| 1. |
- Dalevi, Daniel, 1974, et al.
(författare)
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A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
- 2006
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Ingår i: Statistical Applications in Genetics and Molecular Biology. - : Walter de Gruyter GmbH. - 1544-6115. ; 5:1, s. i-24
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Tidskriftsartikel (refereegranskat)abstract
- Recently Peres and Shields discovered a new method for estimating the order of a stationary fixed order Markov chain. They showed that the estimator is consistent by proving a threshold result. While this threshold is valid asymptotically in the limit, it is not very useful for DNA sequence analysis where data sizes are moderate. In this paper we give a novel interpretation of the Peres-Shields estimator as a sharp transition phenomenon. This yields a precise and powerful estimator that quickly identifies the core dependencies in data. We show that it compares favorably to other estimators, especially in the presence of variable dependencies. Motivated by this last point, we extend the Peres-Shields estimator to Variable Length Markov Chains. We compare it to a well-established estimator and show that it is superior in terms of the predictive likelihood. We give an application to the problem of detecting DNA sequence similarity in plasmids. Copyright ©2006 The Berkeley Electronic Press. All rights reserved.
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| 2. |
- Dalevi, Daniel, 1974, et al.
(författare)
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Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures
- 2006
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 22:5, s. 517-522
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Tidskriftsartikel (refereegranskat)abstract
- Analyses of genomic signatures are gaining attention as they allow studies of species-specific relationships without involving alignments of homologous sequences. A naïve Bayesian classifier was built to discriminate between different bacterial compositions of short oligomers, also known as DNA words. The classifier has proven successful in identifying foreign genes in Neisseria meningitis. In this study we extend the classifier approach using either a fixed higher order Markov model (Mk) or a variable length Markov model (VLMk).
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| 3. |
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| 4. |
- Heinicke, G., et al.
(författare)
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The effect of biological pre-filtration on the performance of conventional surface water treatment
- 2006
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Ingår i: Journal of Water Supply: Research and Technology - Aqua. - 0003-7214. ; 55:2, s. 109-119
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Tidskriftsartikel (refereegranskat)abstract
- Many waterworks that apply conventional treatment of surface water, by flocculation and filtration, have to deal with seasonal changes of the raw water quality, increasing concentrations of natural organic matter (NOM), and the necessity to improve particle removal. A pilot plant was operated to closely resemble the full-scale treatment at a surface water treatment plant in Göteborg, Sweden. Treatment consisted of flocculation, sedimentation and rapid granular activated carbon (GAC) filtration. To assess the effects of biological pre-filtration, the feed water to the pilot plant was switched weekly between surface water and biofiltered water which had passed through adsorptively exhausted GAC at an empty bed contact time (EBCT) of 34 minutes. The processes were investigated with regard to NOM, the bacterial re-growth potential, as well as their function as a barrier for suspended particles that originate from the raw water. Biological pre-filtration improved particle removal and made it less dependent on the post-sedimentation GAC rapid filter, thereby improving robustness. Episodically elevated concentrations of earthy-musty odour compounds, which are not reliably removed by flocculation and filtration, were reduced by the biofilters. The process combination may be of particular interest for waterworks with variable raw water quality.
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| 5. |
- Kämpfer, P, et al.
