of protozoan grazing and bacteriophage lysis on the overall bacterial mortality rate.

  12. Characterization of 15 selected coccal bacteria isolated from Antarctic rock and soil samples from the McMurdo-Dry Valleys (South-Victoria Land)

    NASA Technical Reports Server (NTRS)

    Siebert, J.; Hirsch, P.; Friedmann, E. I. (Principal Investigator)

    1988-01-01

    Approximately 1500 cultures of microorganisms were isolated from rocks and soils of the Ross Desert (McMurdo-Dry Valleys). From these, 15 coccoid strains were chosen for more detailed investigation. They were characterized by morphological, physiological and chemotaxonomical properties. All isolates were Gram-positive, catalase-positive and nonmotile. Six strains showed red pigmentation and could be identified as members of the genera Micrococcus (M. roseus, M. agilis) or Deinococcus. In spite of their coccoid morphology, the remaining nine strains had to be associated with coryneform bacteria (Arthrobacter, Brevibacterium), because of their cell wall composition and G+C ratios. Most of the strains were psychrotrophic, but one strain was even obligately psychrophilic, with a temperature maximum below 20 degrees C. Red cocci had in vitro pH optima above 9.0 although they generally originated from acid samples. Most isolates showed a preference for sugar alcohols and organic acids, compounds which are commonly known to be released by lichens, molds and algae, the other components of the cryptoendolithic ecosystem. These properties indicate that our strains are autochthonous members of the natural Antarctic microbial population.

  13. Molecular Detection of New Delhi Metallo-Beta-Lactamase-1 (NDM-1) Positive Bacteria from Environmental and Drinking Water Samples by Loop Mediated Isothermal Amplification of bla NDM-1.

    PubMed

    Rathinasabapathi, P; Hiremath, Deepak S; Arunraj, Rex; Parani, M

    2015-12-01

    New Delhi metallo-β-lactamase-1 gene (bla NDM-1 ) codes for New Delhi metallo-beta-lactamase-1 (NDM-1) enzyme that cleaves the amide bond of β-lactam ring, and provides resistance against major classes of β-lactam antibiotics. Dissemination of the plasmid borne bla NDM-1 through horizontal gene transfer is a potential threat to the society. In this study, a rapid non-culture method for detecting NDM-1 positive bacteria was developed by Loop Mediated Isothermal Amplification (LAMP) of bla NDM-1 . Sensitivity of this method was found to be one femtogram of plasmid DNA, which translates into 2.6-25.8 copies depending on the size of the plasmid DNA. This method was applied to detect NDM-1 positive bacteria in 81 water samples that were collected from environmental and drinking water sources. NDM-1 positive bacteria were detected in three drinking water samples by LAMP but not by PCR. These three samples were collected from the water sources that were treated with chlorine for decontamination before public distribution. NDM-1 positive bacteria were not detected in lake water samples or in the samples that were collected from the water sources that were purified by reverse osmosis before public distribution. Detection of NDM-1 positive bacteria using LAMP was found to be safe, sensitive and rapid for screening large number of samples from diverse sources. This method could be developed as on-field detection kit by using fluorescent dyes to visualize the amplified bla NDM-1 gene.

  14. Fecal-indicator bacteria in the Yakima River Basin, Washington-An examination of 1999 and 2000 synoptic-sampling data and their relation to historical data

    USGS Publications Warehouse

    Morace, Jennifer L.; McKenzie, Stuart W.

    2002-11-27

    Looking forward relative to future monitoring goals, research needs, and best management practice development, four hypotheses that deal with processes and sources of bacteria were identified: (1) overland runoff transports bacteria from land surfaces to streams, (2) bacteria in the water column tend to associate with suspended matter, (3) with increasing densities of warm-blooded animals, the likelihood of fecal-coliform contamination in streams also increases, and (4) identifi- cation of bacterial sources is difficult, but must be attempted for remediation to be possi

  15. Fecal-indicator bacteria in the Yakima River Basin, Washington-An examination of 1999 and 2000 synoptic-sampling data and their relation to historical data

    USGS Publications Warehouse

    Morace, Jennifer L.; McKenzie, Stuart W.

    2002-11-27

    Looking forward relative to future monitoring goals, research needs, and best management practice development, four hypotheses that deal with processes and sources of bacteria were identified: (1) overland runoff transports bacteria from land surfaces to streams, (2) bacteria in the water column tend to associate with suspended matter, (3) with increasing densities of warm-blooded animals, the likelihood of fecal-coliform contamination in streams also increases, and (4) identifi- cation of bacterial sources is difficult, but must be attempted for remediation to be possible. 

  16. Testing Set-Point Theory in a Swiss National Sample: Reaction and Adaptation to Major Life Events.

    PubMed

    Anusic, Ivana; Yap, Stevie C Y; Lucas, Richard E

    2014-12-01

    Set-point theory posits that individuals react to the experience of major life events, but quickly adapt back to pre-event baseline levels of subjective well-being in the years following the event. A large, nationally representative panel study of Swiss households was used to examine set-point theory by investigating the extent of adaptation following the experience of marriage, childbirth, widowhood, unemployment, and disability. Our results demonstrate that major life events are associated with marked change in life satisfaction and, for some events (e.g., marriage, disability), these changes are relatively long lasting even when accounting for normative, age related change.

  17. Evaluation of a real-time quantitative PCR method with propidium monazide treatment for analyses of viable fecal indicator bacteria in wastewater samples

    EPA Science Inventory

    The U.S. EPA is currently evaluating rapid, real-time quantitative PCR (qPCR) methods for determining recreational water quality based on measurements of fecal indicator bacteria DNA sequences. In order to potentially use qPCR for other Clean Water Act needs, such as updating cri...

  18. Cold Adaptation of Zinc Metalloproteases in the Thermolysin Family from Deep Sea and Arctic Sea Ice Bacteria Revealed by Catalytic and Structural Properties and Molecular Dynamics

    PubMed Central

    Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2009-01-01

    Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, kcat/Km (10–40 °C), followed the order pseudolysin < MCP-02 < E495 with a ratio of ∼1:2:4. MCP-02 and E495 have the same optimal temperature (Topt, 57 °C, 5 °C lower than pseudolysin) and apparent melting temperature (Tm = 64 °C, ∼10 °C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility. PMID:19181663

  19. A Keck Adaptive Optics Survey of a Representative Sample of Gravitationally Lensed Star-forming Galaxies: High Spatial Resolution Studies of Kinematics and Metallicity Gradients

    NASA Astrophysics Data System (ADS)

    Leethochawalit, Nicha; Jones, Tucker A.; Ellis, Richard S.; Stark, Daniel P.; Richard, Johan; Zitrin, Adi; Auger, Matthew

    2016-04-01

    We discuss spatially resolved emission line spectroscopy secured for a total sample of 15 gravitationally lensed star-forming galaxies at a mean redshift of z≃ 2 based on Keck laser-assisted adaptive optics observations undertaken with the recently improved OSIRIS integral field unit (IFU) spectrograph. By exploiting gravitationally lensed sources drawn primarily from the CASSOWARY survey, we sample these sub-L{}* galaxies with source-plane resolutions of a few hundred parsecs ensuring well-sampled 2D velocity data and resolved variations in the gas-phase metallicity. Such high spatial resolution data offer a critical check on the structural properties of larger samples derived with coarser sampling using multiple-IFU instruments. We demonstrate how kinematic complexities essential to understanding the maturity of an early star-forming galaxy can often only be revealed with better sampled data. Although we include four sources from our earlier work, the present study provides a more representative sample unbiased with respect to emission line strength. Contrary to earlier suggestions, our data indicate a more diverse range of kinematic and metal gradient behavior inconsistent with a simple picture of well-ordered rotation developing concurrently with established steep metal gradients in all but merging systems. Comparing our observations with the predictions of hydrodynamical simulations suggests that gas and metals have been mixed by outflows or other strong feedback processes, flattening the metal gradients in early star-forming galaxies.

  20. Mobile membrane introduction tandem mass spectrometry for on-the-fly measurements and adaptive sampling of VOCs around oil and gas projects in Alberta, Canada

    NASA Astrophysics Data System (ADS)

    Krogh, E.; Gill, C.; Bell, R.; Davey, N.; Martinsen, M.; Thompson, A.; Simpson, I. J.; Blake, D. R.

    2012-12-01

    The release of hydrocarbons into the environment can have significant environmental and economic consequences. The evolution of smaller, more portable mass spectrometers to the field can provide spatially and temporally resolved information for rapid detection, adaptive sampling and decision support. We have deployed a mobile platform membrane introduction mass spectrometer (MIMS) for the in-field simultaneous measurement of volatile and semi-volatile organic compounds. In this work, we report instrument and data handling advances that produce geographically referenced data in real-time and preliminary data where these improvements have been combined with high precision ultra-trace VOCs analysis to adaptively sample air plumes near oil and gas operations in Alberta, Canada. We have modified a commercially available ion-trap mass spectrometer (Griffin ICX 400) with an in-house temperature controlled capillary hollow fibre polydimethylsiloxane (PDMS) polymer membrane interface and in-line permeation tube flow cell for a continuously infused internal standard. The system is powered by 24 VDC for remote operations in a moving vehicle. Software modifications include the ability to run continuous, interlaced tandem mass spectrometry (MS/MS) experiments for multiple contaminants/internal standards. All data are time and location stamped with on-board GPS and meteorological data to facilitate spatial and temporal data mapping. Tandem MS/MS scans were employed to simultaneously monitor ten volatile and semi-volatile analytes, including benzene, toluene, ethylbenzene and xylene (BTEX), reduced sulfur compounds, halogenated organics and naphthalene. Quantification was achieved by calibrating against a continuously infused deuterated internal standard (toluene-d8). Time referenced MS/MS data were correlated with positional data and processed using Labview and Matlab to produce calibrated, geographical Google Earth data-visualizations that enable adaptive sampling protocols

  1. A New Framework for Adaptive Sampling and Analysis During Long-Term Monitoring and Remedial Action Management

    SciTech Connect

    Minsker, Barbara; Albert Valocchi; Barbara Bailey

    2008-01-27

    DOE and other Federal agencies are making a significant investment in the development of field analytical techniques, nonintrusive technologies, and sensor technologies that will have a profound impact on the way environmental monitoring is conducted. Monitoring and performance evaluation networks will likely be base on suites of in situ sensors, with physical sampling playing a much more limited role. Designing and using these types of networks effectively will require development of a new paradigm for sampling and analysis of remedial actions, which is the overall goal of this project.

  2. Identification of Bacteria in Biofilm and Bulk Water Samples from a Nonchlorinated Model Drinking Water Distribution System: Detection of a Large Nitrite-Oxidizing Population Associated with Nitrospira spp.

    PubMed Central

    Martiny, Adam C.; Albrechtsen, Hans-Jørgen; Arvin, Erik; Molin, Søren

    2005-01-01

    In a model drinking water distribution system characterized by a low assimilable organic carbon content (<10 μg/liter) and no disinfection, the bacterial community was identified by a phylogenetic analysis of rRNA genes amplified from directly extracted DNA and colonies formed on R2A plates. Biofilms of defined periods of age (14 days to 3 years) and bulk water samples were investigated. Culturable bacteria were associated with Proteobacteria and Bacteriodetes, whereas independently of cultivation, bacteria from 12 phyla were detected in this system. These included Acidobacteria, Nitrospirae, Planctomycetes, and Verrucomicrobia, some of which have never been identified in drinking water previously. A cluster analysis of the population profiles from the individual samples divided biofilms and bulk water samples into separate clusters (P = 0.027). Bacteria associated with Nitrospira moscoviensis were found in all samples and encompassed 39% of the sequenced clones in the bulk water and 25% of the biofilm community. The close association with Nitrospira suggested that a large part of the population had an autotrophic metabolism using nitrite as an electron donor. To test this hypothesis, nitrite was added to biofilm and bulk water samples, and the utilization was monitored during 15 days. A first-order decrease in nitrite concentration was observed for all samples with a rate corresponding to 0.5 × 105 to 2 × 105 nitrifying cells/ml in the bulk water and 3 × 105 cells/cm2 on the pipe surface. The finding of an abundant nitrite-oxidizing microbial population suggests that nitrite is an important substrate in this system, potentially as a result of the low assimilable organic carbon concentration. This finding implies that microbial communities in water distribution systems may control against elevated nitrite concentrations but also contain large indigenous populations that are capable of assisting the depletion of disinfection agents like chloramines. PMID

  3. Demonstration of sequential adaptation strategy for developing salt tolerance in bacteria for wastewater treatment: a study using Escherichia coli as model.

    PubMed

    Puranik, Sampada; Shaligram, Shraddha; Paliwal, Vasundhara; Raje, Dhananjay V; Kapley, Atya; Purohit, Hemant J

    2012-10-01

    A wastewater isolate identified as Escherichia coli HPC781 was adapted for high salt concentration through sequential transfers in Luria Broth (LB). The cells were grown in LB with 5% sodium chloride (NaCl) and were analyzed for the acquired salt resistance network through gene expression profiles. Microarray studies revealed TCA, glyoxylate shunt and acetyl Co-A metabolism as key nodes for stress combat to arrive at compromised physiology. It also proposed that the cells were receiving signals from salt environment via OmpR-EnvZ two component systems and stress dependent general regulatory protein rpoH and rpoE. The salt adapted culture, when challenged with wastewater having additional 5% salt showed growth. The work represents a tactic to adjust biochemical network towards stress and reveals its applicability via real-time PCR measurement of genes in wastewater. The study proposes that the recycled biomass with an adaptation strategy could be applied for treatment of wastewater with high salt levels.

  4. Detection of antibiotic residues and association of cefquinome residues with the occurrence of Extended-Spectrum β-Lactamase (ESBL)-producing bacteria in waste milk samples from dairy farms in England and Wales in 2011.

    PubMed

    Randall, Luke; Heinrich, Katharina; Horton, Robert; Brunton, Lucy; Sharman, Matthew; Bailey-Horne, Victoria; Sharma, Meenaxi; McLaren, Ian; Coldham, Nick; Teale, Chris; Jones, Jeff

    2014-02-01

    Waste milk samples from 103 farms in England and Wales were examined for the presence of β-lactam antibiotics and ESBL-producing Enterobacteriaceae. Approximately 10 months after the initial sampling, further waste milk, environmental and faecal samples from farms shown to be positive for CTX-M Escherichia coli were investigated further. Isolates with an ESBL phenotype were tested by PCR for the presence of blaCTX-M, blaOXA, blaSHV and blaTEM genes. Isolates positive for blaCTX-M were sequenced to determine CTX-M type. Representative isolates were further examined by PFGE, plasmid replicon typing and serotyping. Of particular interest, 21.4% of waste milk samples contained residues of the cephalosporin cefquinome, which was significantly associated with CTX-M bacteria. Such bacteria occurred in 5.8% of the waste milk samples (including 3.9% CTX-M E. coli). CTX-M types identified were 1, 14, 14b and 15, but none of the E. coli were serotype O25, the serotype of the human pandemic strain.

  5. Adaptation of triple axis neutron spectrometer for SANS measurements using alumina samples at TRIGA reactor of Bangladesh

    NASA Astrophysics Data System (ADS)

    Ahmed, F. U.; Kamal, I.; Yunus, S. M.; Datta, T. K.; Azad, A. K.; Zakaria, A. K. M.; Goyal, P. S.

    2005-09-01

    Double crystal method known as Bonse and Hart's technique has been employed to develop small angle neutron scattering (SANS) facility on a triple axis neutron spectrometer at TRIGA Mark II (3 MW) research reactor of Atomic Energy Research Establishment (AERE), Savar, Dhaka, Bangladesh. Two Si(1 1 1) crystals with very small mosaic spread ∼1 min have been used for this purpose. At an incident neutron wavelength of 1.24 Å, this device is useful for SANS in the Q range between 1.6×10 -3 and 10 -1 Å -1. This Q range allows investigating particle sizes and interparticle correlations on a length scale of ∼200 Å. Results of SANS experiments on three alumina (Al 2O 3) samples as performed using above setup are presented. It is seen that Al 2O 3 particles, indeed, scatter neutrons in regions of small angles. It is also seen that scattering is different for different samples showing that it changes with a change in particle size.

  6. Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

    PubMed Central

    Cao, Youfang; Liang, Jie

    2013-01-01

    Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively

  7. Purification of bacterial genomic DNA in less than 20 min using chelex-100 microwave: examples from strains of lactic acid bacteria isolated from soil samples.

    PubMed

    Reyes-Escogido, Lourdes; Balam-Chi, Mario; Rodríguez-Buenfil, Ingrid; Valdés, Jesús; Kameyama, Luis; Martínez-Pérez, Francisco

    2010-11-01

    We established a Chelex 100-Microwave method for the purification of bacterial genomic DNA (gDNA) in less than 20 min with high yield and good quality, useful for multiple purposes. It combines Chelex 100, proteinase K, RNase A and heating in a microwave oven. The resulting gDNA was used directly to identify bacterial species of the Order Lactobacillales by means of PCR amplification of their 16S rDNA gene, isolated from sediments on the Yucatan Peninsula, Mexico. This method produced gDNA free of phenolic and protein residual contaminants from 100 of these isolated bacteria. 16S rDNA amplification and sequencing showed Pediococcus acidilactici to prevail in inland lagoons, and Pediococcus pentosaceus, Lactobacillus plantarum, Lactobacillus sp., and Lactobacillus fermentum to be most abundant in the soils of livestock farms. The combination of Chelex 100, enzymes and microwave heating used in the Chelex 100-Microwave method produced large amounts of highly pure gDNA from Gram-positive and Gram-negative bacteria, in less than 20 min.

  8. Magnetic Bacteria.

    ERIC Educational Resources Information Center

    Nelson, Jane Bray; Nelson, Jim

    1992-01-01

    Describes the history of Richard Blakemore's discovery of magnetotaxic organisms. Discusses possible reasons why the magnetic response in bacteria developed. Proposes research experiments integrating biology and physics in which students investigate problems using cultures of magnetotaxic organisms. (MDH)

  9. SELF-REPORT OF EMPATHY: A SHORTENED FRENCH ADAPTATION OF THE INTERPERSONAL REACTIVITY INDEX (IRI) USING TWO LARGE BELGIAN SAMPLES.

    PubMed

    Braun, Stéphanie; Rosseel, Yves; Kempenaers, Chantal; Loas, Gwenole; Linkowski, Paul

    2015-12-01

    For more than 30 years, the Interpersonal Reactivity Index (IRI) has been used to measure the multidimensional aspects of empathy. But the 28-item, 4-factor model of Davis (1980 ) is currently contested because of methodological issues and for theoretical reasons. Confirmatory (CFA) and exploratory factor analyses (EFA) were applied in two French-speaking Belgian student samples (1,244 participants in the first and 729 in the second study) to test this model and to propose a shortened version. A non-optimal fit was found with respect to the CFI value (Study 1). By splitting the student group into two random subsamples, EFA and then CFA were used to propose a 15-item, 4-factor model with good fit indices. A CFA on the second student group (Study 2) replicated this model. Results are discussed considering the influence of social desirability response bias, an absence of strong invariance across sex and the usefulness of self-report scales to measure empathy. PMID:26595295

  10. Simple chamber facilitates chemiluminescent detection of bacteria

    NASA Technical Reports Server (NTRS)

    Marts, E. C.; Wilkins, J. R.

    1970-01-01

    Test chamber enables rapid estimation of bacteria in a test sample through the reaction of luminol and an oxidant with the cytochrome C portion of certain species of bacteria. Intensity of the light emitted in the reaction is a function of the specific bacteria in the test sample.

  11. High Efficiency Light Harvesting by Carotenoids in the LH2 Complex from Photosynthetic Bacteria: Unique Adaptation to Growth under Low-Light Conditions

    PubMed Central

    2015-01-01

    Rhodopin, rhodopinal, and their glucoside derivatives are carotenoids that accumulate in different amounts in the photosynthetic bacterium, Rhodoblastus (Rbl.) acidophilus strain 7050, depending on the intensity of the light under which the organism is grown. The different growth conditions also have a profound effect on the spectra of the bacteriochlorophyll (BChl) pigments that assemble in the major LH2 light-harvesting pigment–protein complex. Under high-light conditions the well-characterized B800-850 LH2 complex is formed and accumulates rhodopin and rhodopin glucoside as the primary carotenoids. Under low-light conditions, a variant LH2, denoted B800-820, is formed, and rhodopinal and rhodopinal glucoside are the most abundant carotenoids. The present investigation compares and contrasts the spectral properties and dynamics of the excited states of rhodopin and rhodopinal in solution. In addition, the systematic differences in pigment composition and structure of the chromophores in the LH2 complexes provide an opportunity to explore the effect of these factors on the rate and efficiency of carotenoid-to-BChl energy transfer. It is found that the enzymatic conversion of rhodopin to rhodopinal by Rbl. acidophilus 7050 grown under low-light conditions results in nearly 100% carotenoid-to-BChl energy transfer efficiency in the LH2 complex. This comparative analysis provides insight into how photosynthetic systems are able to adapt and survive under challenging environmental conditions. PMID:25171303

  12. High efficiency light harvesting by carotenoids in the LH2 complex from photosynthetic bacteria: unique adaptation to growth under low-light conditions.

