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  • Bacteria
  • Ambleside, UK  (16)
  • Wiley-Blackwell  (16)
  • American Chemical Society
  • International Union of Crystallography (IUCr)
Collection
  • 1
    ISSN: 0886-9383
    Keywords: Pattern recognition ; SIMCA ; PCA ; Classification ; Bacteria ; Pyrolysis mass spectra ; Recall ; Cross-validation ; Indicator function ; Pseudo random data sets ; Leave-x-out ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As part of a critical evaluation of the pattern recognition method SIMCA, three data sets containing pyrolysis mass spectra from bacteria were analysed using the SIMCA classifier. Each set consisted of two classes, Pseudomonas and Serratia bacteria, each class containing ten mass spectra and each mass spectrum having 285 spectral features.The results indicate that for these py-MS data sets, with low object/feature ratio, the SIMCA classifier produces satisfactory results at the first classification level. At the second level, however, the classification results are not reliable, even after deleting outliers. A comparison of the cross-validation method and Malinowski's indicator function for the determination of the number of significant principal components showed that the cross-validation method is less stable and therefore less reliable than the indicator function.
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  • 2
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Journal of High Resolution Chromatography 11 (1988), S. 668-670 
    ISSN: 0935-6304
    Keywords: Gas chromatography, capillary ; Sample extraction ; Membrane filter ; Bacteria ; Fatty acids ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 2 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electroanalysis 7 (1995), S. 904-906 
    ISSN: 1040-0397
    Keywords: Phenol ; Biosensors ; Bacteria ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An amperometric phenol sensor, where Pseudomonus putida bacteria were immobilized on an amperometric oxygen sensor is described. Theoretical considerations of the steady-state concentration distribution of oxygen and substrate in diffusion-controlled microbial sensors are given. Validation of the theory was evaluated by comparing the experimental and theoretical data.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Microscopy Research and Technique 25 (1993), S. 267-275 
    ISSN: 1059-910X
    Keywords: Agarose encapsulation ; TEM specimen preparation ; Bacteria ; Yeast ; Mitochondria ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Natural Sciences in General
    Notes: Agarose, agar, and gelatin were initially compared as encapsulation media for 3 structurally diverse particulate specimens: bacteria, yeast, and mitochondria. Agarose proved superior to both gelatin and agar for ease of handling and overall image quality (minimum background). All sample types exhibited high quality fixation and structural detail with no heat damage from the agarose medium. Based on this finding, we further characterized agarose encapsulation as affected by post-fixation, en bloc staining and resin type. Osmium tetroxide post-fixation, followed by en bloc uranyl acetate staining, could be performed without an increase in the electron density of the encapsulation medium. Agarose proved successful as an encapsulation medium regardless of the resin type or preparation protocol, thus providing flexibility in experimental design and excellent results over a range of variables. © 1993 Wiley-Liss, Inc.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Microscopy Research and Technique 24 (1993), S. 400-422 
    ISSN: 1059-910X
    Keywords: Cryofixation ; Freeze substitution ; Low temperature embedding ; Lowicryl ; Fine structural preservation ; Extracellular material ; Bacteria ; Algae ; Cyanobacteria ; Fungi ; Transgenic plants ; Wheat ; Barley ; Tobacco ; Conidia ; Hyphae ; Haustoria ; Plant pathogen interface ; Molecular preservation ; Retention diffusible elements ; Microanalysis ; Autoradiography ; Fungicides ; Lipids ; Immunocytochemistry ; Protein antigenicity ; Elicitor ; Extensin ; Foreign proteins ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Natural Sciences in General
    Notes: Considering the increasing necessity for improved preparation techniques in biological electron microscopy as a basis for the identification and localization of cellular substances within the compartments of the cell, this review is focussed on the method of freeze substitution as an important link between the cryofixation (ultrarapid freezing) and resin embedding of biological specimens. The theory and practice of freeze substitution is summarized with particular interest in the physical and thermodynamic as well as in the chemical basis of this technique. A survey of practical aspects of the technical process of freeze substitution concerning the equipment and various protocols successfully applied in biological systems is also given. The main advantage of freeze substitution versus conventional chemical fixation is seen in the maintenance of the hydration shell of molecules and macromolecular structures. This results in an improved fine structural preservation, superior retention of the antigenicity of proteins and decreased loss of unbound, diffusible cellular components. Examples of excellent visualization of the ultrastructure of macro-molecular complexes (nucleic acids, extracellular material, membranes etc.), small organisms (bacteria, algae, cyanobacteria and fungi) and large biological samples such as plant and animal tissue as well as the plant-pathogen (fungus) interface and infection structures are presented. Recent data on the molecular characterization of freeze-substituted biological tissue are exemplified with special emphasis on the subcellular detection of soluble components (elements, lipids, proteins and drugs) and the inter-/intracellular localization of proteins including foreign proteins in transgenic plants. The molecular analysis of freeze-substituted specimens is achieved by the combination of low temperature preparation techniques in biological electron microscopy with various detection methods such as X-ray microanalysis, immunocytochemistry and high resolution autoradiography. © 1993 Wiley-Liss, Inc.