(författare)
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Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water
- 2007
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 57:7, s. 1510-1515
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Tidskriftsartikel (refereegranskat)abstract
- Two Gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (strains CCUG 49009T and CCUG 49012), both isolated from drinking water, were characterized. On the basis of chemotaxonomic data [major ubiquinone, Q-8; predominant polyamines, putrescine and 2-hydroxyputrescine; major polar lipids, phosphatidylethanolamine, moderate amounts of diphosphatidylglycerol and phosphatidylglycerol and minor amounts of three aminolipids and phosphatidylserine; major fatty acids, C16 : 0 and summed feature 3 (C16 : 1ω7c/C15 : 0 iso 2-OH)] and 16S rRNA gene sequence similarities, both strains clearly belong to the family Oxalobacteraceae of the Betaproteobacteria. 16S rRNA gene sequence similarities with members of the most closely related genera of this group (Herminiimonas, Massilia, Duganella, Telluria, Herbaspirillum, Janthinobacterium, Naxibacter and Paucimonas) were less than 96.5 % for both strains. The two strains also shared a relatively low 16S rRNA gene sequence similarity (96.8 %). Although phylogenetic analysis based on 16S rRNA gene sequence similarities clearly showed that the two organisms formed a separate branch, their phenotypes (including chemotaxonomic features) were hardly distinguishable and showed high similarities to those reported for the most closely related genera. On the basis of DNA–DNA hybridization results, the two strains were shown to represent separate species (sharing only 20 % DNA–DNA relatedness), but they could not be clearly differentiated phenotypically from each other. It is evident that these organisms represent a new genus, Undibacterium gen. nov., with one species, Undibacterium pigrum sp. nov. The type strain of Undibacterium pigrum is strain CCUG 49009T (=CIP 109318T). Strain CCUG 49012 (=CIP 108976) probably represents a second species of this genus, but is described here as a second genomovar of this species because of the lack of differentiating characters.
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| 6. |
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| 7. |
- Nylund, Göran M., 1974, et al.
(författare)
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Seaweed defence against bacteria: a poly-brominated 2-heptanone from the red alga Bonnemaisonia hamifera inhibits bacterial colonisation
- 2008
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Ingår i: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 369, s. 39-50
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Tidskriftsartikel (refereegranskat)abstract
- It has previously been shown that the red alga Bonnemaisonia hamifera is less fouled by bacteria relative to co-occurring seaweeds and that surface extracts of B. hamifera inhibit bacterial growth at natural concentrations. In the present study, we isolated the antibacterial metabolite by bioassay-guided fractionation of extracts of B. hamifera using standard chromatographic methods. Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry were used for molecular identification. The antibacterial activity in the extracts was caused by a previously described poly-halogenated 2-heptanone: 1,1,3,3-tetrabromo-2-heptanone. To further investigate the role of this compound as an ecologically relevant antifoulant against bacterial colonisation, we quantified it on the surface of B. hamifera specimens collected in the field. Levels of 1,1,3,3-tetrabromo-2-heptanone on the surface of the algae were on average 3.6 µg cm–2. Natural surface concentrations of this secondary metabolite were used to test for growth-inhibiting effects against 18 bacterial strains isolated from red algae co-occurring with B. hamifera. The test indicated a phylogenetic specificity of the metabolite, and gram-positive bacteria and flavobacteria proved to be particularly sensitive. In a further test, natural surface concentrations of 1,1,3,3-tetrabromo-2-heptanone were applied to artificial panels and incubated in the sea. After 4 and 7 d, the number of settled bacteria was significantly lower on all treated panels compared to controls. Thus, this study shows that 1,1,3,3-tetrabromo-2-heptanone has an ecologically relevant role as an antifoulant against bacterial colonisation on the surface of B. hamifera. This study is also one of only a few to quantify natural surface concentrations of a seaweed secondary metabolite.
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| 8. |
- Persson, Frank, 1970, et al.
(författare)
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Characterisation of the behaviour of particles in biofilters for pre-treatment of drinking water
- 2005
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Ingår i: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 39:16, s. 3791-3800
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Tidskriftsartikel (refereegranskat)abstract
- Biofiltration of surface water was examined using granular activated carbon (GAC) and expanded clay (EC). Particle removal was 60-90%, measured by flow cytometry, which enabled discrimination between total- and autofluorescent particles (microalgae) in size ranges of 0.4-1 and 1-15 mu m, and measured by on-line particle counting. Total particles were removed at a higher degree than autofluorescent particles. The biofilters were also challenged with 1 mu m fluorescent microspheres with hydrophobic and hydrophilic surface characteristics and bacteriophages (Salmonella typhimurium 2813). Added microspheres were removed at 97-99% (hydrophobic) and 85-89% (hydrophilic) after 5 hydraulic residence times (HRT) and microspheres retained in the biofilter media were slowly detaching into the filtrate for a long time after the addition. Removal of bacteriophages (5 HRT) was considerably lower at 40-59%, and no long-lasting detachment was observed. A comparison of experimental data with theoretical predictions for removal of particles in clean granular media filters revealed a similar or higher removal of particles around 1 mu m in size than predicted, while bacteriophages were removed at a similar or lesser extent than predicted. The results highlight the selectivity and dynamic behaviour of the particle removal processes and have implications for operation and microbial risk assessment of a treatment train with biofilters as pre-treatment. (c) 2005 Elsevier Ltd. All rights reserved.