    PubMed

    Magdaong, Nikki M; LaFountain, Amy M; Greco, Jordan A; Gardiner, Alastair T; Carey, Anne-Marie; Cogdell, Richard J; Gibson, George N; Birge, Robert R; Frank, Harry A

    2014-09-25

    Rhodopin, rhodopinal, and their glucoside derivatives are carotenoids that accumulate in different amounts in the photosynthetic bacterium, Rhodoblastus (Rbl.) acidophilus strain 7050, depending on the intensity of the light under which the organism is grown. The different growth conditions also have a profound effect on the spectra of the bacteriochlorophyll (BChl) pigments that assemble in the major LH2 light-harvesting pigment-protein complex. Under high-light conditions the well-characterized B800-850 LH2 complex is formed and accumulates rhodopin and rhodopin glucoside as the primary carotenoids. Under low-light conditions, a variant LH2, denoted B800-820, is formed, and rhodopinal and rhodopinal glucoside are the most abundant carotenoids. The present investigation compares and contrasts the spectral properties and dynamics of the excited states of rhodopin and rhodopinal in solution. In addition, the systematic differences in pigment composition and structure of the chromophores in the LH2 complexes provide an opportunity to explore the effect of these factors on the rate and efficiency of carotenoid-to-BChl energy transfer. It is found that the enzymatic conversion of rhodopin to rhodopinal by Rbl. acidophilus 7050 grown under low-light conditions results in nearly 100% carotenoid-to-BChl energy transfer efficiency in the LH2 complex. This comparative analysis provides insight into how photosynthetic systems are able to adapt and survive under challenging environmental conditions.

  13. Computationally efficient video restoration for Nyquist sampled imaging sensors combining an affine-motion-based temporal Kalman filter and adaptive Wiener filter.

    PubMed

    Rucci, Michael; Hardie, Russell C; Barnard, Kenneth J

    2014-05-01

    In this paper, we present a computationally efficient video restoration algorithm to address both blur and noise for a Nyquist sampled imaging system. The proposed method utilizes a temporal Kalman filter followed by a correlation-model based spatial adaptive Wiener filter (AWF). The Kalman filter employs an affine background motion model and novel process-noise variance estimate. We also propose and demonstrate a new multidelay temporal Kalman filter designed to more robustly treat local motion. The AWF is a spatial operation that performs deconvolution and adapts to the spatially varying residual noise left in the Kalman filter stage. In image areas where the temporal Kalman filter is able to provide significant noise reduction, the AWF can be aggressive in its deconvolution. In other areas, where less noise reduction is achieved with the Kalman filter, the AWF balances the deconvolution with spatial noise reduction. In this way, the Kalman filter and AWF work together effectively, but without the computational burden of full joint spatiotemporal processing. We also propose a novel hybrid system that combines a temporal Kalman filter and BM3D processing. To illustrate the efficacy of the proposed methods, we test the algorithms on both simulated imagery and video collected with a visible camera.

  14. Adaptation, equivalence, and validation of the changes in sexual functioning questionnaire-drugs in a sample of drug-dependent men.

    PubMed

    Vallejo-Medina, Pablo; Sierra, Juan Carlos

    2013-01-01

    This study aimed to adapt and validate the changes in sexual functioning questionnaire-short form in a sample of drug-dependent men, achieving equivalence. Participants were 301 drug-dependent and 202 non-drug-dependent men took part in this study. The analysis of invariance revealed strong factor equivalence (RMSEA = .06; χ2/df = 2.66 and ΔCFI = -.01) for the 4-factor model (desire, pleasure, arousal, and orgasm). This model has shown the best fit indices. No items showed differential item functioning (ΔR (2) Nagelkerke < .035). Reliability ranged from α = 0.83 for pleasure to α = 0.61 for orgasm. A comparison between the scores of control and experimental participants showed significant differences (CI = 99%) in all the dimensions. Thus, a worse sexual functioning has been observed in the drug consumer group. The adaptation of the Changes in Sexual Functioning Questionnaire-short form to drug-dependent individuals showed good psychometric properties. PMID:23421763

  15. Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study.

    PubMed

    Aguilera-Arreola, Ma Guadalupe; Martínez-Peña, Marcos Daniel; Hernández-Martínez, Fabiola; Juárez Enriques, Sara R; Rico Verdín, Beatriz; Majalca-Martínez, Cristina; Castro-Escarpulli, Graciela; Albarrán-Fernández, Enrique; Serrano-López, S Cecilia

    2016-01-01

    Administration of empirical antibiotic therapy prior to microbiological diagnosis is thought to be associated the failure of subsequent bacterial growth in culture. The aim of this study was to detect bacterial pathogens via direct amplification and sequencing of the 16S rDNA gene in samples showing negative culture results as alternative diagnostic tools to troubleshoot difficult samples. Twenty-three (7.66 %) positive samples were detected, most of which were monomicrobial infections; 15 of the cases were identified as HAIs, 6 had catheter colonisation, and 2 had sample colonisation. The pathogens identified included Escherichia, Salmonella, Pseudomonas spp., Enterococcus spp. and coagulase-negative staphylococci (CoNS). The most frequent infections were bacteraemia and urinary tract infection, but meningitis, warm infection and soft tissue infection were also documented. These findings emphasise the efficacy and usefulness of molecular diagnosis, thus 16S rDNA gene analysis is strongly indicated by HAIs diagnostics. PMID:27065040

  16. Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study.

    PubMed

    Aguilera-Arreola, Ma Guadalupe; Martínez-Peña, Marcos Daniel; Hernández-Martínez, Fabiola; Juárez Enriques, Sara R; Rico Verdín, Beatriz; Majalca-Martínez, Cristina; Castro-Escarpulli, Graciela; Albarrán-Fernández, Enrique; Serrano-López, S Cecilia

    2016-01-01

    Administration of empirical antibiotic therapy prior to microbiological diagnosis is thought to be associated the failure of subsequent bacterial growth in culture. The aim of this study was to detect bacterial pathogens via direct amplification and sequencing of the 16S rDNA gene in samples showing negative culture results as alternative diagnostic tools to troubleshoot difficult samples. Twenty-three (7.66 %) positive samples were detected, most of which were monomicrobial infections; 15 of the cases were identified as HAIs, 6 had catheter colonisation, and 2 had sample colonisation. The pathogens identified included Escherichia, Salmonella, Pseudomonas spp., Enterococcus spp. and coagulase-negative staphylococci (CoNS). The most frequent infections were bacteraemia and urinary tract infection, but meningitis, warm infection and soft tissue infection were also documented. These findings emphasise the efficacy and usefulness of molecular diagnosis, thus 16S rDNA gene analysis is strongly indicated by HAIs diagnostics.

  17. Insights into the Mechanism of Homeoviscous Adaptation to Low Temperature in Branched-Chain Fatty Acid-Containing Bacteria through Modeling FabH Kinetics from the Foodborne Pathogen Listeria monocytogenes

    PubMed Central

    Saunders, Lauren P.; Sen, Suranjana; Wilkinson, Brian J.; Gatto, Craig

    2016-01-01

    The psychrotolerant foodborne pathogen Listeria monocytogenes withstands the stress of low temperatures and can proliferate in refrigerated food. Bacteria adapt to growth at low temperatures by increasing the production of fatty acids that increase membrane fluidity. The mechanism of homeoviscous increases in unsaturated fatty acid amounts in bacteria that predominantly contain straight-chain fatty acids is relatively well understood. By contrast the analogous mechanism in branched-chain fatty acid-containing bacteria, such as L. monocytogenes, is poorly understood. L. monocytogenes grows at low temperatures by altering its membrane composition to increase membrane fluidity, primarily by decreasing the length of fatty acid chains and increasing the anteiso to iso fatty acid ratio. FabH, the initiator of fatty acid biosynthesis, has been identified as the primary determinant of membrane fatty acid composition, but the extent of this effect has not been quantified. In this study, previously determined FabH steady-state parameters and substrate concentrations were used to calculate expected fatty acid compositions at 30°C and 10°C. FabH substrates 2-methylbutyryl-CoA, isobutyryl-CoA, and isovaleryl-CoA produce the primary fatty acids in L. monocytogenes, i.e., anteiso-odd, iso-even, and iso-odd fatty acids, respectively. In vivo concentrations of CoA derivatives were measured, but not all were resolved completely. In this case, estimates were calculated from overall fatty acid composition and FabH steady-state parameters. These relative substrate concentrations were used to calculate the expected fatty acid compositions at 10°C. Our model predicted a higher level of anteiso lipids at 10°C than was observed, indicative of an additional step beyond FabH influencing fatty acid composition at low temperatures. The potential for control of low temperature growth by feeding compounds that result in the production of butyryl-CoA, the precursor of SCFAs that rigidify the

  18. Insights into the Mechanism of Homeoviscous Adaptation to Low Temperature in Branched-Chain Fatty Acid-Containing Bacteria through Modeling FabH Kinetics from the Foodborne Pathogen Listeria monocytogenes.

    PubMed

    Saunders, Lauren P; Sen, Suranjana; Wilkinson, Brian J; Gatto, Craig

    2016-01-01

    The psychrotolerant foodborne pathogen Listeria monocytogenes withstands the stress of low temperatures and can proliferate in refrigerated food. Bacteria adapt to growth at low temperatures by increasing the production of fatty acids that increase membrane fluidity. The mechanism of homeoviscous increases in unsaturated fatty acid amounts in bacteria that predominantly contain straight-chain fatty acids is relatively well understood. By contrast the analogous mechanism in branched-chain fatty acid-containing bacteria, such as L. monocytogenes, is poorly understood. L. monocytogenes grows at low temperatures by altering its membrane composition to increase membrane fluidity, primarily by decreasing the length of fatty acid chains and increasing the anteiso to iso fatty acid ratio. FabH, the initiator of fatty acid biosynthesis, has been identified as the primary determinant of membrane fatty acid composition, but the extent of this effect has not been quantified. In this study, previously determined FabH steady-state parameters and substrate concentrations were used to calculate expected fatty acid compositions at 30°C and 10°C. FabH substrates 2-methylbutyryl-CoA, isobutyryl-CoA, and isovaleryl-CoA produce the primary fatty acids in L. monocytogenes, i.e., anteiso-odd, iso-even, and iso-odd fatty acids, respectively. In vivo concentrations of CoA derivatives were measured, but not all were resolved completely. In this case, estimates were calculated from overall fatty acid composition and FabH steady-state parameters. These relative substrate concentrations were used to calculate the expected fatty acid compositions at 10°C. Our model predicted a higher level of anteiso lipids at 10°C than was observed, indicative of an additional step beyond FabH influencing fatty acid composition at low temperatures. The potential for control of low temperature growth by feeding compounds that result in the production of butyryl-CoA, the precursor of SCFAs that rigidify the

  19. Insights into the Mechanism of Homeoviscous Adaptation to Low Temperature in Branched-Chain Fatty Acid-Containing Bacteria through Modeling FabH Kinetics from the Foodborne Pathogen Listeria monocytogenes

    PubMed Central

    Saunders, Lauren P.; Sen, Suranjana; Wilkinson, Brian J.; Gatto, Craig

    2016-01-01

    The psychrotolerant foodborne pathogen Listeria monocytogenes withstands the stress of low temperatures and can proliferate in refrigerated food. Bacteria adapt to growth at low temperatures by increasing the production of fatty acids that increase membrane fluidity. The mechanism of homeoviscous increases in unsaturated fatty acid amounts in bacteria that predominantly contain straight-chain fatty acids is relatively well understood. By contrast the analogous mechanism in branched-chain fatty acid-containing bacteria, such as L. monocytogenes, is poorly understood. L. monocytogenes grows at low temperatures by altering its membrane composition to increase membrane fluidity, primarily by decreasing the length of fatty acid chains and increasing the anteiso to iso fatty acid ratio. FabH, the initiator of fatty acid biosynthesis, has been identified as the primary determinant of membrane fatty acid composition, but the extent of this effect has not been quantified. In this study, previously determined FabH steady-state parameters and substrate concentrations were used to calculate expected fatty acid compositions at 30°C and 10°C. FabH substrates 2-methylbutyryl-CoA, isobutyryl-CoA, and isovaleryl-CoA produce the primary fatty acids in L. monocytogenes, i.e., anteiso-odd, iso-even, and iso-odd fatty acids, respectively. In vivo concentrations of CoA derivatives were measured, but not all were resolved completely. In this case, estimates were calculated from overall fatty acid composition and FabH steady-state parameters. These relative substrate concentrations were used to calculate the expected fatty acid compositions at 10°C. Our model predicted a higher level of anteiso lipids at 10°C than was observed, indicative of an additional step beyond FabH influencing fatty acid composition at low temperatures. The potential for control of low temperature growth by feeding compounds that result in the production of butyryl-CoA, the precursor of SCFAs that rigidify the

  20. Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier

    PubMed Central

    Rossetti, Valentina; Bagheri, Homayoun C.

    2013-01-01

    An understanding of bacterial diversity and evolution in any environment requires knowledge of phenotypic diversity. In this study, the underlying factors leading to phenotypic clustering were analyzed and interpreted using a novel approach based on a four-tiered graph. Bacterial isolates were organized into equivalence classes based on their phenotypic profile. Likewise, phenotypes were organized in equivalence classes based on the bacteria that manifest them. The linking of these equivalence classes in a four-tiered graph allowed for a quick visual identification of the phenotypic measurements leading to the clustering patterns deduced from principal component analyses. For evaluation of the method, we investigated phenotypic variation in enzyme production and carbon assimilation of members of the genera Pseudomonas and Serratia, isolated from the Aletsch Glacier in Switzerland. The analysis indicates that the genera isolated produce at least six common enzymes and can exploit a wide range of carbon resources, though some specialist species within the pseudomonads were also observed. We further found that pairwise distances between enzyme profiles strongly correlate with distances based on carbon profiles. However, phenotypic distances weakly correlate with phylogenetic distances. The method developed in this study facilitates a more comprehensive understanding of phenotypic clustering than what would be deduced from principal component analysis alone. PMID:23741454

  1. Hydroxy fatty acids in fresh snow samples from northern Japan: long-range atmospheric transport of Gram-negative bacteria by Asian winter monsoon

    NASA Astrophysics Data System (ADS)

    Tyagi, P.; Yamamoto, S.; Kawamura, K.

    2015-08-01

    Hydroxy fatty acids (FAs) in fresh snow from Sapporo, one of the heaviest snowfall regions in the world, have been studied to ascertain the airborne bacterial endotoxin concentrations and their biomass. The presence of β-hydroxy FAs (C9-C28), constituents of Gram-negative bacteria (GNB), suggests long-range transport of soil microbes. Likewise, the occurrence of α- and ω-hydroxy FAs (C9-C30 and C9-C28, respectively) in snow reveals their contribution from epicuticular waxes and soil microorganisms. Estimated endotoxin and GNB mass can aid in assessing their possible impacts on the diversity and functioning of aquatic and terrestrial ecosystems, as well as lethal effects on pedestrians through dispersal of microbes. Air mass back trajectories together with hydroxy FAs unveil their sources from Siberia, Russian Far East and North China by the Asian monsoon. This study highlights the role of fresh snow that reduces the human health risk of GNB and endotoxin by scavenging from the air.

  2. Improvement of near infrared spectroscopic (NIRS) analysis of caffeine in roasted Arabica coffee by variable selection method of stability competitive adaptive reweighted sampling (SCARS)

    NASA Astrophysics Data System (ADS)

    Zhang, Xuan; Li, Wei; Yin, Bin; Chen, Weizhong; Kelly, Declan P.; Wang, Xiaoxin; Zheng, Kaiyi; Du, Yiping

    2013-10-01

    Coffee is the most heavily consumed beverage in the world after water, for which quality is a key consideration in commercial trade. Therefore, caffeine content which has a significant effect on the final quality of the coffee products requires to be determined fast and reliably by new analytical techniques. The main purpose of this work was to establish a powerful and practical analytical method based on near infrared spectroscopy (NIRS) and chemometrics for quantitative determination of caffeine content in roasted Arabica coffees. Ground coffee samples within a wide range of roasted levels were analyzed by NIR, meanwhile, in which the caffeine contents were quantitative determined by the most commonly used HPLC-UV method as the reference values. Then calibration models based on chemometric analyses of the NIR spectral data and reference concentrations of coffee samples were developed. Partial least squares (PLS) regression was used to construct the models. Furthermore, diverse spectra pretreatment and variable selection techniques were applied in order to obtain robust and reliable reduced-spectrum regression models. Comparing the respective quality of the different models constructed, the application of second derivative pretreatment and stability competitive adaptive reweighted sampling (SCARS) variable selection provided a notably improved regression model, with root mean square error of cross validation (RMSECV) of 0.375 mg/g and correlation coefficient (R) of 0.918 at PLS factor of 7. An independent test set was used to assess the model, with the root mean square error of prediction (RMSEP) of 0.378 mg/g, mean relative error of 1.976% and mean relative standard deviation (RSD) of 1.707%. Thus, the results provided by the high-quality calibration model revealed the feasibility of NIR spectroscopy for at-line application to predict the caffeine content of unknown roasted coffee samples, thanks to the short analysis time of a few seconds and non

  3. Improvement of near infrared spectroscopic (NIRS) analysis of caffeine in roasted Arabica coffee by variable selection method of stability competitive adaptive reweighted sampling (SCARS).

    PubMed

    Zhang, Xuan; Li, Wei; Yin, Bin; Chen, Weizhong; Kelly, Declan P; Wang, Xiaoxin; Zheng, Kaiyi; Du, Yiping

    2013-10-01

    Coffee is the most heavily consumed beverage in the world after water, for which quality is a key consideration in commercial trade. Therefore, caffeine content which has a significant effect on the final quality of the coffee products requires to be determined fast and reliably by new analytical techniques. The main purpose of this work was to establish a powerful and practical analytical method based on near infrared spectroscopy (NIRS) and chemometrics for quantitative determination of caffeine content in roasted Arabica coffees. Ground coffee samples within a wide range of roasted levels were analyzed by NIR, meanwhile, in which the caffeine contents were quantitative determined by the most commonly used HPLC-UV method as the reference values. Then calibration models based on chemometric analyses of the NIR spectral data and reference concentrations of coffee samples were developed. Partial least squares (PLS) regression was used to construct the models. Furthermore, diverse spectra pretreatment and variable selection techniques were applied in order to obtain robust and reliable reduced-spectrum regression models. Comparing the respective quality of the different models constructed, the application of second derivative pretreatment and stability competitive adaptive reweighted sampling (SCARS) variable selection provided a notably improved regression model, with root mean square error of cross validation (RMSECV) of 0.375 mg/g and correlation coefficient (R) of 0.918 at PLS factor of 7. An independent test set was used to assess the model, with the root mean square error of prediction (RMSEP) of 0.378 mg/g, mean relative error of 1.976% and mean relative standard deviation (RSD) of 1.707%. Thus, the results provided by the high-quality calibration model revealed the feasibility of NIR spectroscopy for at-line application to predict the caffeine content of unknown roasted coffee samples, thanks to the short analysis time of a few seconds and non

  4. Methanotrophic bacteria.

    PubMed Central

    Hanson, R S; Hanson, T E

    1996-01-01

    Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene. PMID:8801441

  5. [Methanotrophic bacteria of acid sphagnum bogs].