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  • 6
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electroanalysis 9 (1997), S. 395-398 
    ISSN: 1040-0397
    Keywords: DNA biosensor ; Escherichia coli ; Bacteria ; Water quality ; Sequence-specific detection ; Hybridization ; Environmental monitoring ; Screen-printed electrode ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An electrochemical biosensor for the specific detection of short DNA sequences from the E. coli pathogen is described. This hybridization device relies on the immobilization of a 25-mer oligonucleotide probe, from the E. coli lacZ gene, onto a screen-printed carbon electrode. Chronopotentiometric detection of the Co(bpy)3+3 indicator is used for monitoring the hybridization event. Numerous variables of the assay protocol, including those of the probe immobilization step, the hybridization event, and the indicator association/detection, are characterized and optimized. Hybridization times of 2- and 30-min are sufficient for detecting 300- and 50 ng/mL, respectively, of the E. coli DNA target. Applicability to analysis of untreated environmental water samples is illustrated. Such single-use electrochemical sensors hold great promise for decentralized environmental and food testing for the E. coli pathogen.
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  • 7
    ISSN: 0173-0835
    Keywords: ATPase ; Bacteria ; Sequence data analysis ; Elongation factor Tu ; Phylogeny ; Tree reconstruction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.
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  • 8
    ISSN: 0173-0835
    Keywords: Outer membrane proteins ; Bacteria ; Postantibiotic effect ; Meropenem ; Capillary electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Persistent inhibition of bacterial growth, called postantibiotic effect (PAE), after a short exposure to a new carbapenem, meropenem, was determined in different strains of the Enterobacteriaceae family. Capillary electrophoresis (CE), as well as sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were used to study the outer membrane protein (OMP) profiles before and after meropenem treatment. CE proved to be suitable for the characterization of the OMP profiles of bacteria. Significant changes in the electrophoretic patterns were observed, showing the consequential effect of meropenem on bacteria.
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  • 9
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Angewandte Chemie International Edition in English 18 (1979), S. 337-350 
    ISSN: 0570-0833
    Keywords: Permeability ; Membranes ; Bacteria ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The outer membrane of Gram-negative bacteria is an attractive system for the study of the structure-function relationships in biological membranes. This membrane has, inter alia, the task of regulating the inflow of nutrients and outflow of waste products. Investigations with the aid of mutants showed that there are at least two general pathways for the diffusion of small molecules across the outer membrane: one for hydrophobic and one for hydrophilic compounds. In the case of the “hydrophobic pathway” the hydrophobic compound dissolves in the interior of the membrane and then crosses the membrane in accordance with the partition coefficient. In wild-type forms of enteric bacteria this pathway cannot be used - presumably owing to the absence of regions with phospholipid bilayers. Small hydrophilic molecules, on the other hand, penetrate the membrane through water-filled pores.
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  • 10
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Angewandte Chemie International Edition in English 27 (1988), S. 1040-1049 
    ISSN: 0570-0833
    Keywords: Protein phosphorylation ; Phosphorylation ; Bacteria ; Gene expression ; Metabolism ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The importance of protein phosphorylation to the regulation of physiological processes in eukaryotic cells has been known for almost half a century. In contrast, the first conclusive evidence for functionally relevant protein phosphorylation in bacteria was obtained less than a decade ago. To date, only five functionally well-characterized bacterial proteins have been shown to be regulated by reversible phosphorylation. (1) Phosphorylation of isocitrate dehydrogenase in Escherichia coli controls the relative flux of carbon through the Krebs cycle and the glyoxylate shunt. (2) In gram-positive bacteria, phosphorylation of HPr, a phosphoryl carrier protein of the phosphoenolypyruvate-dependent sugar phosphotransferase system, regulates carbohydrate uptake via this system. (3) Phosphorylation of glycerol kinase in Streptococcus faecalis probably serves to regulate the degradation of glycerol. (4) Phosphorylation of the nitrogen regulatory protein I (NR1) in E. coli controls expression of genes encoding the enzymes which participate in nitrogen metabolism. (5) Phosphorylation of citrate lyase ligase in Clostridium sphenoides regulates the conversion of citrate lyase from the inactive sulfhydryl form to the active acetylated form. Recent investigations have shown that more than one hundred proteins in E. coli are phosphorylated. It can therefore be anticipated that protein phosphorylation will prove to be as important to the regulation of physiological processes in bacteria as it is in eukaryotes.