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| 9. |
- Persson, Frank, 1970, et al.
(författare)
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Performance of direct biofiltration of surface water for reduction of biodegradable organic matter and biofilm formation potential
- 2006
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Ingår i: Environmental Technology. - 0959-3330 .- 1479-487X. ; 27:9, s. 1037-1045
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Tidskriftsartikel (refereegranskat)abstract
- Direct biofiltration of surface water may be considered as pre-treatment for membrane filtration, in order to reduce fouling. The biofiltration process was investigated with regard to biodegradable organic matter and biofilm formation, covering the annual variations under moderately cold climate conditions. Granular activated carbon (GAC) and two types of crushed expanded clay (EC) were compared as filter media. To assess the biological properties of the biofilters, viable biomass and respiratory activity was examined. Biofiltration removed assimilable organic carbon (AOC) and biodegradable dissolved organic carbon (BDOC) by about 30% and also reduced the bacterial concentration in the water phase. Also, biofilm formation in the treated water was reduced by 80-90% during summer and winter conditions. The reductions in the investigated parameters were similar in the biofilters with GAC and EC. Likewise, a similar amount and development of biomass was found in the GAC and EC biofilters of comparable grain size with a pronounced stratification from top to bottom of the filter bed. The specific respiratory activity of the biofilter biomass was dependent on raw water temperature. Even though slight correlations between BDOC removal and temperature or respiratory activity were observed, AOC and BDOC removals were mainly dependent on the feed water concentrations of these compounds. The results indicate that direct biofiltration of surface water, by reducing AOC, BDOC and biofilm formation in the water, may be an advantageous pre-treatment for membrane filtration processes.
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| 10. |
- Persson, Frank, 1970, et al.
(författare)
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Removal of geosmin and MIB by biofiltration - An investigation discriminating between adsorption and biodegradation
- 2007
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Ingår i: Environmental Technology. - 0959-3330 .- 1479-487X. ; 28:1, s. 95-104
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Tidskriftsartikel (refereegranskat)abstract
- Geosmin and 2-methylisoborneol (MIB) are two substances causing earthy/musty odours that are difficult to remove by conventional chemical drinking water treatment. In this study removal of geosmin and MIB by biofiltration of untreated surface water was investigated using granular activated carbon (GAC) and crushed expanded clay (EC) as filter media. Biofiltration through both GAC and EC removed geosmin and MIB present at low (20 ng l(-1)) concentrations by at least 97% at an empty bed contact time of 30 minutes and a temperature of 15 degrees C. At lower temperature (6-12 degrees C) and simultaneously lower biomass concentrations, removal efficiency was similar in the GAC but considerably lower in the EC biofilter, pointing to a second mechanism different from biodegradation. Consequently, microbial activity was suppressed with azide to enable discrimination between biodegradation and adsorption. During azide dosage, the GAC biofilters still removed geosmin and MIB nearly unaffectedly. In the EC biofilter, however, removal of both odorants ceased completely. Methylene blue adsorption confirmed that the GAC, even after almost four years of operation receiving surface water, had capacity to remove geosmin and MlB by adsorption. Since odour episodes commonly occur during the warm season when microbiological activity is high, EC constitutes a viable option as carrier medium for direct biological filtration of surface water. The additional GAC adsorption capacity however adds robustness to the removal process.
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