    PubMed

    Dedysh, S N

    2002-01-01

    Acid sphagnum bogs cover a considerable part of the territory of Russia and are an important natural source of biogenic methane, which is formed in their anaerobic layers. A considerable portion of this methane is consumed in the aerobic part of the bog profile by acidophilic methanotrophic bacteria, which comprise the methane filter of sphagnum bogs and decrease CH4 emission to the atmosphere. For a long time, these bacteria escaped isolation, which became possible only after the elucidation of the optimal conditions of their functioning in situ: pH 4.5 to 5.5; temperature, from 15 to 20 degrees C; and low salt concentration in the solution. Reproduction of these conditions and rejection of earlier used media with a high content of biogenic elements allowed methanotrophic bacteria of two new genera and species--Methylocella palustris and Methylocapsa acidophila--to be isolated from the peat of sphagnum bogs of the northern part of European Russia and West Siberia. These bacteria are well adapted to the conditions in cold, acid, oligotrophic sphagnum bogs. They grow in a pH range of 4.2-7.5 with an optimum at 5.0-5.5, prefer moderate temperatures (15-25 degrees C) and media with a low content of mineral salts (200-500 mg/l), and are capable of active nitrogen fixation. Design of fluorescently labeled 16S rRNA-targeted oligonucleotide probes for the detection of Methylocella palustris and Methylocapsa acidophila and their application to the analysis of sphagnum peat samples showed that these bacteria represent dominant populations of methanotrophs with a density of 10(5)-10(6) cells/g peat. In addition to Methylocella and Methylocapsa populations, one more abundant population of methanotrophs was revealed (10(6) cells/g peat), which were phylogenetically close to the genus Methylocystis. PMID:12526194

  6. Quantification of Propionibacterium acidipropionici P169 bacteria in environmental samples by use of strain-specific primers derived by suppressive subtractive hybridization.

    PubMed

    Peng, Min; Smith, Alexandra H; Rehberger, Thomas G

    2011-06-01

    A quantitative PCR (qPCR) assay targeting a gene identified by suppressive subtractive hybridization (SSH) was developed to detect Propionibacterium acidipropionici P169, with a threshold of 10(4) CFU/U of dairy feed or rumen fluid. The report is the first using a molecular marker generated by SSH to quantify a bacterial strain in environmental samples.

  7. Stress responses of bacteria.

    PubMed

    Marles-Wright, Jon; Lewis, Richard J

    2007-12-01

    Bacteria, irrespective of natural habitat, are exposed to constant fluctuations in their growth conditions. Consequently they have developed sophisticated responses, modulated by the re-modelling of protein complexes and by phosphorylation-dependent signal transduction systems, to adapt to and to survive a variety of insults. Ultimately these signalling systems affect transcriptional regulons either by activating an alternative sigma factor subunit of RNA polymerase, for example, sigma E (sigma(E)) of Escherichia coli and sigma B (sigma(B)) and sigma F (sigma(F)) in Bacillus subtilis or by activating DNA-binding two-component response regulators. Recent structure determinations, and systems biology analysis of key regulators in well-characterised stress-responsive pathways, illustrate conserved and novel mechanisms in these representative model bacteria.

  8. Pulse transient hot strip technique adapted for slab sample geometry to study anisotropic thermal transport properties of μm-thin crystalline films.

    PubMed

    Ma, Y; Gustavsson, J S; Haglund, A; Gustavsson, M; Gustafsson, S E

    2014-04-01

    A new method based on the adaptation of the Pulse Transient Hot Strip technique to slab sample geometry has been developed for studying thermal conductivity and thermal diffusivity of anisotropic thin film materials (<50 μm) with thermal conductivity in the 0.01-100 W/mK range, deposited on thin substrates (i.e., wafers). Strength of this technique is that it provides a well-controlled thermal probing depth, making it possible to probe a predetermined depth of the sample layer and thereby avoiding the influence from material(s) deeper down in the sample. To verify the technique a series of measurements were conducted on a y-cut single crystal quartz wafer. A Hot Strip sensor (32-μm wide, 3.2-mm long) was deposited along two orthogonal crystallographic (x- and z-) directions and two independent pulse transients were recorded. Thereafter, the data was fitted to our theoretical model, and the anisotropic thermal transport properties were determined. Using a thermal probing depth of only 30 μm, we obtained a thermal conductivity along the perpendicular (parallel) direction to the z-, i.e., optic axis of 6.48 (11.4) W/mK, and a thermal diffusivity of 3.62 (6.52) mm(2)/s. This yields a volumetric specific heat of 1.79 MJ/mK. These values agree well with tabulated data on bulk crystalline quartz supporting the accuracy of the technique, and the obtained standard deviation of less than 2.7% demonstrates the precision of this new measurement technique.

  9. Computational Improvements to Quantum Wave Packet ab Initio Molecular Dynamics Using a Potential-Adapted, Time-Dependent Deterministic Sampling Technique.

    PubMed

    Jakowski, Jacek; Sumner, Isaiah; Iyengar, Srinivasan S

    2006-09-01

    In a recent publication, we introduced a computational approach to treat the simultaneous dynamics of electrons and nuclei. The method is based on a synergy between quantum wave packet dynamics and ab initio molecular dynamics. Atom-centered density-matrix propagation or Born-Oppenheimer dynamics can be used to perform ab initio dynamics. In this paper, wave packet dynamics is conducted using a three-dimensional direct product implementation of the distributed approximating functional free-propagator. A fundamental computational difficulty in this approach is that the interaction potential between the two components of the methodology needs to be calculated frequently. Here, we overcome this problem through the use of a time-dependent deterministic sampling measure that predicts, at every step of the dynamics, regions of the potential which are important. The algorithm, when combined with an on-the-fly interpolation scheme, allows us to determine the quantum dynamical interaction potential and gradients at every dynamics step in an extremely efficient manner. Numerical demonstrations of our sampling algorithm are provided through several examples arranged in a cascading level of complexity. Starting from a simple one-dimensional quantum dynamical treatment of the shared proton in [Cl-H-Cl](-) and [CH3-H-Cl](-) along with simultaneous dynamical treatment of the electrons and classical nuclei, through a complete three-dimensional treatment of the shared proton in [Cl-H-Cl](-) as well as treatment of a hydrogen atom undergoing donor-acceptor transitions in the biological enzyme, soybean lipoxygenase-1 (SLO-1), we benchmark the algorithm thoroughly. Apart from computing various error estimates, we also compare vibrational density of states, inclusive of full quantum effects from the shared proton, using a novel unified velocity-velocity, flux-flux autocorrelation function. In all cases, the potential-adapted, time-dependent sampling procedure is seen to improve the

  10. Effect of Surface Sampling and Recovery of Viruses and Non-Spore-Forming Bacteria on a Quantitative Microbial Risk Assessment Model for Fomites.

    PubMed

    Weir, Mark H; Shibata, Tomoyuki; Masago, Yoshifumi; Cologgi, Dena L; Rose, Joan B

    2016-06-01

    Quantitative microbial risk assessment (QMRA) is a powerful decision analytics tool, yet it faces challenges when modeling health risks for the indoor environment. One limitation is uncertainty in fomite recovery for evaluating the efficiency of decontamination. Addressing this data gap has become more important as a result of response and recovery from a potential malicious pathogen release. To develop more accurate QMRA models, recovery efficiency from non-porous fomites (aluminum, ceramic, glass, plastic, steel, and wood laminate) was investigated. Fomite material, surface area (10, 100, and 900 cm(2)), recovery tool (swabs and wipes), initial concentration on the fomites and eluent (polysorbate 80, trypticase soy broth, and beef extract) were evaluated in this research. Recovery was shown to be optimized using polysorbate 80, sampling with wipes, and sampling a surface area of 10-100 cm(2). The QMRA model demonstrated, through a relative risk comparison, the need for recovery efficiency to be used in these models to prevent underestimated risks.

  11. The relative importance of Staphylococcus saprophyticus as a urinary tract pathogen: distribution of bacteria among urinary samples analysed during 1 year at a major Swedish laboratory.

    PubMed

    Eriksson, Andreas; Giske, Christian G; Ternhag, Anders

    2013-01-01

    To determine the distribution of urinary tract pathogens with focus on Staphylococcus saprophyticus and analyse the seasonality, antibiotic susceptibility, and gender and age distributions in a large Swedish cohort. S. saprophyticus is considered an important causative agent of urinary tract infection (UTI) in young women, and some earlier studies have reported up to approximately 40% of UTIs in this patient group being caused by S. saprophyticus. We hypothesized that this may be true only in very specific outpatient settings. During the year 2010, 113,720 urine samples were sent for culture to the Karolinska University Hospital, from both clinics in the hospital and from primary care units. Patient age, gender and month of sampling were analysed for S. saprophyticus, Escherichia coli, Klebsiella pneumoniae and Proteus mirabilis. Species data were obtained for 42,633 (37%) of the urine samples. The most common pathogens were E. coli (57.0%), Enterococcus faecalis (6.5%), K. pneumoniae (5.9%), group B streptococci (5.7%), P. mirabilis (3.0%) and S. saprophyticus (1.8%). The majority of subjects with S. saprophyticus were women 15-29 years of age (63.8%). In this age group, S. saprophyticus constituted 12.5% of all urinary tract pathogens. S. saprophyticus is a common urinary tract pathogen in young women, but its relative importance is low compared with E. coli even in this patient group. For women in other ages and for men, growth of S. saprophyticus is a quite uncommon finding.

  12. Evaluation of PCR primer selectivity and phylogenetic specificity by using amplification of 16S rRNA genes from betaproteobacterial ammonia-oxidizing bacteria in environmental samples.

    PubMed

    Junier, Pilar; Kim, Ok-Sun; Hadas, Ora; Imhoff, Johannes F; Witzel, Karl-Paul

    2008-08-01

    The effect of primer specificity for studying the diversity of ammonia-oxidizing betaproteobacteria (betaAOB) was evaluated. betaAOB represent a group of phylogenetically related organisms for which the 16S rRNA gene approach is especially suitable. We used experimental comparisons of primer performance with water samples, together with an in silico analysis of published sequences and a literature review of clone libraries made with four specific PCR primers for the betaAOB 16S rRNA gene. With four aquatic samples, the primers NitA/NitB produced the highest frequency of ammonia-oxidizing-bacterium-like sequences compared to clone libraries with products amplified with the primer combinations betaAMOf/betaAMOr, betaAMOf/Nso1255g, and NitA/Nso1225g. Both the experimental examination of ammonia-oxidizing-bacterium-specific 16S rRNA gene primers and the literature search showed that neither specificity nor sensitivity of primer combinations can be evaluated reliably only by sequence comparison. Apparently, the combination of sequence comparison and experimental data is the best approach to detect possible biases of PCR primers. Although this study focused on betaAOB, the results presented here more generally exemplify the importance of primer selection and potential primer bias when analyzing microbial communities in environmental samples.

  13. The examination of urine samples for pathogenic microbes by the luciferase assay for ATP. 1: The effect of the presence of fungi, fungal like bacteria and kidney cells in urine samples

    NASA Technical Reports Server (NTRS)

    Bush, V. N.

    1973-01-01

    A method for accurately determining urinary tract infections in man is introduced. The method is based on adenosine triphosphate (ATP) concentration in urine samples after removing nonbacterial ATP. Adenosine triphosphate concentration is measured from the bioluminescent reaction of luciferase when mixed with ATP. An examination was also made of the effectiveness of rupturing agents on monkey kidney cells Candia albicans, a Rhodotorula species, and a Streptomyces species in determining whether these cells could contribute ATP to the bacterial ATP value of a urine sample.

  14. Effect of Surface Sampling and Recovery of Viruses and Non-Spore-Forming Bacteria on a Quantitative Microbial Risk Assessment Model for Fomites.

    PubMed

    Weir, Mark H; Shibata, Tomoyuki; Masago, Yoshifumi; Cologgi, Dena L; Rose, Joan B

    2016-06-01

    Quantitative microbial risk assessment (QMRA) is a powerful decision analytics tool, yet it faces challenges when modeling health risks for the indoor environment. One limitation is uncertainty in fomite recovery for evaluating the efficiency of decontamination. Addressing this data gap has become more important as a result of response and recovery from a potential malicious pathogen release. To develop more accurate QMRA models, recovery efficiency from non-porous fomites (aluminum, ceramic, glass, plastic, steel, and wood laminate) was investigated. Fomite material, surface area (10, 100, and 900 cm(2)), recovery tool (swabs and wipes), initial concentration on the fomites and eluent (polysorbate 80, trypticase soy broth, and beef extract) were evaluated in this research. Recovery was shown to be optimized using polysorbate 80, sampling with wipes, and sampling a surface area of 10-100 cm(2). The QMRA model demonstrated, through a relative risk comparison, the need for recovery efficiency to be used in these models to prevent underestimated risks. PMID:27154208

  15. Improvement of the identification of four heavy metals in environmental samples by using predictive decision tree models coupled with a set of five bioluminescent bacteria.

    PubMed

    Jouanneau, Sulivan; Durand, Marie-José; Courcoux, Philippe; Blusseau, Thomas; Thouand, Gérald

    2011-04-01

    A primary statistical model based on the crossings between the different detection ranges of a set of five bioluminescent bacterial strains was developed to identify and quantify four metals which were at several concentrations in different mixtures: cadmium, arsenic III, mercury, and copper. Four specific decision trees based on the CHAID algorithm (CHi-squared Automatic Interaction Detector type) which compose this model were designed from a database of 576 experiments (192 different mixture conditions). A specific software, 'Metalsoft', helped us choose the best decision tree and a user-friendly way to identify the metal. To validate this innovative approach, 18 environmental samples containing a mixture of these metals were submitted to a bioassay and to standardized chemical methods. The results show on average a high correlation of 98.6% for the qualitative metal identification and 94.2% for the quantification. The results are particularly encouraging, and our model is able to provide semiquantitative information after only 60 min without pretreatments of samples. PMID:21355529

  16. Fast simulated annealing and adaptive Monte Carlo sampling based parameter optimization for dense optical-flow deformable image registration of 4DCT lung anatomy

    NASA Astrophysics Data System (ADS)

    Dou, Tai H.; Min, Yugang; Neylon, John; Thomas, David; Kupelian, Patrick; Santhanam, Anand P.

    2016-03-01

    Deformable image registration (DIR) is an important step in radiotherapy treatment planning. An optimal input registration parameter set is critical to achieve the best registration performance with the specific algorithm. Methods In this paper, we investigated a parameter optimization strategy for Optical-flow based DIR of the 4DCT lung anatomy. A novel fast simulated annealing with adaptive Monte Carlo sampling algorithm (FSA-AMC) was investigated for solving the complex non-convex parameter optimization problem. The metric for registration error for a given parameter set was computed using landmark-based mean target registration error (mTRE) between a given volumetric image pair. To reduce the computational time in the parameter optimization process, a GPU based 3D dense optical-flow algorithm was employed for registering the lung volumes. Numerical analyses on the parameter optimization for the DIR were performed using 4DCT datasets generated with breathing motion models and open-source 4DCT datasets. Results showed that the proposed method efficiently estimated the optimum parameters for optical-flow and closely matched the best registration parameters obtained using an exhaustive parameter search method.

  17. The possible role of nannobacteria (dwarf bacteria) in clay-mineral diagenesis and the importance of careful sample preparation in high-magnification SEM study

    SciTech Connect

    Folk, R.L.; Lynch, F.L.

    1997-05-01

    Bacterial textures are present on clay minerals in Oligocene Frio Formation sandstones from the subsurface of the Corpus Christi area, Texas. In shallower samples, beads 0.05--0.1 {micro}m in diameter rim the clay flakes; at greater depth these beads become more abundant and eventually are perched on the ends of clay filaments of the same diameter. The authors believe that the beads are nannobacteria (dwarf forms) that have precipitated or transformed the clay minerals during burial of the sediments. Rosettes of chlorite also contain, after HCl etching, rows of 0.1 {micro}m bodies. In contrast, kaolinite shows no evidence of bacterial precipitation. The authors review other examples of bacterially precipitated clay minerals. A danger present in interpretation of earlier work (and much work of others) is the development of nannobacteria-looking artifacts caused by gold coating times in excess of one minute; the authors strongly recommend a 30-second coating time. Bacterial growth of clay minerals may be a very important process both in the surface and subsurface.

  18. Cultivable alginate lyase-excreting bacteria associated with the Arctic brown alga Laminaria.

    PubMed

    Dong, Sheng; Yang, Jie; Zhang, Xi-Ying; Shi, Mei; Song, Xiao-Yan; Chen, Xiu-Lan; Zhang, Yu-Zhong

    2012-11-01

    Although some alginate lyases have been isolated from marine bacteria, alginate lyases-excreting bacteria from the Arctic alga have not yet been investigated. Here, the diversity of the bacteria associated with the brown alga Laminaria from the Arctic Ocean was investigated for the first time. Sixty five strains belonging to nine genera were recovered from six Laminaria samples, in which Psychrobacter (33/65), Psychromonas (10/65) and Polaribacter (8/65) were the predominant groups. Moreover, 21 alginate lyase-excreting strains were further screened from these Laminaria-associated bacteria. These alginate lyase-excreting strains belong to five genera. Psychromonas (8/21), Psedoalteromonas (6/21) and Polaribacter (4/21) are the predominant genera, and Psychrobacter, Winogradskyella, Psychromonas and Polaribacter were first found to produce alginate lyases. The optimal temperatures for the growth and algiante lyase production of many strains were as low as 10–20 °C, indicating that they are psychrophilic bacteria. The alginate lyases produced by 11 strains showed the highest activity at 20–30 °C, indicating that these enzymes are cold-adapted enzymes. Some strians showed high levels of extracellular alginate lyase activity around 200 U/mL. These results suggest that these algiante lyase-excreting bacteria from the Arctic alga are good materials for studying bacterial cold-adapted alginate lyases. PMID:23203272

  19. Thriving While Engaging in Risk? Examining Trajectories of Adaptive Functioning, Delinquency, and Substance Use in a Nationally Representative Sample of U.S. Adolescents

    ERIC Educational Resources Information Center

    Warren, Michael T.; Wray-Lake, Laura; Rote, Wendy M.; Shubert, Jennifer

    2016-01-01

    Recent advances in positive youth development theory and research explicate complex associations between adaptive functioning and risk behavior, acknowledging that high levels of both co-occur in the lives of some adolescents. However, evidence on nuanced overlapping developmental trajectories of adaptive functioning and risk has been limited to 1…

  20. The relationship between land management, fecal indicator bacteria, and the occurrence of Campylobacter and Listeria spp. in water and sediments during synoptic sampling in the S. Fork Broad River Watershed, N.E. Georgia, U.S.A

    NASA Astrophysics Data System (ADS)

    Bradshaw, J. K.; Molina, M.; Sidle, R. C.; Sullivan, K.; Oakley, B.; Berrang, M.; Meinersmann, R.

    2013-12-01

    Fecal indicator bacteria (FIB) and pathogens stored in the bed sediments of streams and rivers may be mobilized into the water column affecting overall water quality. Furthermore, land management may play an important role in the concentrations of FIB and the occurrence of pathogens in stream water and sediments. The purpose of this study was to determine the relationship between FIB and pathogens in stream water and sediment based on three land management-affected categories: agricultural, forest, and waters receiving treated municipal wastewater. Two synoptic sampling events were conducted under baseflow conditions (<0.64 cm of rain within 24h) between October-November, 2012 and May-June, 2013. Counts of the E. coli and E. faecalis and occurrences of the enteric pathogens Campylobacter and Listeria spp. were measured in stream water and sediment samples collected at 15 locations (six agricultural (AG); six forested (FORS); and three receiving discharge from water pollution control plants (WPCP)) in the S. Fork Broad River watershed located in northeast Georgia, USA. Mean E. coli and E. faecalis concentrations were highest in the AG stream water samples (3.08 log MPN 100 mL -1 for E. coli and 3.07 log CFU 100 mL -1 for E. faecalis ) and lowest in the FORS water samples for E. coli (2.37 log MPN 100 mL -1 ) and WPCP water samples for E. faecalis (2.53 log CFU 100 mL -1 ). E. coli concentrations (2.74 log MPN 100 mL -1 ) in the WPCP streams were intermediate. Similar to water samples, E. coli concentrations were highest in the AG sediments (4.31 log MPN g -1 ), intermediate in the WPCP sediments (4.06 log MPN g -1 ), and lowest in the FORS sediments (3.46 log MPN g -1 ). In contrast to E. coli, E. faecalis concentrations were lower (1.10 to 1.31 log CFU g -1 ) and relatively more constant than E. coli in sediments over the three land management categories. Campylobacter was detected in 27% of the water samples and 8% of the sediment samples. The highest occurrence

  1. Advances in the detection of as in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope: arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria.