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  • 11
    ISSN: 0570-0833
    Keywords: Lipopolysaccharides ; Lipopolysaccharides ; Polysaccharides ; Bacteria ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Lipopolysaccharides, which are located in the cell wall of gram-negative bacteria, are characterized by their biological versatility. They represent the O antigens of the bacteria, they are potent endotoxins, and they often function as the receptor sites for bacteriophages. The study of the mode of action of lipopolysaccharides and the search for structures in the macromolecules that are responsible for biological activity became promising when principles of the chemical fine structure of lipopolysaccharides were identified. The following review summarizes the results of recent investigations regarding the structure of lipopolysaccharides, their biosynthesis and its genetic determination.
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  • 12
    ISSN: 0570-0833
    Keywords: Lipids ; Tubercle bacillus ; Bacteria ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The extensive studies of R.J. Anderson between 1926 and 1946 nad the subsequent work of Stenhagen, Polgar, and Cason, and of the author's laboratory have demonstrated the astonishing abilities of the tubercle bacillus in synthetizing lipids. Numerous branched-chain fatty acids, glycolipids, peptidolipids, and peptidoglycolipds have been isolated, and their structures more or less elucidated. Such work is of interest not only to natural-priduct chemists, and biochemists, but especially to biologists and pathologists who are concerned with the harmful effects caused by the tubercle bacillus. The present article discusses chiefly three points: 1. The biogenesis of the branched-chain fatty acids. - 2. The structures of several glyco-, peptido-, and peptidoglycolipids. - 3. Adjuvant activity and immunization by the lipids of the tubercle bacillus.
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  • 13
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 16 (1995), S. 135-148 
    ISSN: 0173-0835
    Keywords: Two-dimensional polyacrylamide gel electrophoresis ; Haemophilus influenzae ; Bacteria ; Protein database ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The proteins of nontypable and type b Haemophilus influenzae isolates were characterised using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Coomassie Brilliant Blue R-250 was used for protein detection. Two hundred and twenty eight proteins were resolved from whole cell lysates prepared from a standard nontypable H. influenzae strain (designated HI-64443) when isoelectric focusing was used for the first-dimensional separation of 2-D PAGE. When nonequilibrium pH gel electrophoresis (NEPHGE) was used to separate basic proteins in the first dimension, 50 proteins were detected for HI-64443; 20 of the basic proteins detected were considered to be unique for this separation protocol. The apparent molecular weights and isoelectric points were determined for 82 of the proteins resolved for HI-64443. The variation of the proteins from the standard bacterial strain (HI-64443) was determined for nontypable H. influenzae isolates. On the basis of their electrophoretic mobilities, 17.5% of the proteins of HI-64443 were shared by four other non-typable H. influenzae strains analysed. These data identified both conserved and variable proteins among the nontypable H. influenzae isolates analysed. The results obtained indicated that 2-D PAGE was able to discriminate nontypable H. influenzae into population clones identified by other procedures. The 2-D protein profiles obtained for type b H. influenzae strains were similar to those obtained for nontypable H. influenzae strains. The extent of the protein variation observed between type b and nontypable H. influenzae strain was similar to that observed among nontypable strains alone. These data are discussed in relation to the application of 2-D PAGE as a tool for studies on bacterial epidemiology and for the analysis of the genome structure and gene expression of Haemophilus influenzae.
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  • 14
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 2317-2323 
    ISSN: 0173-0835
    Keywords: Protein profile ; Bacteria ; Capillary electrophoresis ; Lysate ; Enterobacteriaceae family ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: A fast and reproducible method was developed to characterize cell lysates by their electrophoretic profiles using capillary electrophoresis (CE). Characteristic and reproducible patterns were recorded for each bacterial strains when “dynamic sieving” CE, using a polymer solution in the capillary, was applied to distinguish four strains of the Enterobacteriaceae family. The electropherograms showed distinct differences when comparing them to the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) protein profiles. This is certainly a result of the differences in the separation principles and in the detection methods of the two techniques.