    PubMed

    Hitchcock, A P; Obst, M; Wang, J; Lu, Y S; Tyliszczak, T

    2012-03-01

    Speciation and quantitative mapping of elements, organic and inorganic compounds, and mineral phases in environmental samples at high spatial resolution is needed in many areas of geobiochemistry and environmental science. Scanning transmission X-ray microscopes (STXMs) provide a focused beam which can interrogate samples at a fine spatial scale. Quantitative chemical information can be extracted using the transmitted and energy-resolved X-ray fluorescence channels simultaneously. Here we compare the relative merits of transmission and low-energy X-ray fluorescence detection of X-ray absorption for speciation and quantitative analysis of the spatial distribution of arsenic(V) within cell-mineral aggregates formed by Acidovorax sp. strain BoFeN1, an anaerobic nitrate-reducing Fe(II)-oxidizing β-proteobacteria isolated from the sediments of Lake Constance. This species is noted to be highly tolerant to high levels of As(V). Related, As-tolerant Acidovorax-strains have been found in As-contaminated groundwater wells in Bangladesh and Cambodia wherein they might influence the mobility of As by providing sorption sites which might have different properties as compared to chemically formed Fe-minerals. In addition to demonstrating the lower detection limits that are achieved with X-ray fluorescence relative to transmission detection in STXM, this study helps to gain insights into the mechanisms of As immobilization by biogenic Fe-mineral formation and to further the understanding of As-resistance of anaerobic Fe(II)-oxidizing bacteria.

  2. Bioreporter bacteria for landmine detection

    SciTech Connect

    Burlage, R.S.; Youngblood, T.; Lamothe, D.

    1998-04-01

    Landmines (and other UXO) gradually leak explosive chemicals into the soil at significant concentrations. Bacteria, which have adapted to scavenge low concentrations of nutrients, can detect these explosive chemicals. Uptake of these chemicals results in the triggering of specific bacterial genes. The authors have created genetically recombinant bioreporter bacteria that detect small concentrations of energetic chemicals. These bacteria are genetically engineered to produce a bioluminescent signal when they contact specific explosives. A gene for a brightly fluorescent compound can be substituted for increased sensitivity. By finding the fluorescent bacteria, you find the landmine. Detection might be accomplished using stand-off illumination of the minefield and GPS technology, which would result in greatly reduced risk to the deminers. Bioreporter technology has been proven at the laboratory scale, and will be tested under field conditions in the near future. They have created a bacterial strain that detects sub-micromolar concentrations of o- and p-nitrotoluene. Related bacterial strains were produced using standard laboratory protocols, and bioreporters of dinitrotoluene and trinitrotoluene were produced, screening for activity with the explosive compounds. Response time is dependent on the growth rate of the bacteria. Although frill signal production may require several hours, the bacteria can be applied over vast areas and scanned quickly, producing an equivalent detection speed that is very fast. This technology may be applicable to other needs, such as locating buried explosives at military and ordnance/explosive manufacturing facilities.

  3. Reanimation of Ancient Bacteria

    SciTech Connect

    Vreeland, Russell H.

    2009-01-09

    Recent highly publicized experiments conducted on salt crystals taken from the Permian Salado Formation in Southeastern New Mexico have shown that some ancient crystals contain viable microorganisms trapped within fluid inclusions. Stringent geological and microbiological selection criteria were used to select crystals and conduct all sampling. This talk will focus on how each of these lines of data support the conclusion that such isolated bacteria are as old as the rock in which they are trapped. In this case, the isolated microbes are salt tolerant bacilli that grow best in media containing 8% NaCl, and respond to concentrated brines by forming spores. One of the organisms is phylogenetically related to several bacilli, but does have several unique characteristics. This talk will trace the interdisciplinary data and procedures supporting these discoveries, and describe the various isolated bacteria.

  4. Radioresistant Bacteria Came From Mars?

    NASA Astrophysics Data System (ADS)

    Pavlov, A.; Kalinin, V.; Konstantinov, A.; Shelegedin, V.

    We propose that the radioresistant bacteria (i.e. Deinococcus radiodurans) has been originated on Mars. This bacteria possesses an ability which should have been ab- solutely "unnecessary" in the Earth environment. It can survive very high doses of the ionizing radiation. Our experiments demonstrate that different kinds of non- radioresistant bacteria are able to develop very high radioresistance ability also. To develop radioresistance we exposed different bacterial cultures to several dozens of cycles of high irradiation. Therefore, radioresistance is not a result of some early spontaneous bacterial mutation but rather a consequence of the very specific plane- tary environment. Polar regions of Mars are the most probable (if not the only) place in the Solar System for such a periodical high-dosage irradiation process. We pro- pose a plausible scenario of where and when such an adaptation process could have taken place and also discuss indirect arguments of the Martian origin of Deinococcus Radiodurans based on their specific genetic structure.

  5. An adaptive-in-temperature method for on-the-fly sampling of thermal neutron scattering data in continuous-energy Monte Carlo codes

    NASA Astrophysics Data System (ADS)

    Pavlou, Andrew Theodore

    The Monte Carlo simulation of full-core neutron transport requires high fidelity data to represent not only the various types of possible interactions that can occur, but also the temperature and energy regimes for which these data are relevant. For isothermal conditions, nuclear cross section data are processed in advance of running a simulation. In reality, the temperatures in a neutronics simulation are not fixed, but change with respect to the temperatures computed from an associated heat transfer or thermal hydraulic (TH) code. To account for the temperature change, a code user must either 1) compute new data at the problem temperature inline during the Monte Carlo simulation or 2) pre-compute data at a variety of temperatures over the range of possible values. Inline data processing is computationally inefficient while pre-computing data at many temperatures can be memory expensive. An alternative on-the-fly approach to handle the temperature component of nuclear data is desired. By on-the-fly we mean a procedure that adjusts cross section data to the correct temperature adaptively during the Monte Carlo random walk instead of before the running of a simulation. The on-the-fly procedure should also preserve simulation runtime efficiency. While on-the-fly methods have recently been developed for higher energy regimes, the double differential scattering of thermal neutrons has not been examined in detail until now. In this dissertation, an on-the-fly sampling method is developed by investigating the temperature dependence of the thermal double differential scattering distributions. The temperature dependence is analyzed with a linear least squares regression test to develop fit coefficients that are used to sample thermal scattering data at any temperature. The amount of pre-stored thermal scattering data has been drastically reduced from around 25 megabytes per temperature per nuclide to only a few megabytes per nuclide by eliminating the need to compute data

  6. Magnetic bacteria against MIC

    SciTech Connect

    Javaherdashti, R.

    1997-12-01

    In this article, it is suggested to use the sensitivity of magnetotactic bacteria to changes of magnetic field direction and the natural ability of this bacteria in rapid growth during relatively short time intervals against corrosion-enhancing bacteria and especially sulfate-reducing bacteria. If colonies of sulfate-reducing bacteria could be packed among magnetotactic bacteria, then, by applying sufficiently powerful magnetic field (about 0.5 gauss), all of these bacteria (magnetic and non-magnetic) will be oriented towards an Anti-bacteria agent (oxygen or biocide). So, Microbiologically-Influenced Corrosion in the system would be controlled to a large extent.

  7. Back To Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    1997-01-01

    Explores new research about bacteria. Discusses bacterial genomes, archaea, unusual environments, evolution, pathogens, bacterial movement, biofilms, bacteria in the body, and a bacterial obsession. Contains 29 references. (JRH)

  8. Behavioral Regulation, Visual Spatial Maturity in Kindergarten, and the Relationship of School Adaptation in the First Grade for a Sample of Turkish Children.

    PubMed

    Özer, Serap

    2016-04-01

    Behavioral regulation has recently become an important variable in research looking at kindergarten and first-grade achievement of children in private and public schools. The purpose of this study was to examine a measure of behavioral regulation, the Head Toes Knees Shoulders Task, and to evaluate its relationship with visual spatial maturity at the end of kindergarten. Later, in first grade, teachers were asked to rate the children (N = 82) in terms of academic and behavioral adaptation. Behavioral regulation and visual spatial maturity were significantly different between the two school types, but ratings by the teachers in the first grade were affected by children's visual spatial maturity rather than by behavioral regulation. Socioeducational opportunities provided by the two types of schools may be more important to school adaptation than behavioral regulation.

  9. Adaptation and Validation of the Brief Sexual Opinion Survey (SOS) in a Colombian Sample and Factorial Equivalence with the Spanish Version

    PubMed Central

    Sierra, Juan Carlos; Soler, Franklin

    2016-01-01

    Attitudes toward sexuality are a key variable for sexual health. It is really important for psychology and education to have adapted and validated questionnaires to evaluate these attitudes. Therefore, the objective of this research was to adapt, validate and calculate the equivalence of the Colombia Sexual Opinion Survey as compared to the same survey from Spain. To this end, a total of eight experts were consulted and 1,167 subjects from Colombia and Spain answered the Sexual Opinion Survey, the Sexual Assertiveness Scale, the Massachusetts General Hospital-Sexual Functioning Questionnaire, and the Sexuality Scale. The evaluation was conducted by online and the results show adequate qualitative and quantitative properties of the items, with adequate reliability and external validity and compliance with the strong invariance between the two countries. Consequently, the Colombia Sexual Opinion Survey is a valid and reliable scale and its scores can be compared with the ones from the Spain survey, with minimum bias. PMID:27627114

  10. Adaptation and Validation of the Brief Sexual Opinion Survey (SOS) in a Colombian Sample and Factorial Equivalence with the Spanish Version.

    PubMed

    Vallejo-Medina, Pablo; Marchal-Bertrand, Laurent; Gómez-Lugo, Mayra; Espada, José Pedro; Sierra, Juan Carlos; Soler, Franklin; Morales, Alexandra

    2016-01-01

    Attitudes toward sexuality are a key variable for sexual health. It is really important for psychology and education to have adapted and validated questionnaires to evaluate these attitudes. Therefore, the objective of this research was to adapt, validate and calculate the equivalence of the Colombia Sexual Opinion Survey as compared to the same survey from Spain. To this end, a total of eight experts were consulted and 1,167 subjects from Colombia and Spain answered the Sexual Opinion Survey, the Sexual Assertiveness Scale, the Massachusetts General Hospital-Sexual Functioning Questionnaire, and the Sexuality Scale. The evaluation was conducted by online and the results show adequate qualitative and quantitative properties of the items, with adequate reliability and external validity and compliance with the strong invariance between the two countries. Consequently, the Colombia Sexual Opinion Survey is a valid and reliable scale and its scores can be compared with the ones from the Spain survey, with minimum bias. PMID:27627114

  11. Behavioral Regulation, Visual Spatial Maturity in Kindergarten, and the Relationship of School Adaptation in the First Grade for a Sample of Turkish Children.

    PubMed

    Özer, Serap

    2016-04-01

    Behavioral regulation has recently become an important variable in research looking at kindergarten and first-grade achievement of children in private and public schools. The purpose of this study was to examine a measure of behavioral regulation, the Head Toes Knees Shoulders Task, and to evaluate its relationship with visual spatial maturity at the end of kindergarten. Later, in first grade, teachers were asked to rate the children (N = 82) in terms of academic and behavioral adaptation. Behavioral regulation and visual spatial maturity were significantly different between the two school types, but ratings by the teachers in the first grade were affected by children's visual spatial maturity rather than by behavioral regulation. Socioeducational opportunities provided by the two types of schools may be more important to school adaptation than behavioral regulation. PMID:27154368

  12. Adaptive antennas

    NASA Astrophysics Data System (ADS)

    Barton, P.

    1987-04-01

    The basic principles of adaptive antennas are outlined in terms of the Wiener-Hopf expression for maximizing signal to noise ratio in an arbitrary noise environment; the analogy with generalized matched filter theory provides a useful aid to understanding. For many applications, there is insufficient information to achieve the above solution and thus non-optimum constrained null steering algorithms are also described, together with a summary of methods for preventing wanted signals being nulled by the adaptive system. The three generic approaches to adaptive weight control are discussed; correlation steepest descent, weight perturbation and direct solutions based on sample matrix conversion. The tradeoffs between hardware complexity and performance in terms of null depth and convergence rate are outlined. The sidelobe cancellor technique is described. Performance variation with jammer power and angular distribution is summarized and the key performance limitations identified. The configuration and performance characteristics of both multiple beam and phase scan array antennas are covered, with a brief discussion of performance factors.

  13. Hydrocarbon degradation by antarctic bacteria

    SciTech Connect

    Cavanagh, J.A.E.; Nichols, P.D.; McMeekin, T.A.; Franzmann, P.D.

    1996-12-31

    Bacterial cultures obtained from sediment samples collected during a trial oil spill experiment conducted at Airport beach, Eastern Antarctica were selectively enriched for n-alkane-degrading and phenanthrenedegrading bacteria. Samples were collected from a control site and sites treated with different hydrocarbon mixtures - Special Antarctic blend (SAB), BP-Visco and orange roughy oils. One set of replicate sites was also treated with water from Organic Lake which had previously been shown to contain hydrocarbon-degrading bacteria. No viable bacteria were obtained from samples collected from sites treated with orange roughy oil. Extensive degradation of n-alkanes by enrichment cultures obtained from sites treated with SAB and BP-Visco occurred at both 25{degrees}C and 10{degrees}C. Extensive degradation of phenanthrene also occurred in enrichment cultures from these sites grown at 25{degrees}C. Concurrent increases of polar lipid in these cultures were also observed. The presence of 1,4-naphthaquinone and 1-naphthol during the growth of the cultures on phenanthrene is unusual and warrants further investigation of the mechanism of phenanthrene-degradation by these Antarctic bacteria.

  14. Endophytic bacteria in Coffea arabica L.

    PubMed

    Vega, Fernando E; Pava-Ripoll, Monica; Posada, Francisco; Buyer, Jeffrey S

    2005-01-01

    Eighty-seven culturable endophytic bacterial isolates in 19 genera were obtained from coffee plants collected in Colombia (n = 67), Hawaii (n = 17), and Mexico (n = 3). Both Gram positive and Gram negative bacteria were isolated, with a greater percentage (68%) being Gram negative. Tissues yielding bacterial endophytes included adult plant leaves, various parts of the berry (e.g., crown, pulp, peduncle and seed), and leaves, stems, and roots of seedlings. Some of the bacteria also occurred as epiphytes. The highest number of bacteria among the berry tissues sampled was isolated from the seed, and includes Bacillus , Burkholderia , Clavibacter , Curtobacterium , Escherichia , Micrococcus , Pantoea , Pseudomonas , Serratia , and Stenotrophomonas . This is the first survey of the endophytic bacteria diversity in various coffee tissues, and the first study reporting endophytic bacteria in coffee seeds. The possible role for these bacteria in the biology of the coffee plant remains unknown.

  15. Bacteria isolated from amoebae/bacteria consortium

    DOEpatents

    Tyndall, R.L.

    1995-05-30

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  16. Bacteria isolated from amoebae/bacteria consortium

    DOEpatents

    Tyndall, Richard L.

    1995-01-01

    New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

  17. ACETOGENIC BACTERIA ASSOCIATED WITH SEAGRASS ROOTS

    EPA Science Inventory

    Seagrasses are adapted to being rooted in reduced, anoxic sediments with high rates of sulfate reduction. During the day, an oxygen gradient is generated around the roots, becoming anoxic at night. Thus, obligate anaerobic bacteria in the rhizosphere have to tolerate elevated oxy...

  18. Adaptation and Psychometric Properties of the Self-Efficacy/Social Support for Activity for Persons with Intellectual Disability Scale (SE/SS-AID) in a Spanish Sample

    ERIC Educational Resources Information Center

    Cuesta-Vargas, Antonio Ignacio; Paz-Lourido, Berta; Lee, Miyoung; Peterson-Besse, Jana J.

    2013-01-01

    Background: In this study we aimed to develop a Spanish version of the Self-Efficacy/Social Support Scales for Activity for persons with Intellectual Disability (SE/SS-AID). Method: A cross-sectional study was carried out in a sample of 117 individuals with intellectual disability (ID). The SE/SS-AID scales were translated into Spanish and their…

  19. Bacteriophages of methanotrophic bacteria

    SciTech Connect

    Tyutikow, F.M.; Bespalova, I.A.; Rebentish, B.A.; Aleksandrushkina, N.N.; Krivisky, A.S.

    1980-10-01

    Bacteriophages of methanotrophic bacteria have been found in 16 out of 88 studied samples (underground waters, pond water, soil, gas and oil installation waters, fermentor cultural fluids, bacterial paste, and rumen of cattle) taken in different geographic zones of the Soviet Union. Altogether, 23 phage strains were isolated. By fine structure, the phages were divided into two types (with very short or long noncontractile tails); by host range and serological properties, they fell into three types. All phages had guanine- and cytosine-rich double-stranded deoxyribonucleic acid consisting of common nitrogen bases. By all of the above-mentioned properties, all phages within each of the groups were completely identical to one another, but differed from phages of other groups.

  20. The Relationship Between Land Management, Fecal Indicator Bacteria, and the Occurrence of Campylobacter and Listeria Spp. in Water and Sediments During Synoptic Sampling In The South Fork Broad River Watershed, Northeast Georgia, U.S.A.

    EPA Science Inventory

    Fecal indicator bacteria (FIB) and pathogens stored in the bed sediments of streams and rivers may be mobilized into the water column affecting overall water quality. Furthermore, land management may play an important role in the concentrations of FIB and the occurrence of pathog...

  1. Spanish version of the Rotterdam Symptom Check List: cross-cultural adaptation and preliminary validity in a sample of terminal cancer patients.

    PubMed

    Agra, Y; Badía, X

    1998-01-01

    We report on the process of adaptation into Spanish of the Rotterdam Symptom Check List (RSCL). The original version was translated and back-translated by professional bilingual translators. A quantitative rating method was used to select the items to include in the final Spanish version. Validity (discriminant and construction) and reliability were test in 118 terminal cancer patients. In addition to the RSCL the Nottingham Health Profile (NHP) and the Karnofsky Performance Status (KPS) were used. The RSCL showed different ratings on all scales according to the functional level of the patients. The scales were moderately to highly correlated with the NHP (from 0.48 to 0.71). Internal consistency, measured by Cronbach's alpha coefficient ranged from 0.74 (physical) to 0.90 (activity). Twenty-four hours test-retest intraclass correlation coefficient ranged from 0.71 to 0.88. The results of this study suggest that the Spanish version of the RSCL is conceptually equivalent to the original. More research is needed to assess the responsiveness of the version before using it in clinical trials.

  2. Low incidence of clonality in cold water corals revealed through the novel use of standardized protocol adapted to deep sea sampling

    USGS Publications Warehouse

    Becheler, Ronan; Cassone, Anne-Laure; Noel, Philippe; Mouchel, Olivier; Morrison, Cheryl; Arnaud-Haond, Sophie

    2016-01-01

    Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6–7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.

  3. Zooming-in on floral nectar: a first exploration of nectar-associated bacteria in wild plant communities.

    PubMed

    Alvarez-Pérez, Sergio; Herrera, Carlos M; de Vega, Clara

    2012-06-01

    Floral nectar of some animal-pollinated plants usually harbours highly adapted yeast communities which can profoundly alter nectar characteristics and, therefore, potentially have significant impacts on plant reproduction through their effects on insect foraging behaviour. Bacteria have also been occasionally observed in floral nectar, but their prevalence, phylogenetic diversity and ecological role within plant-pollinator-yeast systems remains unclear. Here we present the first reported survey of bacteria in floral nectar from a natural plant community. Culturable bacteria occurring in a total of 71 nectar samples collected from 27 South African plant species were isolated and identified by 16S rRNA gene sequencing. Rarefaction-based analyses were used to assess operational taxonomic units (OTUs) richness at the plant community level using nectar drops as sampling units. Our results showed that bacteria are common inhabitants of floral nectar of South African plants (53.5% of samples yielded growth), and their communities are characterized by low species richness (18 OTUs at a 16S rRNA gene sequence dissimilarity cut-off of 3%) and moderate phylogenetic diversity, with most isolates belonging to the Gammaproteobacteria. Furthermore, isolates showed osmotolerance, catalase activity and the ability to grow under microaerobiosis, three traits that might help bacteria to overcome important factors limiting their survival and/or growth in nectar.

  4. Adaptive Learning and Risk Taking

    ERIC Educational Resources Information Center

    Denrell, Jerker

    2007-01-01

    Humans and animals learn from experience by reducing the probability of sampling alternatives with poor past outcomes. Using simulations, J. G. March (1996) illustrated how such adaptive sampling could lead to risk-averse as well as risk-seeking behavior. In this article, the author develops a formal theory of how adaptive sampling influences risk…

  5. Fast Raman single bacteria identification: toward a routine in-vitro diagnostic

    NASA Astrophysics Data System (ADS)

    Douet, Alice; Josso, Quentin; Marchant, Adrien; Dutertre, Bertrand; Filiputti, Delphine; Novelli-Rousseau, Armelle; Espagnon, Isabelle; Kloster-Landsberg, Meike; Mallard, Frédéric; Perraut, Francois

    2016-04-01

    Timely microbiological results are essential to allow clinicians to optimize the prescribed treatment, ideally at the initial stage of the therapeutic process. Several approaches have been proposed to solve this issue and to provide the microbiological result in a few hours directly from the sample such as molecular biology. However fast and sensitive those methods are not based on single phenotypic information which presents several drawbacks and limitations. Optical methods have the advantage to allow single-cell sensitivity and to probe the phenotype of measured cells. Here we present a process and a prototype that allow automated single-bacteria phenotypic analysis. This prototype is based on the use of Digital In-line Holography techniques combined with a specially designed Raman spectrometer using a dedicated device to capture bacteria. The localization of single-cell is finely determined by using holograms and a proper propagation kernel. Holographic images are also used to analyze bacteria in the sample to sort potential pathogens from flora dwelling species or other biological particles. This accurate localization enables the use of a small confocal volume adapted to the measurement of single-cell. Along with the confocal volume adaptation, we also have modified every components of the spectrometer to optimize single-bacteria Raman measurements. This optimization allowed us to acquire informative single-cell spectra using an integration time of 0.5s only. Identification results obtained with this prototype are presented based on a 65144 Raman spectra database acquired automatically on 48 bacteria strains belonging to 8 species.

  6. Rain sampling device

    DOEpatents

    Nelson, Danny A.; Tomich, Stanley D.; Glover, Donald W.; Allen, Errol V.; Hales, Jeremy M.; Dana, Marshall T.

    1991-01-01

    The present invention constitutes a rain sampling device adapted for independent operation at locations remote from the user which allows rainfall to be sampled in accordance with any schedule desired by the user. The rain sampling device includes a mechanism for directing wet precipitation into a chamber, a chamber for temporarily holding the precipitation during the process of collection, a valve mechanism for controllably releasing samples of said precipitation from said chamber, a means for distributing the samples released from the holding chamber into vessels adapted for permanently retaining these samples, and an electrical mechanism for regulating the operation of the device.

  7. Rain sampling device

    DOEpatents

    Nelson, D.A.; Tomich, S.D.; Glover, D.W.; Allen, E.V.; Hales, J.M.; Dana, M.T.

    1991-05-14

    The present invention constitutes a rain sampling device adapted for independent operation at locations remote from the user which allows rainfall to be sampled in accordance with any schedule desired by the user. The rain sampling device includes a mechanism for directing wet precipitation into a chamber, a chamber for temporarily holding the precipitation during the process of collection, a valve mechanism for controllably releasing samples of the precipitation from the chamber, a means for distributing the samples released from the holding chamber into vessels adapted for permanently retaining these samples, and an electrical mechanism for regulating the operation of the device. 11 figures.

  8. Bacteria under simulated Martian conditions.

    PubMed

    Young, R S; Deal, P H; Bell, J; Allen, J L

    1964-01-01

    The behavior of organisms in simulated Martian conditions is of great importance to exobiology for two reasons: (1) Because of the extreme environment of Mars, the likelihood of contamination of the planet by earth organisms is considered slight by some scientists. To date, there has been little evidence to contradict this supposition. Such evidence is presented. (2) The selection and adaptation of earth bacteria to Martian conditions is potentially significant in understanding Martian life, if it exists, and may be helpful in designing life-detection techniques and devices. Of course, simulation attempts, based on current knowledge of the Mars environment, may be far from the actual conditions, and extrapolations made from such situations of no real significance. However, generalizations can be made and cautious interpretation of the results of those experiments seems well worth reporting. A new technique for simulation of known parameters of the Martian environment is discussed along with possible biological implications. The response of bacteria to such simulation is demonstrated in terms of survival and growth, showing that certain bacteria will not only survive, but grow during simulated Martian freeze-thaw cycling if water is present. Ways are demonstrated in which water can be present on Mars although not detectable with current technology. Plans for future experimentation are discussed.

  9. Nucleic acid extraction from polluted estuarine water for detection of viruses and bacteria by PCR and RT-PCR analysis.

    PubMed

    Petit, F; Craquelin, S; Guespin-Michel, J; Buffet-Janvresse, C

    1999-03-01

    We describe an extraction protocol for genomic DNA and RNA of both viruses and bacteria from polluted estuary water. This procedure was adapted to the molecular study of microflora of estuarine water where bacteria and viruses are found free, forming low-density biofilms, or intimately associated with organo-mineral particles. The sensitivity of the method was determined with seeded samples for RT-PCR and PCR analysis of viruses (10 virions/mL), and bacteria (1 colony-forming unit mL). We report an example of molecular detection of both poliovirus and Salmonella in the Seine estuary (France) and an approach to studying their association with organo-mineral particles.

  10. Chemotactic selection of pollutant degrading soil bacteria

    DOEpatents

    Hazen, T.C.

    1991-03-04

    A method is described for identifying soil microbial strains which may be bacterial degraders of pollutants. This method includes: Placing a concentration of a pollutant in a substantially closed container; placing the container in a sample of soil for a period of time ranging from one minute to several hours; retrieving the container and collecting its contents; microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to innoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

  11. PCR detection of uncultured rumen bacteria.

    PubMed

    Rosero, Jaime A; Strosová, Lenka; Mrázek, Jakub; Fliegerová, Kateřina; Kopečný, Jan

    2012-07-01

    16S rRNA sequences of ruminal uncultured bacterial clones from public databases were phylogenetically examined. The sequences were found to form two unique clusters not affiliated with any known bacterial species: cluster of unidentified sequences of free floating rumen fluid uncultured bacteria (FUB) and cluster of unidentified sequences of bacteria associated with rumen epithelium (AUB). A set of PCR primers targeting 16S rRNA of ruminal free uncultured bacteria and rumen epithelium adhering uncultured bacteria was designed based on these sequences. FUB primers were used for relative quantification of uncultured bacteria in ovine rumen samples. The effort to increase the population size of FUB group has been successful in sulfate reducing broth and culture media supplied with cellulose.

  12. Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

    PubMed Central

    Adams, Heather E.; Crump, Byron C.; Kling, George W.

    2014-01-01

    To understand mechanisms linking ecosystem processes and microbial diversity in freshwater ecosystems, bacterial productivity and the metacommunity dynamics of species sorting and mass effects were investigated in an 18 ha headwater lake in northern Alaska. On most sampling dates, the phylogenetic composition of bacterial communities in inflowing streams (inlets) was strikingly different than that in the lake and the outflowing stream (outlet) (16S DGGE fingerprinting), demonstrating the shift in composition that occurs as these communities transit the lake. Outlet and downstream communities were also more productive than inlet and upstream communities (14C-leucine incorporation). Inlet bacteria transplanted to the outlet stream in dialysis bags were equally or less productive than control bacteria, suggesting that the inlet bacteria are capable of growing under lake conditions, but do not remain abundant because of species sorting in the lake. Outlet bacteria (representative of epilimnetic bacteria) transplanted to the inlet stream were less productive than control bacteria, suggesting that lake bacteria are not as well adapted to growing under inlet conditions. Based on water density, inlet stream water and bacteria generally entered the lake at the base of the epilimnion. However, during low to medium flow in the inlet stream the residence time of the epilimnion was too long relative to bacterial doubling times for these allochthonous bacteria to have a mass effect on the composition of outlet bacteria. The highest community similarity between inlet and outlet bacteria was detected after a large rain event in 2003, with over 61% similarity (average non-storm similarities were 39 ± 8%). While mass effects may be important during large storm events, species sorting appears to be the predominant mechanism structuring bacterial communities within the lake, leading to the assembly of a lake community that has lost some ability to function in stream habitats. PMID

  13. Validation of a simplified field-adapted procedure for routine determinations of methyl mercury at trace levels in natural water samples using species-specific isotope dilution mass spectrometry.

    PubMed

    Lambertsson, Lars; Björn, Erik

    2004-12-01

    A field-adapted procedure based on species-specific isotope dilution (SSID) methodology for trace-level determinations of methyl mercury (CH(3)Hg(+)) in mire, fresh and sea water samples was developed, validated and applied in a field study. In the field study, mire water samples were filtered, standardised volumetrically with isotopically enriched CH(3) (200)Hg(+), and frozen on dry ice. The samples were derivatised in the laboratory without further pre-treatment using sodium tetraethyl borate (NaB(C(2)H(5))(4)) and the ethylated methyl mercury was purge-trapped on Tenax columns. The analyte was thermo-desorbed onto a GC-ICP-MS system for analysis. Investigations preceding field application of the method showed that when using SSID, for all tested matrices, identical results were obtained between samples that were freeze-preserved or analysed unpreserved. For DOC-rich samples (mire water) additional experiments showed no difference in CH(3)Hg(+) concentration between samples that were derivatised without pre-treatment or after liquid extraction. Extractions of samples for matrix-analyte separation prior to derivatisation are therefore not necessary. No formation of CH(3)Hg(+) was observed during sample storage and treatment when spiking samples with (198)Hg(2+). Total uncertainty budgets for the field application of the method showed that for analyte concentrations higher than 1.5 pg g(-1) (as Hg) the relative expanded uncertainty (REU) was approximately 5% and dominated by the uncertainty in the isotope standard concentration. Below 0.5 pg g(-1) (as Hg), the REU was >10% and dominated by variations in the field blank. The uncertainty of the method is sufficiently low to accurately determine CH(3)Hg(+) concentrations at trace levels. The detection limit was determined to be 4 fg g(-1) (as Hg) based on replicate analyses of laboratory blanks. The described procedure is reliable, considerably faster and simplified compared to non-SSID methods and thereby very

  14. Taking Advantage of Electric Field Induced Bacterial Aggregation for the Study of Interactions between Bacteria and Macromolecules by Capillary Electrophoresis.

    PubMed

    Sisavath, Nicolas; Got, Patrice; Charrière, Guillaume M; Destoumieux-Garzon, Delphine; Cottet, Hervé

    2015-07-01

    The quantification of interaction stoichiometry and binding constant between bacteria (or other microorganism) and (macro)molecules remains a challenging issue for which only a few adapted methods are available. In this paper, a new methodology was developed for the determination of the interaction stoichiometry and binding constant between bacteria and (macro)molecules. The originality of this work is to take advantage of the bacterial aggregation phenomenon to directly quantify the free ligand concentration in equilibrated bacteria-ligand mixtures using frontal analysis continuous capillary electrophoresis. The described methodology does not require any sample preparation such as filtration step or centrifugation. It was applied to the study of interactions between Erwinia carotovora and different generations of dendrigraft poly-L-lysines leading to quantitative information (i.e., stoichiometry and binding site constant). High stoichiometries in the order of 10(6)-10(7) were determined between nanometric dendrimer-like ligands and the rod-shaped micrometric bacteria. The effect of the dendrimer generation on the binding constant and the stoichiometry is discussed. Stoichiometries were compared with those obtained by replacing the bacteria by polystyrene microbeads to demonstrate the internalization of the ligands inside the bacteria and the increase of the specific surface via the formation of vesicles. PMID:26086209

  15. Heterotrophic bacteria in drinking water distribution system: a review.

    PubMed

    Chowdhury, Shakhawat

    2012-10-01

    The microbiological quality of drinking water in municipal water distribution systems (WDS) depends on several factors. Free residual chlorine and/or chloramines are typically used to minimize bacterial recontamination and/or regrowth in WDS. Despite such preventive measures, regrowth of heterotrophic (HPC) and opportunistic bacteria in bulk water and biofilms has yet to be controlled completely. No approach has shown complete success in eliminating biofilms or HPC bacteria from bulk water and pipe surfaces. Biofilms can provide shelter for pathogenic bacteria and protect these bacteria from disinfectants. Some HPC bacteria may be associated with aesthetic and non-life threatening diseases. Research to date has achieved important success in understanding occurrence and regrowth of bacteria in bulk water and biofilms in WDS. To achieve comprehensive understanding and to provide efficient control against bacteria regrowth, future research on bacteria regrowth dynamics and their implications is warranted. In this study, a review was performed on the literature published in this area. The findings and limitations of these papers are summarized. Occurrences of bacteria in WDS, factors affecting bacteria regrowth in bulk water and biofilms, bacteria control strategies, sources of nutrients, human health risks from bacterial exposure, modelling of bacteria regrowth and methods of bacteria sampling and detection and quantification are investigated. Advances to date are noted, and future research needs are identified. Finally, research directions are proposed to effectively control HPC and opportunistic bacteria in bulk water and biofilms in WDS.

  16. Plants as sources of airborne bacteria, including ice nucleation-active bacteria.

    PubMed

    Lindemann, J; Constantinidou, H A; Barchet, W R; Upper, C D

    1982-11-01

    Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m over young corn and wet soil to 663 colony-forming units per m over dry soil and 6,500 colony-forming units per m over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.

  17. Ecological Differentiation within a Cosmopolitan Group of Planktonic Freshwater Bacteria (SOL Cluster, Saprospiraceae, Bacteroidetes)†

    PubMed Central

    Schauer, Michael; Kamenik, Christian; Hahn, Martin W.

    2005-01-01

    Members of the monophyletic SOL cluster are large filamentous bacteria inhabiting the pelagic zone of many freshwater habitats. The abundances of SOL bacteria and compositions of SOL communities in samples from 115 freshwater ecosystems around the globe were determined by fluorescence in situ hybridization with cluster- and subcluster-specific oligonucleotide probes. The vast majority (73%) of sampled ecosystems harbored SOL bacteria, and all three previously described SOL subclusters (LD2, HAL, and GKS2-217) were detected. The morphometric and chemicophysical parameters and trophic statuses of ecosystems were related to the occurrence and subcluster-specific composition of SOL bacteria by multivariate statistical methods. SOL bacteria did not occur in acidic lakes (pH < 6), and their abundance was negatively related to high trophy and pH. The subcluster-specific variation in the compositions of SOL communities could be related to the pH, electrical conductivity, altitude, and trophic status of ecosystems. All three known SOL subclusters differed in respect to their tolerated ranges of pH and conductivity. Complete niche separation was observed between the vicarious subclusters GKS2-217 and LD2; the former occurred in soft-water lakes, whereas the latter was found in a broad range of hard-water habitats. The third subgroup (HAL) showed a wide environmental tolerance and was usually found sympatrically with the LD2 or GKS2-217 subcluster. Ecological differentiation of SOL bacteria at the subcluster level was most probably driven by differential adaptation to water chemistry. The distribution of the two vicarious taxa seems to be predominantly controlled by the geological backgrounds of the catchment areas of the habitats. PMID:16204503

  18. Bacteria detection instrument and method

    NASA Technical Reports Server (NTRS)

    Renner, W.; Fealey, R. D. (Inventor)

    1972-01-01

    A method and apparatus for screening a sample fluid for bacterial presence are disclosed wherein the fluid sample is mixed with culture media of sufficient quantity to permit bacterial growth in order to obtain a test solution. The concentration of oxygen dissolved in the test solution is then monitored using the potential difference between a reference electrode and a noble metal electrode which are in contact with the test solution. The change in oxygen concentration which occurs during a period of time as indicated by the electrode potential difference is compared with a detection criterion which exceeds the change which would occur absent bacteria.

  19. Adaptive Management

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive managem...

  20. Rapid, quantitative determination of bacteria in water. [adenosine triphosphate

    NASA Technical Reports Server (NTRS)

    Chappelle, E. W.; Picciolo, G. L.; Thomas, R. R.; Jeffers, E. L.; Deming, J. W. (Inventor)

    1978-01-01

    A bioluminescent assay for ATP in water borne bacteria is made by adding nitric acid to a water sample with concentrated bacteria to rupture the bacterial cells. The sample is diluted with sterile, deionized water, then mixed with a luciferase-luciferin mixture and the resulting light output of the bioluminescent reaction is measured and correlated with bacteria present. A standard and a blank also are presented so that the light output can be correlated to bacteria in the sample and system noise can be substracted from the readings. A chemiluminescent assay for iron porphyrins in water borne bacteria is made by adding luminol reagent to a water sample with concentrated bacteria and measuring the resulting light output of the chemiluminescent reaction.

  1. Pathogenic bacteria and timing of laying

    PubMed Central

    Møller, Anders Pape; Soler, Juan J; Nielsen, Jan Tøttrup; Galván, Ismael

    2015-01-01

    Pathogenic bacteria constitute a serious threat to viability of many organisms. Because growth of most bacteria is favored by humid and warm environmental conditions, earlier reproducers in seasonal environments should suffer less from the negative consequences of pathogenic bacteria. These relationships, and the effects on reproductive success, should be particularly prominent in predators because they are frequently exposed to pathogenic microorganisms from sick prey. Here, we presented and tested this hypothesis by sampling bacteria on adult and nestling goshawks Accipiter gentilis. We predicted that early breeders and their offspring should have fewer bacteria than those reproducing later during the breeding season. Adult goshawks with a high abundance of Staphylococcus on their beak and claws were easier to capture and their laying date was delayed. Moreover, goshawks that laid their eggs later had offspring with more Staphylococcus on their beaks and claws. The strength of the association between laying date and bacterial density of nestlings was stronger during the warm spring of 2013, when nestlings suffered from a higher abundance of pathogenic bacteria. Hatching failure and fledging failure were more common in nests with a higher abundance of Staphylococcus independently of the number of years occupied, laying date, and age of the female nest owner. These findings imply that timing of reproduction may be under the influence of pathogenic bacteria. Because early breeding goshawks produce more recruits than later breeders, our results suggest a role for pathogenic bacteria in the optimal timing of reproduction. PMID:25937910

  2. Genomics of Probiotic Bacteria

    NASA Astrophysics Data System (ADS)

    O'Flaherty, Sarah; Goh, Yong Jun; Klaenhammer, Todd R.

    Probiotic bacteria from the Lactobacillus and Bifidobacterium species belong to the Firmicutes and the Actinobacteria phylum, respectively. Lactobacilli are members of the lactic acid bacteria (LAB) group, a broadly defined family of microorganisms that ferment various hexoses into primarily lactic acid. Lactobacilli are typically low G + C gram-positive species which are phylogenetically diverse, with over 100 species documented to date. Bifidobacteria are heterofermentative, high G + C content bacteria with about 30 species of bifidobacteria described to date.

  3. Bioconjugated magnetic nanoparticles for the detection of bacteria.

    PubMed

    Chu, Yu W; Engebretson, David A; Carey, James R

    2013-12-01

    Blood culture is traditionally a time-consuming method and has not changed significantly in several decades. Using nanotechnology, such as the use of magnetic nanoparticles (MNPs), the blood culture process may be streamlined. An important advantage of using MNPs to capture bacteria is the simple separation of bacteria from biological samples using magnets. Indeed, high bacteria capture efficiencies have been realized using MNPs. The binding events between MNPs and bacteria can be tightly controlled through carefully selected biorecognition events, using molecules such as vancomycin, daptomycin, antibodies, and others. These biomolecules can be readily conjugated onto MNPs followed by tethering to bacteria, thus enabling detection using the beacon produced by the bacteria conjugated MNPs. Methods to prepare bioconjugated MNPs and their performance with bacteria are reviewed. Finally, future directions on bacteria detection using giant magnetoresistance (GMR) biosensors are discussed.

  4. Fireplace adapters

    SciTech Connect

    Hunt, R.L.

    1983-12-27

    An adapter is disclosed for use with a fireplace. The stove pipe of a stove standing in a room to be heated may be connected to the flue of the chimney so that products of combustion from the stove may be safely exhausted through the flue and outwardly of the chimney. The adapter may be easily installed within the fireplace by removing the damper plate and fitting the adapter to the damper frame. Each of a pair of bolts has a portion which hooks over a portion of the damper frame and a threaded end depending from the hook portion and extending through a hole in the adapter. Nuts are threaded on the bolts and are adapted to force the adapter into a tight fit with the adapter frame.

  5. Relation of bacteria in limestone aquifers to septic systems in Berkeley County, West Virginia

    USGS Publications Warehouse

    Mathes, M.V.

    2000-01-01

    Water samples collected from 50 wells in Berkeley County, West Virginia, during June 2000 were analyzed for indicator bacteria. Of the 50 wells sampled, 62 percent (31 wells) contained total coliform bacteria, 32 percent (16 wells) contained Escherichia coli, and 30 percent (15 wells) contained fecal coliform bacteria. Although bacteria were present in many wells regardless of the number of septic systems in a 5-acre circular area around each well, no apparent correlation was detected between septic-system density and concentrations of bacteria colonies. There was also little difference in the frequency of total coliform bacteria detection between shallow and deep wells; however, the highest concentrations of E. coli and fecal coliform bacteria were found in the shallowest wells. At least one of the three bacteria types was found in samples of untreated water in 32 of the 50 wells. At 21 of the 32 wells with bacteria present, there was no treatment of the ground water to remove bacteria.