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  • 15
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Angewandte Chemie International Edition in English 32 (1993), S. 1398-1408 
    ISSN: 0570-0833
    Keywords: Bacteria ; Degradation ; Environmental chemistry ; Hydrocarbons ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The natural potential of bacteria for the biological degradation of synthetic compounds is greater than is commonly supposed and extends to many heteroarenes and even some chloroarenes. An increase in the number of substituents on the aromatic ring or a certain substitution pattern is what confers xenobiotic character to a compound. In addition, when enzymes with low substrate specificity encounter foreign compounds with random variations, products with very strong xenobiotic character often result. In this case, changing the conditions or introducing a cooperation between several different types of bacteria can be used to degrade these compounds. Finally, mineralization, the complete breakdown of organic substances into carbon dioxide and inorganic salts, of xenobiotics previously regarded as persistent can be achieved by taking advantage of natural or induced gene transfer to construct hybrid degradative pathways. After an introduction to the world of bacteria and their place in Nature, we will describe their natural potential for biodegradation with reference to aliphatic and aromatic hydrocarbons. The discussion will then turn to the types of the substituents that confer xenobiotic properties to compounds and how these compounds are degraded despite their xenobiotic character.
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  • 16
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Angewandte Chemie International Edition in English 12 (1973), S. 517-528 
    ISSN: 0570-0833
    Keywords: Extrachromosomal DNA ; Bacteria ; DNA ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In addition to chromosomal DNA carrying the genetic information of the cell, many bacterial cells contain smaller circular DNA factors known as plasmids or episomes. These genetic elements endow the cell with additional biochemical capabilities. The fertility factors (F and F′), the antibiotic resistance factors (R), the colicinogenic factors (Col), the hemolytic factors (Hly), and other extrachromosomal DNA systems are described. These small DNA molecules can be isolated, and are therefore particularly suitable for the investigation of DNA replication and the stable establishment of genetic material in the bacterial cell.
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  • 17
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5287 | 1256 | 2011-09-29 15:12:00 | 5287 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Restoration of water-bodies from eutrophication has proved to be extremely difficult. Mathematical models have been used extensively to provide guidance for management decisions. The aim of this paper is to elucidate important problems of using models for predicting environmental changes. First, the necessity for a proper uncertainty assessment of the model, upon calibration, has not been widely recognized. Predictions must not be a single time trajectory; they should be a band, expressing system uncertainty and natural variability. Availability of this information may alter the decision to be taken. Second, even with well-calibrated models, there is no guarantee they will give correct projections in situations where the model is used to predict the effects of measures designed to bring the system into an entirely different ”operating point”, as is typically the case in eutrophication abatement. The concept of educated speculation is introduced to partially overcome this difficulty. Lake Veluwe is used as a case to illustrate the point. Third, as questions become more detailed, such as ”what about expected algal composition”, there is a greater probability of running into fundamental problems that are associated with predicting the behaviour of complex non-linear systems. Some of these systems show extreme initial condition sensitivity and even, perhaps, chaotic behaviour, and are therefore fundamentally unpredictable.
    Keywords: Ecology ; Limnology ; Pollution ; Eutrophication ; Algal blooms ; Phytoplankton ; Freshwater lakes ; Models ; Growth ; Modelling ; Equations ; Bacteria ; Prediction ; Netherlands ; Veluwemeer Lake
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  • 18
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5301 | 1256 | 2011-09-29 15:07:11 | 5301 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: The cyanobacteria that cause problems in water supply are principally the colonial forms that are buoyed up by gas vesicles. The success of these organisms is due, in part, to their gas vesicles, which enable them to perform vertical migrations or to maintain themselves in the euphotic zone. The gas vesicles are also the root cause of the problems. In calm periods they cause the cyanobacteria to float to the water surface forming noxious scums, and they may prevent the colonies from sedimenting in water treatment plants. Gas vesicles are hollow, gas-filled structures; they are rigid but can be collapsed by the application of pressure. Their critical collapse pressure is influenced by their dimensions, which vary in different organisms. Gas vesicles are formed by the assembly of two types of protein, which determine their mechanical and physical properties. Methods for collapsing gas vesicles in natural populations of cyanobacteria will be considered. They may have application to the control of cyanobacteria in water supply.