  6. Bleach vs. Bacteria

    MedlinePlus

    ... Inside Life Science > Bleach vs. Bacteria Inside Life Science View All Articles | Inside Life Science Home Page Bleach vs. Bacteria By Sharon Reynolds ... For Proteins, Form Shapes Function This Inside Life Science article also appears on LiveScience . Learn about related ...

  7. Bacteria turn tiny gears

    SciTech Connect

    2009-01-01

    Swarms of bacteria turn two 380-micron long gears, opening the possibility of building hybrid biological machines at the microscopic scale. Read more at Wired: http://www.wired.com/wiredscience/2009/12/bacterial-micro-machine/#more-15684 or Scientific American: http://www.scientificamerican.com/article.cfm?id=brownian-motion-bacteria

  8. Some Bacteria Are Beneficial!

    USGS Publications Warehouse

    McMahon, Peter B.

    1995-01-01

    Most people would agree that bacteria usually spell trouble where the quality of drinking water is con cerned. However, recent studies conducted by the U.S. Geological Survey (USGS) under the National Water-Quality Assessment (NAWQA) program have shown that some bacteria can improve the quality of water.

  9. Apparatus and method for handheld sampling

    DOEpatents

    Staab, Torsten A.

    2005-09-20

    The present invention includes an apparatus, and corresponding method, for taking a sample. The apparatus is built around a frame designed to be held in at least one hand. A sample media is used to secure the sample. A sample media adapter for securing the sample media is operated by a trigger mechanism connectively attached within the frame to the sample media adapter.

  10. Real-time quantification of viable bacteria in liquid medium using infrared thermography

    NASA Astrophysics Data System (ADS)

    Salaimeh, Ahmad A.; Campion, Jeffrey J.; Gharaibeh, Belal Y.; Evans, Martin E.; Saito, Kozo

    2011-11-01

    Quantifying viable bacteria in liquids is important in environmental, food processing, manufacturing, and medical applications. Since vegetative bacteria generate heat as a result of biochemical reactions associated with cellular functions, thermal sensing techniques, including infrared thermography (IRT), have been used to detect viable cells in biologic samples. We developed a novel method that extends the dynamic range and improves the sensitivity of bacterial quantification by IRT. The approach uses IRT video, thermodynamics laws, and heat transfer mechanisms to directly measure, in real-time, the amount of energy lost as heat from the surface of a liquid sample containing bacteria when the specimen cools to a lower temperature over 2 min. We show that the Energy Content ( EC) of liquid media containing as few as 120 colony-forming units (CFU) of Escherichia coli per ml was significantly higher than that of sterile media ( P < 0.0001), and that EC and viable counts were strongly positively correlated ( r = 0.986) over a range of 120 to approximately 5 × 10 8 CFU/ml. Our IRT approach is a unique non-contact method that provides real-time bacterial enumeration over a wide dynamic range without the need for sample concentration, modification, or destruction. The approach could be adapted to quantify other living cells in a liquid milieu and has the potential for automation and high throughput.

  11. Adaptive Sampling using Support Vector Machines

    SciTech Connect

    D. Mandelli; C. Smith

    2012-11-01

    Reliability/safety analysis of stochastic dynamic systems (e.g., nuclear power plants, airplanes, chemical plants) is currently performed through a combination of Event-Tress and Fault-Trees. However, these conventional methods suffer from certain drawbacks: • Timing of events is not explicitly modeled • Ordering of events is preset by the analyst • The modeling of complex accident scenarios is driven by expert-judgment For these reasons, there is currently an increasing interest into the development of dynamic PRA methodologies since they can be used to address the deficiencies of conventional methods listed above.

  12. Bacterial surface adaptation

    NASA Astrophysics Data System (ADS)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  13. Airborne Bacteria in an Urban Environment

    PubMed Central

    Mancinelli, Rocco L.; Shulls, Wells A.

    1978-01-01

    Samples were taken at random intervals over a 2-year period from urban air and tested for viable bacteria. The number of bacteria in each sample was determined, and each organism isolated was identified by its morphological and biochemical characteristics. The number of bacteria found ranged from 0.013 to 1.88 organisms per liter of air sampled. Representatives of 19 different genera were found in 21 samples. The most frequently isolated organisms and their percent of occurence were Micrococcus (41%), Staphylococcus (11%), and Aerococcus (8%). The bacteria isolated were correlated with various weather and air pollution parameters using the Pearson product-moment correlation coefficient method. Statistically significant correlations were found between the number of viable bacteria isolated and the concentrations of nitric oxide (−0.45), nitrogen dioxide (+0.43), and suspended particulate pollutants (+0.56). Calculated individually, the total number of Micrococcus, Aerococcus, and Staphylococcus, number of rods, and number of cocci isolated showed negative correlations with nitric oxide and positive correlations with nitrogen dioxide and particulates. Statistically significant positive correlations were found between the total number of rods isolated and the concentration of nitrogen dioxide (+0.54) and the percent relative humidity (+0.43). The other parameters tested, sulfur dioxide, hydrocarbons, and temperature, showed no significant correlations. Images PMID:677875

  14. Adaptive SPECT

    PubMed Central

    Barrett, Harrison H.; Furenlid, Lars R.; Freed, Melanie; Hesterman, Jacob Y.; Kupinski, Matthew A.; Clarkson, Eric; Whitaker, Meredith K.

    2008-01-01

    Adaptive imaging systems alter their data-acquisition configuration or protocol in response to the image information received. An adaptive pinhole single-photon emission computed tomography (SPECT) system might acquire an initial scout image to obtain preliminary information about the radiotracer distribution and then adjust the configuration or sizes of the pinholes, the magnifications, or the projection angles in order to improve performance. This paper briefly describes two small-animal SPECT systems that allow this flexibility and then presents a framework for evaluating adaptive systems in general, and adaptive SPECT systems in particular. The evaluation is in terms of the performance of linear observers on detection or estimation tasks. Expressions are derived for the ideal linear (Hotelling) observer and the ideal linear (Wiener) estimator with adaptive imaging. Detailed expressions for the performance figures of merit are given, and possible adaptation rules are discussed. PMID:18541485

  15. Fast detection of coliform bacteria by means of gas chromatography-differential mobility spectrometry.

    PubMed

    Saptalena, Lena Ganda; Kuklya, Andriy; Telgheder, Ursula

    2016-05-01

    In this study, we demonstrate that the combination of an enzymatic method (based on Colilert-18 medium) and gas chromatography-differential mobility spectrometry (GC-DMS) can reduce the time required for detection of coliform bacteria (including Escherichia coli) from 18 to 2.5 h. The presented method includes the incubation (~2.5 h) of the sample containing coliform bacteria in Colilert-18 medium. The incubation time of 2.5 h is required for the activation of the β-galactosidase enzyme. Produced during the incubation biomarker o-nitrophenol (ONP) can be detected by means of GC-DMS within just 200 s. The detection limit for ONP was 45 ng (on-column). The method developed in this work provides significantly shorter analysis time compared with standard methods, and can be potentially adapted to the field conditions. Therefore, this method is a promising tool for an early detection of coliform bacteria (including E. coli). Graphical Abstract Fast detection of coliform bacteria by means of GC-DMS.

  16. Adaptive Computing.

    ERIC Educational Resources Information Center

    Harrell, William

    1999-01-01

    Provides information on various adaptive technology resources available to people with disabilities. (Contains 19 references, an annotated list of 129 websites, and 12 additional print resources.) (JOW)

  17. Contour adaptation.

    PubMed

    Anstis, Stuart

    2013-01-01

    It is known that adaptation to a disk that flickers between black and white at 3-8 Hz on a gray surround renders invisible a congruent gray test disk viewed afterwards. This is contrast adaptation. We now report that adapting simply to the flickering circular outline of the disk can have the same effect. We call this "contour adaptation." This adaptation does not transfer interocularly, and apparently applies only to luminance, not color. One can adapt selectively to only some of the contours in a display, making only these contours temporarily invisible. For instance, a plaid comprises a vertical grating superimposed on a horizontal grating. If one first adapts to appropriate flickering vertical lines, the vertical components of the plaid disappears and it looks like a horizontal grating. Also, we simulated a Cornsweet (1970) edge, and we selectively adapted out the subjective and objective contours of a Kanisza (1976) subjective square. By temporarily removing edges, contour adaptation offers a new technique to study the role of visual edges, and it demonstrates how brightness information is concentrated in edges and propagates from them as it fills in surfaces.

  18. Super-Resolution Imaging of Bacteria in a Microfluidics Device

    PubMed Central

    Valeri, Alessandro; Mignot, Tâm; Nöllmann, Marcelo

    2013-01-01

    Bacteria have evolved complex, highly-coordinated, multi-component cellular engines to achieve high degrees of efficiency, accuracy, adaptability, and redundancy. Super-resolution fluorescence microscopy methods are ideally suited to investigate the internal composition, architecture, and dynamics of molecular machines and large cellular complexes. These techniques require the long-term stability of samples, high signal-to-noise-ratios, low chromatic aberrations and surface flatness, conditions difficult to meet with traditional immobilization methods. We present a method in which cells are functionalized to a microfluidics device and fluorophores are injected and imaged sequentially. This method has several advantages, as it permits the long-term immobilization of cells and proper correction of drift, avoids chromatic aberrations caused by the use of different filter sets, and allows for the flat immobilization of cells on the surface. In addition, we show that different surface chemistries can be used to image bacteria at different time-scales, and we introduce an automated cell detection and image analysis procedure that can be used to obtain cell-to-cell, single-molecule localization and dynamic heterogeneity as well as average properties at the super-resolution level. PMID:24146850

  19. Raman spectroscopic differentiation of planktonic bacteria and biofilms.

    PubMed

    Kusić, Dragana; Kampe, Bernd; Ramoji, Anuradha; Neugebauer, Ute; Rösch, Petra; Popp, Jürgen

    2015-09-01

    Both biofilm formations as well as planktonic cells of water bacteria such as diverse species of the Legionella genus as well as Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli were examined in detail by Raman microspectroscopy. Production of various molecules involved in biofilm formation of tested species in nutrient-deficient media such as tap water was observed and was particularly evident in the biofilms formed by six Legionella species. Biofilms of selected species of the Legionella genus differ significantly from the planktonic cells of the same organisms in their lipid amount. Also, all Legionella species have formed biofilms that differ significantly from the biofilms of the other tested genera in the amount of lipids they produced. We believe that the significant increase in the synthesis of this molecular species may be associated with the ability of Legionella species to form biofilms. In addition, a combination of Raman microspectroscopy with chemometric approaches can distinguish between both planktonic form and biofilms of diverse bacteria and could be used to identify samples which were unknown to the identification model. Our results provide valuable data for the development of fast and reliable analytic methods based on Raman microspectroscopy, which can be applied to the analysis of tap water-adapted microorganisms without any cultivation step.

  20. Evolution of the MIDTAL microarray: the adaption and testing of oligonucleotide 18S and 28S rDNA probes and evaluation of subsequent microarray generations with Prymnesium spp. cultures and field samples.

    PubMed

    McCoy, Gary R; Touzet, Nicolas; Fleming, Gerard T A; Raine, Robin

    2015-07-01

    The toxic microalgal species Prymnesium parvum and Prymnesium polylepis are responsible for numerous fish kills causing economic stress on the aquaculture industry and, through the consumption of contaminated shellfish, can potentially impact on human health. Monitoring of toxic phytoplankton is traditionally carried out by light microscopy. However, molecular methods of identification and quantification are becoming more common place. This study documents the optimisation of the novel Microarrays for the Detection of Toxic Algae (MIDTAL) microarray from its initial stages to the final commercial version now available from Microbia Environnement (France). Existing oligonucleotide probes used in whole-cell fluorescent in situ hybridisation (FISH) for Prymnesium species from higher group probes to species-level probes were adapted and tested on the first-generation microarray. The combination and interaction of numerous other probes specific for a whole range of phytoplankton taxa also spotted on the chip surface caused high cross reactivity, resulting in false-positive results on the microarray. The probe sequences were extended for the subsequent second-generation microarray, and further adaptations of the hybridisation protocol and incubation temperatures significantly reduced false-positive readings from the first to the second-generation chip, thereby increasing the specificity of the MIDTAL microarray. Additional refinement of the subsequent third-generation microarray protocols with the addition of a poly-T amino linker to the 5' end of each probe further enhanced the microarray performance but also highlighted the importance of optimising RNA labelling efficiency when testing with natural seawater samples from Killary Harbour, Ireland.

  1. Antibiotics from predatory bacteria

    PubMed Central

    Korp, Juliane; Vela Gurovic, María S

    2016-01-01

    Summary Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism. PMID:27340451

  2. Antibiotics from predatory bacteria.

    PubMed

    Korp, Juliane; Vela Gurovic, María S; Nett, Markus

    2016-01-01

    Bacteria, which prey on other microorganisms, are commonly found in the environment. While some of these organisms act as solitary hunters, others band together in large consortia before they attack their prey. Anecdotal reports suggest that bacteria practicing such a wolfpack strategy utilize antibiotics as predatory weapons. Consistent with this hypothesis, genome sequencing revealed that these micropredators possess impressive capacities for natural product biosynthesis. Here, we will present the results from recent chemical investigations of this bacterial group, compare the biosynthetic potential with that of non-predatory bacteria and discuss the link between predation and secondary metabolism. PMID:27340451

  3. Close Encounters of Lymphoid Cells and Bacteria

    PubMed Central

    Cruz-Adalia, Aranzazu; Veiga, Esteban

    2016-01-01

    During infections, the first reaction of the host against microbial pathogens is carried out by innate immune cells, which recognize conserved structures on pathogens, called pathogen-associated molecular patterns. Afterward, some of these innate cells can phagocytose and destroy the pathogens, secreting cytokines that would modulate the immune response to the challenge. This rapid response is normally followed by the adaptive immunity, more specific and essential for a complete pathogen clearance in many cases. Some innate immune cells, usually named antigen-presenting cells, such as macrophages or dendritic cells, are able to process internalized invaders and present their antigens to lymphocytes, triggering the adaptive immune response. Nevertheless, the traditional boundary of separated roles between innate and adaptive immunity has been blurred by several studies, showing that very specialized populations of lymphocytes (cells of the adaptive immunity) behave similarly to cells of the innate immunity. These “innate-like” lymphocytes include γδ T cells, invariant NKT cells, B-1 cells, mucosal-associated invariant T cells, marginal zone B cells, and innate response activator cells, and together with the newly described innate lymphoid cells are able to rapidly respond to bacterial infections. Strikingly, our recent data suggest that conventional CD4+ T cells, the paradigm of cells of the adaptive immunity, also present innate-like behavior, capturing bacteria in a process called transinfection. Transinfected CD4+ T cells digest internalized bacteria like professional phagocytes and secrete large amounts of proinflammatory cytokines, protecting for further bacterial challenges. In the present review, we will focus on the data showing such innate-like behavior of lymphocytes following bacteria encounter. PMID:27774092

  4. The Interaction between Heterotrophic Bacteria and Coliform, Fecal Coliform, Fecal Streptococci Bacteria in the Water Supply Networks

    PubMed Central

    AMANIDAZ, Nazak; ZAFARZADEH, Ali; MAHVI, Amir Hossein

    2015-01-01

    Background: This study investigated the interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in water supply networks. Methods: This study was conducted during 2013 on water supply distribution network in Aq Qala City, Golestan Province, Northern Iran and standard methods were applied for microbiological analysis. The surface method was applied to test the heterotrophic bacteria and MPN method was used for coliform, fecal coliform and fecal streptococci bacteria measurements. Results: In 114 samples, heterotrophic bacteria count were over 500 CFU/ml, which the amount of fecal coliform, coliform, and fecal streptococci were 8, 32, and 20 CFU/100 ml, respectively. However, in the other 242 samples, with heterotrophic bacteria count being less than 500 CFU/ml, the amount of fecal coliform, coliform, and fecal streptococci was 7, 23, and 11 CFU/100ml, respectively. The relationship between heterotrophic bacteria, coliforms and fecal streptococci was highly significant (P<0.05). We observed the concentration of coliforms, fecal streptococci bacteria being high, whenever the concentration of heterotrophic bacteria in the water network systems was high. Conclusion: Interaction between heterotrophic bacteria and coliform, fecal coliforms, fecal streptococci bacteria in the Aq Qala City water supply networks was not notable. It can be due to high concentrations of organic carbon, bio-films and nutrients, which are necessary for growth, and survival of all microorganisms. PMID:26811820

  5. Morphological plasticity of bacteria-Open questions.

    PubMed

    Shen, Jie-Pan; Chou, Chia-Fu

    2016-05-01

    Morphological plasticity of bacteria is a cryptic phenomenon, by which bacteria acquire adaptive benefits for coping with changing environments. Some environmental cues were identified to induce morphological plasticity, but the underlying molecular mechanisms remain largely unknown. Physical and chemical factors causing morphological changes in bacteria have been investigated and mostly associated with potential pathways linked to the cell wall synthetic machinery. These include starvation, oxidative stresses, predation effectors, antimicrobial agents, temperature stresses, osmotic shock, and mechanical constraints. In an extreme scenario of morphological plasticity, bacteria can be induced to be shapeshifters when the cell walls are defective or deficient. They follow distinct developmental pathways and transform into assorted morphological variants, and most of them would eventually revert to typical cell morphology. It is suggested that phenotypic heterogeneity might play a functional role in the development of morphological diversity and/or plasticity within an isogenic population. Accordingly, phenotypic heterogeneity and inherited morphological plasticity are found to be survival strategies adopted by bacteria in response to environmental stresses. Here, microfluidic and nanofabrication technology is considered to provide versatile solutions to induce morphological plasticity, sort and isolate morphological variants, and perform single-cell analysis including transcriptional and epigenetic profiling. Questions such as how morphogenesis network is modulated or rewired (if epigenetic controls of cell morphogenesis apply) to induce bacterial morphological plasticity could be resolved with the aid of micro-nanofluidic platforms and optimization algorithms, such as feedback system control. PMID:27375812

  6. Climate adaptation

    NASA Astrophysics Data System (ADS)

    Kinzig, Ann P.

    2015-03-01

    This paper is intended as a brief introduction to climate adaptation in a conference devoted otherwise to the physics of sustainable energy. Whereas mitigation involves measures to reduce the probability of a potential event, such as climate change, adaptation refers to actions that lessen the impact of climate change. Mitigation and adaptation differ in other ways as well. Adaptation does not necessarily have to be implemented immediately to be effective; it only needs to be in place before the threat arrives. Also, adaptation does not necessarily require global, coordinated action; many effective adaptation actions can be local. Some urban communities, because of land-use change and the urban heat-island effect, currently face changes similar to some expected under climate change, such as changes in water availability, heat-related morbidity, or changes in disease patterns. Concern over those impacts might motivate the implementation of measures that would also help in climate adaptation, despite skepticism among some policy makers about anthropogenic global warming. Studies of ancient civilizations in the southwestern US lends some insight into factors that may or may not be important to successful adaptation.

  7. [Darwin and bacteria].

    PubMed

    Ledermann D, Walter

    2009-02-01

    As in 2009 the scientific world celebrates two hundreds years from the birthday of Charles Darwin and one hundred and fifty from the publication of The Origin of Species, an analysis of his complete work is performed, looking for any mention of bacteria. But it seems that the great naturahst never took knowledge about its existence, something rather improbable in a time when the discovery of bacteria shook the medical world, or he deliberately ignored them, not finding a place for such microscopic beings into his theory of evolution. But the bacteria badly affected his familiar life, killing scarlet fever one of his children and worsening to death the evolution of tuberculosis of his favourite Annie. Darwin himself could suffer the sickness of Chagas, whose etiological agent has a similar level to bacteria in the scale of evolution. PMID:19350162

  8. Bacteria subsisting on antibiotics.

    PubMed

    Dantas, Gautam; Sommer, Morten O A; Oluwasegun, Rantimi D; Church, George M

    2008-04-01

    Antibiotics are a crucial line of defense against bacterial infections. Nevertheless, several antibiotics are natural products of microorganisms that have as yet poorly appreciated ecological roles in the wider environment. We isolated hundreds of soil bacteria with the capacity to grow on antibiotics as a sole carbon source. Of 18 antibiotics tested, representing eight major classes of natural and synthetic origin, 13 to 17 supported the growth of clonal bacteria from each of 11 diverse soils. Bacteria subsisting on antibiotics are surprisingly phylogenetically diverse, and many are closely related to human pathogens. Furthermore, each antibiotic-consuming isolate was resistant to multiple antibiotics at clinically relevant concentrations. This phenomenon suggests that this unappreciated reservoir of antibiotic-resistance determinants can contribute to the increasing levels of multiple antibiotic resistance in pathogenic bacteria. PMID:18388292

  9. Indicator For Pseudomonas Bacteria

    NASA Technical Reports Server (NTRS)

    Margalit, Ruth

    1990-01-01

    Characteristic protein extracted and detected. Natural protein marker found in Pseudomonas bacteria. Azurin, protein containing copper readily extracted, purified, and used to prepare antibodies. Possible to develop simple, fast, and accurate test for marker carried out in doctor's office.

  10. [Darwin and bacteria].

    PubMed

    Ledermann D, Walter

    2009-02-01

    As in 2009 the scientific world celebrates two hundreds years from the birthday of Charles Darwin and one hundred and fifty from the publication of The Origin of Species, an analysis of his complete work is performed, looking for any mention of bacteria. But it seems that the great naturahst never took knowledge about its existence, something rather improbable in a time when the discovery of bacteria shook the medical world, or he deliberately ignored them, not finding a place for such microscopic beings into his theory of evolution. But the bacteria badly affected his familiar life, killing scarlet fever one of his children and worsening to death the evolution of tuberculosis of his favourite Annie. Darwin himself could suffer the sickness of Chagas, whose etiological agent has a similar level to bacteria in the scale of evolution.

  11. Gut bacteria and cancer

    PubMed Central

    Erdman, Susan E.; Poutahidis, Theofilos

    2015-01-01

    Microbiota on the mucosal surfaces of the gastrointestinal (GI) tract greatly outnumber the cells in the human body. Effects of antibiotics indicate that GI tract bacteria may be determining the fate of distal cancers. Recent data implicate dysregulated host responses to enteric bacteria leading to cancers in extra-intestinal sites. Together these findings point to novel anti-cancer strategies aimed at promoting GI tract homeostasis. PMID:26050963

  12. Recurrent isolation of extremotolerant bacteria from the clean room where Phoenix spacecraft components were assembled.

    PubMed

    Ghosh, Sudeshna; Osman, Shariff; Vaishampayan, Parag; Venkateswaran, Kasthuri

    2010-04-01

    The microbial burden of the Phoenix spacecraft assembly environment was assessed in a systematic manner via several cultivation-based techniques and a suite of NASA-certified, cultivation-independent biomolecule-based detection assays. Extremotolerant bacteria that could potentially survive conditions experienced en route to Mars or on the planet's surface were isolated with a series of cultivation-based assays that promoted the growth of a variety of organisms, including spore formers, mesophilic heterotrophs, anaerobes, thermophiles, psychrophiles, alkaliphiles, and bacteria resistant to UVC radiation and hydrogen peroxide exposure. Samples were collected from the clean room where Phoenix was housed at three different time points, before (1P), during (2P), and after (3P) Phoenix's presence at the facility. There was a reduction in microbial burden of most bacterial groups, including spore formers, in samples 2P and 3P. Analysis of 262 isolates from the facility demonstrated that there was also a shift in predominant cultivable bacterial populations accompanied by a reduction in diversity during 2P and 3P. It is suggested that this shift was a result of increased cleaning when Phoenix was present in the assembly facility and that certain species, such as Acinetobacter johnsonii and Brevundimonas diminuta, may be better adapted to environmental conditions found during 2P and 3P. In addition, problematic bacteria resistant to multiple extreme conditions, such as Bacillus pumilus, were able to survive these periods of increased cleaning.

  13. Recurrent Isolation of Extremotolerant Bacteria from the Clean Room Where Phoenix Spacecraft Components Were Assembled

    NASA Astrophysics Data System (ADS)

    Ghosh, Sudeshna; Osman, Shariff; Vaishampayan, Parag; Venkateswaran, Kasthuri

    2010-04-01

    The microbial burden of the Phoenix spacecraft assembly environment was assessed in a systematic manner via several cultivation-based techniques and a suite of NASA-certified, cultivation-independent biomolecule-based detection assays. Extremotolerant bacteria that could potentially survive conditions experienced en route to Mars or on the planet's surface were isolated with a series of cultivation-based assays that promoted the growth of a variety of organisms, including spore formers, mesophilic heterotrophs, anaerobes, thermophiles, psychrophiles, alkaliphiles, and bacteria resistant to UVC radiation and hydrogen peroxide exposure. Samples were collected from the clean room where Phoenix was housed at three different time points, before (1P), during (2P), and after (3P) Phoenix's presence at the facility. There was a reduction in microbial burden of most bacterial groups, including spore formers, in samples 2P and 3P. Analysis of 262 isolatisolattivable bacterial populations accompanied by a reduction in diversity during 2P and 3P. It is suggested that this shift was a result of increased cleaning when Phoenix was present in the assembly facility and that certain species, such as Acinetobacter johnsonii and Brevundimonas diminuta, may be better adapted to environmental conditions found during 2P and 3P. In addition, problematic bacteria resistant to multiple extreme conditions, such as Bacillus pumilus, were able to survive these periods of increased cleaning.

  14. Enumeration of total aerobic bacteria and Escherichia coli in minced meat and on carcass surface samples with an automated most-probable-number method compared with colony count protocols.

    PubMed

    Paulsen, P; Schopf, E; Smulders, F J M

    2006-10-01

    An automated most-probable-number (MPN) system for the enumeration of total bacterial flora and Escherichia coli was compared with plate count agar and tryptone-bile-glucuronide (TBX) and ColiID (in-house method) agar methodology. The MPN partitioning of sample aliquots was done automatically on a disposable card containing 48 wells of 3 different volumes, i.e., 16 replicates per volume. Bacterial growth was detected by the formation of fluorescent 4-methylumbilliferone. After incubation, the number of fluorescent wells was read with a separate device, and the MPN was calculated automatically. A total of 180 naturally contaminated samples were tested (pig and cattle carcass surfaces, n = 63; frozen minced meat, n = 62; and refrigerated minced meat, n = 55). Plate count agar results and MPN were highly correlated (r = 0.99), with log MPN = -0.25 + 1.05 x log CFU (plate count agar) (n = 163; range, 2.2 to 7.5 log CFU/g or cm2). Only a few discrepancies were recorded. In two samples (1.1%), the differences were > or = 1.0 log; in three samples (1.7%), the differences were > or = 0.5 log. For E. coli, regression analysis was done for all three methods for 80 minced meat samples, which were above the limit of detection (1.0 log CFU/g): log MPN = 0.18 + 0.98 x log CFU (TBX), r = 0.96, and log MPN = -0.02 + 0.99 x log CFU (ColiID), r = 0.99 (range, 1.0 to 4.2 log CFU/g). Four discrepant results were recorded, with differences of > 0.5 but < 1.0 log unit. These results suggest that the automated MPN method described is a suitable and labor-saving alternative to colony count techniques for total bacterial flora and E. coli determination in minced meat or on carcass surfaces.

  15. Sample rotating turntable kit for infrared spectrometers

    DOEpatents

    Eckels, Joel Del; Klunder, Gregory L.

    2008-03-04

    An infrared spectrometer sample rotating turntable kit has a rotatable sample cup containing the sample. The infrared spectrometer has an infrared spectrometer probe for analyzing the sample and the rotatable sample cup is adapted to receive the infrared spectrometer probe. A reflectance standard is located in the rotatable sample cup. A sleeve is positioned proximate the sample cup and adapted to receive the probe. A rotator rotates the rotatable sample cup. A battery is connected to the rotator.

  16. The fecal bacteria

    USGS Publications Warehouse

    Sadowsky, Michael J.; Whitman, Richard L.

    2011-01-01

    The Fecal Bacteria offers a balanced, integrated discussion of fecal bacteria and their presence and ecology in the intestinal tract of mammals, in the environment, and in the food supply. This volume covers their use in examining and assessing water quality in order to offer protection from illnesses related to swimming in or ingesting contaminated water, in addition to discussing their use in engineering considerations of water quality, modeling, monitoring, and regulations. Fecal bacteria are additionally used as indicators of contamination of ready-to-eat foods and fresh produce. The intestinal environment, the microbial community structure of the gut microbiota, and the physiology and genomics of this broad group of microorganisms are explored in the book. With contributions from an internationally recognized group of experts, the book integrates medicine, public health, environmental, and microbiological topics in order to provide a unique, holistic understanding of fecal bacteria. Moreover, it shows how the latest basic science and applied research findings are helping to solve problems and develop effective management strategies. For example, readers will discover how the latest tools and molecular approaches have led to our current understanding of fecal bacteria and enabled us to improve human health and water quality. The Fecal Bacteria is recommended for microbiologists, clinicians, animal scientists, engineers, environmental scientists, food safety experts, water quality managers, and students. It will help them better understand fecal bacteria and use their knowledge to protect human and environmental health. They can also apply many of the techniques and molecular tools discussed in this book to the study of a broad range of microorganisms in a variety of habitats.

  17. Measuring Adaptation in Ministers' Families: The Modified Family Adaptation Scale.

    ERIC Educational Resources Information Center

    Ostrander, Diane L.; Henry, Carolyn S.

    A modification of the Family Adaptation Scale of Antonovsky and Sourani (1988), was developed for assessing the adaptation of ministers' families. A sample of 317 individuals (ministers, spouses, and children aged 8 to 18) from 135 protestant ministers' families was used to test the scale. The self-report questionnaire was tested for internal…

  18. Toothbrush Adaptations.

    ERIC Educational Resources Information Center

    Exceptional Parent, 1987

    1987-01-01

    Suggestions are presented for helping disabled individuals learn to use or adapt toothbrushes for proper dental care. A directory lists dental health instructional materials available from various organizations. (CB)

  19. [Transport of subsurface bacteria in porous media

    SciTech Connect

    Not Available

    1992-08-01

    This report describes studies undertaken to better understand basic microbiology of deep underground regions with special reference to Savannah River Plant. The studies related herein describe studies to enhance sampling methods of deep aquifers and soil columns, to develop equipment to better understand the migration of bacteria in deep soils, and to improve methods to culturing and maintaining deep isolates.

  20. (Transport of subsurface bacteria in porous media)

    SciTech Connect

    Not Available

    1992-01-01

    This report describes studies undertaken to better understand basic microbiology of deep underground regions with special reference to Savannah River Plant. The studies related herein describe studies to enhance sampling methods of deep aquifers and soil columns, to develop equipment to better understand the migration of bacteria in deep soils, and to improve methods to culturing and maintaining deep isolates.

  1. Distribution and identification of luminous bacteria from the sargasso sea.

    PubMed

    Orndorff, S A; Colwell, R R

    1980-05-01

    Vibrio fischeri and Lucibacterium harveyi constituted 75 of the 83 luminous bacteria isolated from Sargasso Sea surface waters. Photobacterium leiognathi and Photobacterium phosphoreum constituted the remainder of the isolates. Luminescent bacteria were recovered at concentrations of 1 to 63 cells per 100 ml from water samples collected at depths of 160 to 320 m. Two water samples collected at the thermocline yielded larger numbers of viable, aerobic heterotrophic and luminous bacteria. Luminescent bacteria were not recovered from surface microlayer samples. The species distribution of the luminous bacteria reflected previously recognized growth patterns; i.e., L. harveyi and V. fischeri were predominant in the upper, warm waters (only one isolate of P. phosphoreum was obtained from surface tropical waters).

  2. High efficiency recombineering in lactic acid bacteria

    PubMed Central

    van Pijkeren, Jan-Peter; Britton, Robert A.

    2012-01-01

    The ability to efficiently generate targeted point mutations in the chromosome without the need for antibiotics, or other means of selection, is a powerful strategy for genome engineering. Although oligonucleotide-mediated recombineering (ssDNA recombineering) has been utilized in Escherichia coli for over a decade, the successful adaptation of ssDNA recombineering to Gram-positive bacteria has not been reported. Here we describe the development and application of ssDNA recombineering in lactic acid bacteria. Mutations were incorporated in the chromosome of Lactobacillus reuteri and Lactococcus lactis without selection at frequencies ranging between 0.4% and 19%. Whole genome sequence analysis showed that ssDNA recombineering is specific and not hypermutagenic. To highlight the utility of ssDNA recombineering we reduced the intrinsic vancomymycin resistance of L. reuteri >100-fold. By creating a single amino acid change in the d-Ala-d-Ala ligase enzyme we reduced the minimum inhibitory concentration for vancomycin from >256 to 1.5 µg/ml, well below the clinically relevant minimum inhibitory concentration. Recombineering thus allows high efficiency mutagenesis in lactobacilli and lactococci, and may be used to further enhance beneficial properties and safety of strains used in medicine and industry. We expect that this work will serve as a blueprint for the adaptation of ssDNA recombineering to other Gram-positive bacteria. PMID:22328729

  3. Stress-Induced Mutagenesis in Bacteria

    PubMed Central

    Foster, Patricia L.

    2009-01-01

    Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution. PMID:17917873

  4. Petrifilm plates for enumeration of bacteria counts in goat milk

    Technology Transfer Automated Retrieval System (TEKTRAN)

    PetrifilmTM Aerobic Count (AC) and Coliform Count (CC) plates were validated against standard methods for enumeration of coliforms, total bacteria, and psychrotrophic bacteria in raw (n = 39) and pasteurized goat milk (n = 17) samples. All microbiological data were transformed into log form and sta...

  5. EVALUATION OF MEDIA FOR RECOVERY OF AEROSOLIZED BACTERIA

    EPA Science Inventory

    Disease transmission by airborne bacteria is well known.Bacterial burden in indoor air is estimated by sampling the air and estimating Colony Forming Unites (CFU) using a variety of media.In this study, the recovery of bacteria, after aerosolization in an aerosol chamber, and emp...

  6. Anaerobic bacteria in otitis media.

    PubMed

    Fulghum, R S; Daniel, H J; Yarborough, J G

    1977-01-01

    Anaerobic bacteria, Peptostrepotococcus intermedius and Propionibacterium acnes, were found in mixed culture specimens from four to ten tested cases of chronic secretory otitis media. These anaerobic bacteria were in a mixed infection flora with aerobic bacteria most often Staphylococcus epidermidis and Cornybacterium sp. which do not fit any established species. The findings of anaerobic bacteria in otitis media is consistent with the sporadic report of the involvement of anaerobic bacteria in otitis media in the literature since 1898.

  7. Microbial Condition of Water Samples from Foreign Fuel Storage Facilities

    SciTech Connect

    Berry, C.J.; Fliermans, C.B.; Santo Domingo, J.

    1997-10-30

    In order to assess the microbial condition of foreign nuclear fuel storage facilities, fourteen different water samples were received from facilities outside the United States that have sent spent nuclear fuel to SRS for wet storage. Each water sample was analyzed for microbial content and activity as determined by total bacteria, viable aerobic bacteria, viable anaerobic bacteria, viable sulfate- reducing bacteria, viable acid-producing bacteria and enzyme diversity. The results for each water sample were then compared to other foreign samples and to data from the receiving basin for off- site fuel (RBOF) at SRS.

  8. Diarrhea-associated pathogens, lactobacilli and cellulolytic bacteria in equine feces: responses to antibiotic challenge.

    PubMed

    Harlow, Brittany E; Lawrence, Laurie M; Flythe, Michael D

    2013-09-27

    Antibiotics are important to equine medicine, but antibiotic-associated diarrhea (AAD) can lead to poor performance and even mortality. AAD is attributed to disruption of the hindgut microbiota, which permits proliferation of pathogenic microbes. The goal of this study was to evaluate the effects of common antibiotics on cellulolytic bacteria, lactobacilli, and AAD-associated pathogens in the feces of healthy horses. Fifteen horses were assigned to three treatment groups (blocked by age and sex): control (no antibiotics), trimethoprim-sulfadiazine (PO), or ceftiofur (IM). Fecal samples (n=8 per horse) were taken during dietary adaptation (3 weeks), antibiotic challenge (1 week), and withdrawal (1 week). Bacteria were enumerated by serial dilution and viable count. Cellulolytic bacteria decreased by >99% during administration of either antibiotic (P<0.0001) and were still less than controls at the end of the withdrawal period (P<0.0001). Fecal samples from horses challenged with ceftiofur had 75% fewer lactobacilli than those from control horses at the end of the antibiotic challenge period (P<0.05). Antibiotic challenged horses also shed more salmonella than control horses (P<0.05). Antibiotics had no effect on the number of Clostridium perfringens isolates. There was no detectable Clostridium difficile during adaptation or in any control horse. C. difficile increased (P<0.0001) to approximately 10(4)cfu/g when horses were challenged with antibiotics, and were still detectable 1 week after withdrawal. These results indicate that antibiotics can disrupt the normal gastrointestinal microbiota and allow proliferation of Salmonella spp. and C. difficile.

  9. Tooth brushing inhibits oral bacteria in dogs.

    PubMed

    Watanabe, Kazuhiro; Hayashi, Kotaro; Kijima, Saku; Nonaka, Chie; Yamazoe, Kazuaki

    2015-10-01

    In this study, scaling, polishing and daily tooth brushing were performed in 20 beagle dogs, and the number of oral bacteria was determined using a bacterial counter. The dogs were randomized into the scaling (S), scaling + polishing (SP), scaling + tooth daily brushing (SB) and scaling + polishing + tooth daily brushing (SPB) groups. Samples were collected from the buccal surface of the maxillary fourth premolars of the dogs immediately after scaling and every week thereafter from weeks 1 to 8. Throughout the study, the number of bacteria was significantly lower in the SB and SPB groups compared with the S group. The findings suggest that daily tooth brushing inhibited oral bacterial growth in the dogs.

  10. Bacteriophage biosensors for antibiotic-resistant bacteria.

    PubMed

    Sorokulova, Irina; Olsen, Eric; Vodyanoy, Vitaly

    2014-03-01

    An increasing number of disease-causing bacteria are resistant to one or more anti-bacterial drugs utilized for therapy. Early and speedy detection of these pathogens is therefore very important. Traditional pathogen detection techniques, that include microbiological and biochemical assays are long and labor-intensive, while antibody or DNA-based methods require substantial sample preparation and purification. Biosensors based on bacteriophages have demonstrated remarkable potential to surmount these restrictions and to offer rapid, efficient and sensitive detection technique for antibiotic-resistant bacteria.

  11. Differential staining of bacteria: gram stain.

    PubMed

    Moyes, Rita B; Reynolds, Jackie; Breakwell, Donald P

    2009-11-01

    In 1884, Hans Christian Gram, a Danish doctor, developed a differential staining technique that is still the cornerstone of bacterial identification and taxonomic division. This multistep, sequential staining protocol separates bacteria into four groups based on cell morphology and cell wall structure: Gram-positive cocci, Gram-negative cocci, Gram-positive rods, and Gram-negative rods. The Gram stain is useful for assessing bacterial contamination of tissue culture samples or for examining the Gram stain status and morphological features of bacteria isolated from mixed or isolated bacterial cultures.

  12. Homeoviscous Adaptation of Membranes in Archaea.

    PubMed

    Oger, Philippe M

    2015-01-01

    Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Membrane adaptation is achieved by a modification of the membrane lipid composition, a strategy termed homeoviscous adaptation. Homeoviscous adaptation in archaea involves strategies similar to that observed in bacteria and eucarya, such as the regulation of lipid chain length or saturation levels, as well as strategies specific to archaea, such as the regulation of the number of cycles along the isoprenoid chains or the regulation of the ratio between mono and bipolar lipids. Although not described yet described in hyperthermophilic bacteria, it is possible that these two strategies also apply to these latter organisms. PMID:26174392

  13. Adaptive Development

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The goal of this research is to develop and demonstrate innovative adaptive seal technologies that can lead to dramatic improvements in engine performance, life, range, and emissions, and enhance operability for next generation gas turbine engines. This work is concentrated on the development of self-adaptive clearance control systems for gas turbine engines. Researchers have targeted the high-pressure turbine (HPT) blade tip seal location for following reasons: Current active clearance control (ACC) systems (e.g., thermal case-cooling schemes) cannot respond to blade tip clearance changes due to mechanical, thermal, and aerodynamic loads. As such they are prone to wear due to the required tight running clearances during operation. Blade tip seal wear (increased clearances) reduces engine efficiency, performance, and service life. Adaptive sealing technology research has inherent impact on all envisioned 21st century propulsion systems (e.g. distributed vectored, hybrid and electric drive propulsion concepts).

  14. Combined immunofluorescence-DNA-fluorescence staining technique for enumeration of Thiobacillus ferrooxidans in a population of acidophilic bacteria

    SciTech Connect

    Muyzer, G.; De Bruyn, A.; Schmedding, D.J.M.; Bos, P.; Westbroek, P.; Kuenen, G.J.