    Keywords: Ecology ; Limnology ; Pollution ; Eutrophication ; Algal blooms ; Gases ; Buoyancy ; Algae ; Bacteria ; Photosynthesis ; Growth ; Competition
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  • 19
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5317 | 1256 | 2011-09-29 15:05:35 | 5317 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Most microbiological methods require culture to allow organisms to recover or to selectively increase, and target organisms are identified by growth on specific agar media. Many cultural methods take several days to complete and even then the results require confirmation. Alternative techniques include the use of chromogenic and fluorogenic substances to identify bacteria as they are growing, selective capture using antibodies after short periods of growth, molecular techniques, and direct staining with or without flow cytometry for enumeration and identification. Future microbiologists may not use culture but depend on the use of specific probes and sophisticated detection systems.
    Keywords: Engineering ; Limnology ; Pollution ; Water quality ; Microorganisms ; Methodology ; Detection ; Bacteria ; Cultured organisms ; Enzymes ; Immunofluorescence ; Flow cytometry ; Microbiological culture
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  • 20
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5315 | 1256 | 2011-09-29 15:06:22 | 5315 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Improvements in methods for the detection and enumeration of microbes in water, particularly the application of techniques of molecular biology, have highlighted shortcomings in the ”standard methods” for assessing water quality. Higher expectations from the consumer and increased publicity associated with pollution incidents can lead to an uncoupling of the cycle which links methodological development with standard-setting and legislation. The new methodology has also highlighted problems within the water cycle, related to the introduction, growth and metabolism of microbes. A greater understanding of the true diversity of the microbial community and the ability to transmit genetic information within aquatic systems ensures that the subject of this symposium and volume provides an ideal forum to discuss the problems encountered by both researcher and practitioner.
    Keywords: Biology ; Limnology ; Pollution ; Water quality ; Microbiology ; Microorganisms ; Hydrologic cycle ; Methodology ; Bacteria ; Bacterial counters ; Public health ; Microbial contamination ; Primary production ; Fungi ; Cryptosporidium
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5318 | 1256 | 2011-09-29 15:05:37 | 5318 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: It is widely recognised that conventional culture techniques may underestimate true viable bacterial numbers by several orders of magnitude. The basis of this discrepancy is that a culture in or on media of high nutrient concentration is highly selective (either through ”nutrient shock” or failure to provide vital co-factors) and decreases apparent diversity; thus it is unrepresentative of the natural community. In addition, the non-culturable but viable state (NCBV) is a strategy adopted by some bacteria as a response to environmental stress. The basis for the non-culturable state is that cells placed in conditions present in the environment cannot be recultured but can be shown to maintain their viability. Consequently, these cells would not be detected by standard water quality techniques that are based on culture. In the case of pathogens, it may explain outbreaks of disease in populations that have not come into contact with the pathogen. However, the NCBV state is difficult to attribute, due to the failure to distinguish between NCBV and non-viable cells. This article will describe experiences with the fish pathogen Aeromonas salmonicida subsp. salmonicida and the application of molecular techniques for its detection and physiological analysis.
    Keywords: Ecology ; Limnology ; Pollution ; Bacteria ; Bacterial diseases ; Detection ; Methodology ; Molecular biology ; Microbiological culture
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5316 | 1256 | 2011-09-29 15:05:33 | 5316 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: The advent of molecular biology has had a dramatic impact on all aspects of biology, not least applied microbial ecology. Microbiological testing of water has traditionally depended largely on culture techniques. Growing understanding that only a small proportion of microbial species are culturable, and that many microorganisms may attain a viable but non-culturable state, has promoted the development of novel approaches to monitoring pathogens in the environment. This has been paralleled by an increased awareness of the surprising genetic diversity of natural microbial populations. By targeting gene sequences that are specific for particular microorganisms, for example genes that encode diagnostic enzymes, or species-specific domains of conserved genes such as 16S ribosomal RNA coding sequences (rrn genes), the problems of culture can be avoided. Technical developments, notably in the area of in vitro amplification of DNA using the polymerase chain reaction (PCR), now permit routine detection and identification of specific microorganisms, even when present in very low numbers. Although the techniques of molecular biology have provided some very powerful tools for environmental microbiology, it should not be forgotten that these have their own drawbacks and biases in sampling. For example, molecular techniques are dependent on efficient lysis and recovery of nucleic acids from both vegetative forms and spores of microbial species that may differ radically when growing in the laboratory compared with the natural environment. Furthermore, PCR amplification can introduce its own bias depending on the nature of the oligonucleotide primers utilised. However, despite these potential caveats, it seems likely that a molecular biological approach, particularly with its potential for automation, will provide the mainstay of diagnostic technology for the foreseeable future.