    1987-04-01

    An antiserum raised against whole cells of Thiobacillus ferroxidans was allowed to react with a variety of acidophilic and nonacidophilic bacteria in an enzyme-linked immunosorbent assay and an indirect immunofluorescence assay. Both experiments demonstrated that the antiserum was specific at the species level. This preparation was used to evaluate the role of T. ferroooxidans in the microbial desulfurization process. Leaching experiments were performed, and the numbers of T. ferrooxidans cells and other bacteria were estimated by using a combined immunofluorescence-DNA-fluorescence staining technique that was adapted for this purpose. Nonsterile coal samples inoculated with T. ferrooxidans yielded high concentrations of soluble iron after 16 days. After this period, however, T. ferrooxidans cells could no longer be detected by the immunofluorescence assay, whereas the DNA-fluorescence staining procedure demonstrated a large number of microorganisms on the coal particles. These results indicate that T. ferrooxidans is removed by competition with different acidophilic microorganisms that were originally present on the coal.

  15. The secreted fructose 1,6-bisphosphate aldolase as a broad spectrum vaccine candidate against pathogenic bacteria in aquaculture.

    PubMed

    Sun, Zhongyang; Shen, Binbing; Wu, Haizhen; Zhou, Xiangyu; Wang, Qiyao; Xiao, Jingfan; Zhang, Yuanxing

    2015-10-01

    The development of aquaculture has been hampered by different aquatic pathogens that can cause edwardsiellosis, vibriosis, or other diseases. Therefore, developing a broad spectrum vaccine against different fish diseases is necessary. In this study, fructose 1,6-bisphosphate aldolase (FBA), a conserved enzyme in the glycolytic pathway, was demonstrated to be located in the non-cytoplasmic components of five aquatic pathogenic bacteria and exhibited remarkable protection and cross-protection against these pathogens in turbot and zebrafish. Further analysis revealed that sera sampled from vaccinated turbot had a high level of specific antibody and bactericidal activity against these pathogens. Meanwhile, the increased expressions of immune response-related genes associated with antigen recognition and presentation indicated that the adaptive immune response was effectively aroused. Taken together, our results suggest that FBA can be utilized as a broad-spectrum vaccine against various pathogenic bacteria of aquaculture in the future.

  16. Hydrocarbon Mineralization in Sediments and Plasmid Incidence in Sediment Bacteria from the Campeche Bank

    PubMed Central

    Leahy, Joseph G.; Somerville, Charles C.; Cunningham, Kelly A.; Adamantiades, Grammenos A.; Byrd, Jeffrey J.; Colwell, Rita R.

    1990-01-01

    Rates of degradation of radiolabeled hydrocarbons and incidence of bacterial plasmid DNA were investigated in sediment samples collected from the Campeche Bank, Gulf of Mexico, site of an offshore oil field containing several petroleum platforms. Overall rates of mineralization of [14C]hexadecane and [14C]phenanthrene measured for sediments were negligible; <1% of the substrate was converted to CO2 in all cases. Low mineralization rates are ascribed to nutrient limitations and to lack of adaptation by microbial communities to hydrocarbon contaminants. Plasmid frequency data for sediment bacteria similarly showed no correlation with proximity to the oil field, but, instead, showed correlation with water column depth at each sampling site. Significant differences between sites were observed for proportion of isolates carrying single or multiple plasmids and mean number of plasmids per isolate, each of which increased as a function of depth. PMID:16348204

  17. Bacteria-surface interactions

    PubMed Central

    Tuson, Hannah H.; Weibel, Douglas B.

    2013-01-01

    The interaction of bacteria with surfaces has important implications in a range of areas, including bioenergy, biofouling, biofilm formation, and the infection of plants and animals. Many of the interactions of bacteria with surfaces produce changes in the expression of genes that influence cell morphology and behavior, including genes essential for motility and surface attachment. Despite the attention that these phenotypes have garnered, the bacterial systems used for sensing and responding to surfaces are still not well understood. An understanding of these mechanisms will guide the development of new classes of materials that inhibit and promote cell growth, and complement studies of the physiology of bacteria in contact with surfaces. Recent studies from a range of fields in science and engineering are poised to guide future investigations in this area. This review summarizes recent studies on bacteria-surface interactions, discusses mechanisms of surface sensing and consequences of cell attachment, provides an overview of surfaces that have been used in bacterial studies, and highlights unanswered questions in this field. PMID:23930134

  18. Communication among Oral Bacteria

    PubMed Central

    Kolenbrander, Paul E.; Andersen, Roxanna N.; Blehert, David S.; Egland, Paul G.; Foster, Jamie S.; Palmer, Robert J.

    2002-01-01

    Human oral bacteria interact with their environment by attaching to surfaces and establishing mixed-species communities. As each bacterial cell attaches, it forms a new surface to which other cells can adhere. Adherence and community development are spatiotemporal; such order requires communication. The discovery of soluble signals, such as autoinducer-2, that may be exchanged within multispecies communities to convey information between organisms has emerged as a new research direction. Direct-contact signals, such as adhesins and receptors, that elicit changes in gene expression after cell-cell contact and biofilm growth are also an active research area. Considering that the majority of oral bacteria are organized in dense three-dimensional biofilms on teeth, confocal microscopy and fluorescently labeled probes provide valuable approaches for investigating the architecture of these organized communities in situ. Oral biofilms are readily accessible to microbiologists and are excellent model systems for studies of microbial communication. One attractive model system is a saliva-coated flowcell with oral bacterial biofilms growing on saliva as the sole nutrient source; an intergeneric mutualism is discussed. Several oral bacterial species are amenable to genetic manipulation for molecular characterization of communication both among bacteria and between bacteria and the host. A successful search for genes critical for mixed-species community organization will be accomplished only when it is conducted with mixed-species communities. PMID:12209001

  19. PATHOGENICITY OF BIOFILM BACTERIA

    EPA Science Inventory

    There is a paucity of information concerning any link between the microorganisms commonly found in biofilms of drinking water systems and their impacts on human health. For bacteria, culture-based techniques detect only a limited number of the total microorganisms associated wit...

  20. Antibiotic-Resistant Bacteria.

    ERIC Educational Resources Information Center

    Longenecker, Nevin E.; Oppenheimer, Dan

    1982-01-01

    A study conducted by high school advanced bacteriology students appears to confirm the hypothesis that the incremental administration of antibiotics on several species of bacteria (Escherichia coli, Staphylococcus epidermis, Bacillus sublitus, Bacillus megaterium) will allow for the development of antibiotic-resistant strains. (PEB)

  1. Adaptive management

    USGS Publications Warehouse

    Allen, Craig R.; Garmestani, Ahjond S.

    2015-01-01

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive management has explicit structure, including a careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. The process is iterative, and serves to reduce uncertainty, build knowledge and improve management over time in a goal-oriented and structured process.

  2. Tape Cassette Bacteria Detection System

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The design, fabrication, and testing of an automatic bacteria detection system with a zero-g capability and based on the filter-capsule approach is described. This system is intended for monitoring the sterility of regenerated water in a spacecraft. The principle of detection is based on measuring the increase in chemiluminescence produced by the action of bacterial porphyrins (i.e., catalase, cytochromes, etc.) on a luminol-hydrogen peroxide mixture. Since viable as well as nonviable organisms initiate this luminescence, viable organisms are detected by comparing the signal of an incubated water sample with an unincubated control. Higher signals for the former indicate the presence of viable organisms. System features include disposable sealed sterile capsules, each containing a filter membrane, for processing discrete water samples and a tape transport for moving these capsules through a processing sequence which involves sample concentration, nutrient addition, incubation, a 4 Molar Urea wash and reaction with luminol-hydrogen peroxide in front of a photomultiplier tube. Liquids are introduced by means of a syringe needle which pierces a rubber septum contained in the wall of the capsule. Detection thresholds obtained with this unit towards E. coli and S. marcescens assuming a 400 ml water sample are indicated.

  3. Effects of dietary fiber preparations made from maize starch on the growth and activity of selected bacteria from the Firmicutes, Bacteroidetes, and Actinobacteria phyla in fecal samples from obese children.

    PubMed

    Barczynska, Renata; Slizewska, Katarzyna; Litwin, Mieczyslaw; Szalecki, Mieczyslaw; Kapusniak, Janusz

    2016-01-01

    Currently, there is a search for substances that would be very well tolerated by an organism and which could contribute to the activation of the growth of Bacteroidetes and Actinobacteria strains, with simultaneous inhibition of the growth of Firmicutes. High expectations in this regard are raised with the use of fiber preparations from starch - resistant corn dextrins, branched dextrins, resistant maltodextrins and soluble corn fiber. In this paper, the influence of fiber preparations made from corn starch was evaluated on growth and activity of Bacteroidetes, Actinobacteria and Firmicutes strains isolated from obese children. It was demonstrated that in the stool of obese children Firmicutes strains predominate, while Bacteroidetes and Actinobacteria strains were in the minority. A supplementation of fecal culture with fiber preparations did not cause any significant changes in the number of strains of Bacteroidetes and Firmicutes. Addition of fiber preparations to the fecal samples of obese children increased the amount of short-chain fatty acids, especially acetic (p < 0.01), propionic, butyric (p = 0.05) and lactic acid (p < 0.01).

  4. VIRULENCE CHARACTERISTICS OF HETEROTROPHIC BACTERIA COMMONLY ISOLATED FROM POTABLE WATER

    EPA Science Inventory

    Heterotrophic bacteria isolated from drinking water distribution systems were examined to determine if they possessed putative virulence factors such as hemolysins, proteases, or cytotoxins. Representative samples of colonies from several different distribution systems indicated ...

  5. Predominant bacteria diversity in Chinese traditional sourdough.

    PubMed

    Zhang, Guohua; He, Guoqing

    2013-08-01

    The purpose of this study was to identify the major bacteria in Chinese traditional sourdough (CTS). Five CTS samples (Hn-87, Sx-91, Gs-107, Hf-112, and Hr-122) were collected from different Chinese steamed breads shops or private households. The total bacterial DNA was extracted from sourdough samples and sequenced using Illumina Hiseq 2000 system. Illumina tags were assigned to BLASTN server based on 16S rRNA libraries to reveal a genetic profile. Phylogenetic analysis revealed that the bacteria in traditional sourdough samples were dominated by the genera Leuconostoc and Lactobacillus. Beta diversity analysis, principal component analysis, and cluster analysis compared the bacterial differences in traditional sourdough samples. The results showed that Leuconostoc, Lactobacillus, and Weissella were the predominant genera among the 5 samples. This differentiated the sourdoughs into 3 typologies, namely, 1) Gs-107 and Sx-91, 2) Hr-122 and Hn-87, and 3) Hf-112. This study identified 3 unique major bacteria genus in CTS bread ecosystems.

  6. Plasmid copy number underlies adaptive mutability in bacteria.

    PubMed

    Sano, Emiko; Maisnier-Patin, Sophie; Aboubechara, John Paul; Quiñones-Soto, Semarhy; Roth, John R

    2014-11-01

    The origin of mutations under selection has been intensively studied using the Cairns-Foster system, in which cells of an Escherichia coli lac mutant are plated on lactose and give rise to 100 Lac+ revertants over several days. These revertants have been attributed variously to stress-induced mutagenesis of nongrowing cells or to selective improvement of preexisting weakly Lac+ cells with no mutagenesis. Most revertant colonies (90%) contain stably Lac+ cells, while others (10%) contain cells with an unstable amplification of the leaky mutant lac allele. Evidence is presented that both stable and unstable Lac+ revertant colonies are initiated by preexisting cells with multiple copies of the F'lac plasmid, which carries the mutant lac allele. The tetracycline analog anhydrotetracycline (AnTc) inhibits growth of cells with multiple copies of the tetA gene. Populations with tetA on their F'lac plasmid include rare cells with an elevated plasmid copy number and multiple copies of both the tetA and lac genes. Pregrowth of such populations with AnTc reduces the number of cells with multiple F'lac copies and consequently the number of Lac+ colonies appearing under selection. Revertant yield is restored rapidly by a few generations of growth without AnTc. We suggest that preexisting cells with multiple F'lac copies divide very little under selection but have enough energy to replicate their F'lac plasmids repeatedly until reversion initiates a stable Lac+ colony. Preexisting cells whose high-copy plasmid includes an internal lac duplication grow under selection and produce an unstable Lac+ colony. In this model, all revertant colonies are initiated by preexisting cells and cannot be stress induced. PMID:25173846

  7. Genetic adaptation of bacteria to halogenated aliphatic compounds.

    PubMed Central

    Janssen, D B; van der Ploeg, J R; Pries, F

    1995-01-01

    The bacterial degradation and detoxification of chlorinated xenobiotic compounds requires the production of enzymes that are capable of recognizing and converting compounds which do not occur at significant concentrations in nature. We have studied the catabolic route of 1,2-dichloroethane as an example of a pathway for the conversion of such a synthetic compound. In strains of Xanthobacter and Ancylobacter that have been isolated on 1,2-dichloroethane, the first catabolic step is catalyzed by a hydrolytic haloalkane dehalogenase. The enzyme converts 1,2-dichloroethane to 2-chloroethanol but is also active with many other environmentally important haloalkanes such as methylchloride, methylbromide, 1,2-dibromoethane, epichlorohydrin, and 1,3-dichloropropene. Further degradation of 2-chloroethanol proceeds by oxidation to the carboxylic acid and dehalogenation to glycolate. The aldehyde dehydrogenase prevents toxicity of the reactive chloroacetaldehyde that is formed as an intermediate and is necessary for establishing a functional 2-chloroethanol degradative pathway in a strain that is not capable of growth on this compound. PMID:8565904

  8. Genetic adaptation of bacteria to halogenated aliphatic compounds

    SciTech Connect

    Janssen, D.B.; Ploeg, J.R. van der; Pries, F.

    1995-06-01

    The bacterial degradation and detoxification of chlorinated xenobiotic compounds requires the production of enzymes that are capable of recognizing and converting compounds which do not occur at significant concentrations in nature. We have studied the catabolic route of 1,2-dichloroethane as an example of a pathway for the conversion of such a synthetic compound. In strains of Xanthobacter and Ancylobacter that have been isolated on 1,2-dichloroethane, the first catabolic step is catalyzed by a hydrolytic haloalkane dehalogenase. The enzyme converts 1,2-dichloroethane to 2-chloroethanol but is also active with many other environmentally important haloalkanes such as methylchloride, methylbromide, 1,2-dibromoethane, epichlorohydrin, and 1,3-dichloropropene. Further degradation of 2-chloroethanol proceeds by oxidation to the carboxylic acid and dehalogenation to glycolate. The aldehyde dehydrogenase prevents toxicity of the reactive chloroacetaldehyde that is formed as an intermediate and is necessary for establishing a functional 2-chloroethanol degradative pathway in a strain that is not capable of growth on this compound. 27 refs., 3 figs., 1 tab.

  9. Genetic adaptation of bacteria to halogenated aliphatic compounds.

    PubMed

    Janssen, D B; van der Ploeg, J R; Pries, F

    1995-06-01

    The bacterial degradation and detoxification of chlorinated xenobiotic compounds requires the production of enzymes that are capable of recognizing and converting compounds which do not occur at significant concentrations in nature. We have studied the catabolic route of 1,2-dichloroethane as an example of a pathway for the conversion of such a synthetic compound. In strains of Xanthobacter and Ancylobacter that have been isolated on 1,2-dichloroethane, the first catabolic step is catalyzed by a hydrolytic haloalkane dehalogenase. The enzyme converts 1,2-dichloroethane to 2-chloroethanol but is also active with many other environmentally important haloalkanes such as methylchloride, methylbromide, 1,2-dibromoethane, epichlorohydrin, and 1,3-dichloropropene. Further degradation of 2-chloroethanol proceeds by oxidation to the carboxylic acid and dehalogenation to glycolate. The aldehyde dehydrogenase prevents toxicity of the reactive chloroacetaldehyde that is formed as an intermediate and is necessary for establishing a functional 2-chloroethanol degradative pathway in a strain that is not capable of growth on this compound.

  10. Genetic adaptation of bacteria to halogenated aliphatic compounds.

    PubMed

    Janssen, D B; van der Ploeg, J R; Pries, F

    1995-06-01

    The bacterial degradation and detoxification of chlorinated xenobiotic compounds requires the production of enzymes that are capable of recognizing and converting compounds which do not occur at significant concentrations in nature. We have studied the catabolic route of 1,2-dichloroethane as an example of a pathway for the conversion of such a synthetic compound. In strains of Xanthobacter and Ancylobacter that have been isolated on 1,2-dichloroethane, the first catabolic step is catalyzed by a hydrolytic haloalkane dehalogenase. The enzyme converts 1,2-dichloroethane to 2-chloroethanol but is also active with many other environmentally important haloalkanes such as methylchloride, methylbromide, 1,2-dibromoethane, epichlorohydrin, and 1,3-dichloropropene. Further degradation of 2-chloroethanol proceeds by oxidation to the carboxylic acid and dehalogenation to glycolate. The aldehyde dehydrogenase prevents toxicity of the reactive chloroacetaldehyde that is formed as an intermediate and is necessary for establishing a functional 2-chloroethanol degradative pathway in a strain that is not capable of growth on this compound. PMID:8565904

  11. Adaptive Thresholds

    SciTech Connect

    Bremer, P. -T.

    2014-08-26

    ADAPT is a topological analysis code that allow to compute local threshold, in particular relevance based thresholds for features defined in scalar fields. The initial target application is vortex detection but the software is more generally applicable to all threshold based feature definitions.

  12. Bytes and Bugs: Integrating Computer Programming with Bacteria Identification.

    ERIC Educational Resources Information Center

    Danciger, Michael

    1986-01-01

    By using a computer program to identify bacteria, students sharpen their analytical skills and gain familiarity with procedures used in laboratories outside the university. Although it is ideal for identifying a bacterium, the program can be adapted to many other disciplines. (Author)

  13. Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency

    PubMed Central

    Sebastián, Marta; Smith, Alastair F; González, José M; Fredricks, Helen F; Van Mooy, Benjamin; Koblížek, Michal; Brandsma, Joost; Koster, Grielof; Mestre, Mireia; Mostajir, Behzad; Pitta, Paraskevi; Postle, Anthony D; Sánchez, Pablo; Gasol, Josep M; Scanlan, David J; Chen, Yin

    2016-01-01

    Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean. PMID:26565724

  14. Chemotactic selection of pollutant degrading soil bacteria

    DOEpatents

    Hazen, Terry C.

    1994-01-01

    A method for identifying soil microbial strains which may be bacterial degraders of pollutants comprising the steps of placing a concentration of a pollutant in a substantially closed container, placing the container in a sample of soil for a period of time ranging from one minute to several hours, retrieving the container, collecting the contents of the container, and microscopically determining the identity of the bacteria present. Different concentrations of the pollutant can be used to determine which bacteria respond to each concentration. The method can be used for characterizing a polluted site or for looking for naturally occurring biological degraders of the pollutant. Then bacteria identified as degraders of the pollutant and as chemotactically attracted to the pollutant are used to inoculate contaminated soil. To enhance the effect of the bacteria on the pollutant, nutrients are cyclicly provided to the bacteria then withheld to alternately build up the size of the bacterial colony or community and then allow it to degrade the pollutant.

  15. Monitoring of antimicrobial resistance in pathogenic bacteria from livestock animals.

    PubMed

    Wallmann, Jürgen

    2006-06-01

    Facing the problem of development and spreading of bacterial resistance, preventive strategies are considered the most appropriate means to counteract. The establishment of corresponding management options relies on scientifically defensible efforts to obtain objective data on the prevalence of bacterial resistance in healthy and diseased livestock. Additionally, detailed statistics are needed on the overall amount of antimicrobial agents dispensed in Germany. The collection of valid data on the prevalence of resistance requires representative and cross-sectional studies. The German national antimicrobial resistance monitoring of the Federal Office of Consumer Protection and Food Safety (BVL) determines the current quantitative resistance level of life-stock pathogens, in order to permit the evaluation and surveillance of the distribution of resistances on a valid basis. Essential key features determining the design of these studies comprise (1) a statistically valid sampling program. This incorporates regional differences in animal population density, (2) the avoidance of "copy strains", (3) testing of no more than two bacterial strains belonging to one species per herd, (4) testing only if no antimicrobial therapy preceded sample collection, and (5) the use of standardized methods [e.g. microdilution broth method to determine the minimal inhibitory concentration (MIC)]. The analysis and interpretation of this data permits reliable identification and definition of epidemiological characteristics of resistance and its development in animal associated bacteria, such as geographically and time wise differentiated profiles on its prevalence, the emergence of unknown phenotypes of resistance and an assessment of the threat resistant bacteria from animals pose for humans. In applied antimicrobial therapy, the data can serve as a decision guidance in choosing the antimicrobial agent most adapted to the prevailing epidemiological situation. The susceptibility testing