    Keywords: Engineering ; Limnology ; Pollution ; Water quality ; Microbiology ; Microorganisms ; Methodology ; Molecular biology ; DNA ; Polymerase chain reaction ; Detection ; RNA ; Bacteria ; Bacterial diseases
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  • 23
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5323 | 1256 | 2011-09-29 15:05:12 | 5323 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: In drinking water distribution systems, three groups of living organisms are usually found in the biofilm and circulating water: heterotrophic bacteria, free-living protozoa, and macro-invertebrates. Indirect evidence suggests that protozoa grazing in distribution systems can partially eliminate biomass production and accidental microbiological pollution. This paper examines the biodiversit in drinking water distribution systems.
    Keywords: Biology ; Limnology ; Water supply ; Biodiversity ; Food chains ; Bacteria ; Invertebrate larvae ; Escherichia coli
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  • 24
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5322 | 1256 | 2011-09-29 15:05:32 | 5322 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: The direct measurement of in situ respiring bacteria using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) shows that, especially for Gram-negative bacteria, large numbers of viable but non-culturable (VBNC) bacteria are present in finished water from a conventional water treatment plant, and the regrowth of bacteria along distribution networks can be seen rapidly by using this very sensitive technique. The level of bacterial inactivation with chlorine is much less important than has been previously supposed (based on experiments with non-injured laboratory strains of bacteria and classical culture techniques). Threshold values of VBNC bacteria leaving water treatment plants or regrowing along distribution systems have to be determined for better control of coliform regrowth and health- risks associated with the consumption of drinking water.
    Keywords: Biology ; Health ; Limnology ; Water supply ; Water treatment ; Bacteria ; Microbiological culture ; Bacterial counters ; Staining ; Growth curves ; France
    Repository Name: AquaDocs
    Type: book_section , FALSE
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    Format: 54-62
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5333 | 1256 | 2011-09-29 15:04:52 | 5333 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Interest in the identification and characterisation of cyanobacteria and dinoflagellates in aquatic environments is increasing rapidly due to the perceived roles of these organisms in primary production and nuisance aspects in terms of water treatment and public health. Techniques for the identification and quantification of these organisms currently are limited, and the application of molecular approaches provides fundamental taxonomic information and techniques of practical value. Antigenic properties of algal cells may be useful taxonomic markers. Immunodetection techniques utilise the specificity of the antibody/antigen association as a probe for recognising and distinguishing between microorganisms according to their cell- surface chemistry. Immunofluorescent detection of unicellular cyanobacteria and dinoflagellates has been studied with success in marine and freshwater ecosystems and a range of techniques and results are presented and discussed. The most recent advances in the study of planktonic algae have come with the application of continuous flow cytometric methods (CFC). Flow cytometry makes use of the autofluorescence properties of the algal cells, which alone can be used to demonstrate their presence and permit their quantification in natural water samples. When used in conjunction with immunolabelling techniques, the potential of CFC analysis is broadened to study the serological/strain composition of plankters in natural populations. Changes in algal strains represented within and between waters over periods of time are reported and discussed, along with the ecological issues thus raised.
    Keywords: Ecology ; Limnology ; Bacteria ; Methodology ; Algae ; Plankton ; Immunology ; Detection ; Toxicity tests ; Immunofluorescence ; Synechococcus ; Alexandrium tamarens ; Prorocentrum micans
    Repository Name: AquaDocs
    Type: book_section , FALSE
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    Format: application/pdf
    Format: 92-103
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5161 | 3949 | 2011-09-29 15:17:51 | 5161 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: Actinomycetes are a group of micro-organisms which lie, in classification, half-way between the fungi and the bacteria. They may be isolated from the plating of leaf washings, water samples and mud dilutions on to nutrient agar (with incorporated actidione to eliminate fungi). The predominant genus varied with the source of the sample. An attempt was also made to isolate the phages of some Actinomycetes. A search was made in the typical environments of the host, for the virus. In this way actinophage were also isolated; and shown to be capable of being transmitted from one host strain to another host strain within 1 sp or from one host to another within 1 genus; i.e. polyvalent.
    Keywords: Biology ; Ecology ; Environment ; Bacteria ; Fungi ; Microbiological culture ; Viruses ; Actinomycetes ; Annual report
    Repository Name: AquaDocs
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5208 | 1256 | 2011-09-29 15:16:34 | 5208 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: This project investigated the production of nitrate (nitrification) by bacteria in lakes. The work was undertaken as nitrification is a key process in the nitrogen cycle and previous estimates of rates of nitrification were unreliable. When different methods were used to estimate rates of nitrification within sediment deposits different results were obtained. Investigation' of specific aspects of these methodologies has allowed some rationalization of these observations and also enabled comparisons of previously published data which, beforehand, was not possible. However, it was not clear which methods gave the most reliable rate estimates. Calculation of a nitrate budget for Grasmere lake indicated that the use of methods which involved the mixing of surface sediments (and therefore disrupted preformed nutrient gradients) overestimated the rate of nitrification. The study concludes that slight changes in the method used to prepare sediment slurries can result in large changes, in the measured nitrifying activity. This makes comparisons between studies, using different methods, extremely difficult. Methods to study sediment nitrification processes which do not disrupt preformed substrate gradients within the sediment provide the most reliable rate estimates.
    Keywords: Ecology ; Limnology ; Bacteria ; Nitrification ; Freshwater lakes ; Sediment samples ; Slurries ; Seasonal variations ; Methodology ; England ; Grasmere Lake
    Repository Name: AquaDocs
    Type: monograph
    Format: application/pdf
    Format: application/pdf
    Format: 47
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5239 | 3949 | 2011-09-29 15:13:47 | 5239 | Freshwater Biological Association
    Publication Date: 2021-06-24
    Description: This review discusses the processes involved in the decomposition of organic carbon derived initially from structural components of algae and other primary producers. It describes how groups of bacteria interact in time and space in a eutrophic lake. The relative importance of anaerobic and aerobic processes are discussed. The bulk of decomposition occurs within the sediment. The role of bacteria in the nitrogen cycle and the iron cycle, and in sulphate reduction and methanogenesis as the terminal metabolism of organic carbon are described.
    Keywords: Biology ; Chemistry ; Anaerobic bacteria ; Bacteria ; Biodegradation ; Carbon cycle ; Eutrophic lakes ; Fresh water ; Geochemical cycle ; Iron ; Manganese ; Nitrates ; Nitrogen cycle ; Organic carbon ; Oxygen consumption ; Partical size ; Sedimentation ; Sulphates ; Sulphur ; Annual report
    Repository Name: AquaDocs
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    Format: application/pdf
    Format: 31-44
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5319 | 1256 | 2011-09-29 15:05:39 | 5319 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Tap water is not sterile; it contains organisms which grow in water distribution systems or inside taps and their fittings. The absence of known pathogenic bacteria is assured by the absence of the indicator organisms but concerns have been raised in the past few years that drinking water fulfilling the standards laid down in the EC Directive ECC 80/778 may still cause disease. These concerns have arisen from several sources: the fact that a cause has been identified in only half of all suspected waterborne outbreaks of disease; reports have suggested that heterotrophic bacteria possessing single pathogenic mechanisms such as haemolysin may cause disease; reports of heterotrophic organisms causing water contact diseases in hospitals. These concerns led to a reappraisal of the pathogenic potential of heteretrophic bacteria, by carrying out an extensive literature search and review commissioned by the UK Water Research Company. This research identified many papers showing an association between drinking water and heterotrophic bacteria but only very few reports of suspected waterborne disease associated with the heterotrophs. The organisms demonstrating potential to cause disease were species of Aeromonas and Yersinia, but typing of organisms identified in patients and isolated from the water revealed very few similarities. The potential of Aeromonas and Yersinia to cause waterborne disease is thought to be very low and the Communicable Disease Surveillance Centre database of laboratory infections due to these two genera of organisms was analysed to produce population-related incidences for each health region in England and Wales. Additionally a laboratory questionnaire revealed different levels of ascertainment of these two organisms in different laboratories of the Public Health Laboratory Service.
    Keywords: Ecology ; Health ; Limnology ; Public health ; Microbial contamination ; Water pollution treatment ; Bacteria ; Bacterial diseases ; Water supply ; Water policy ; Heterotrophic organisms
    Repository Name: AquaDocs
    Type: book_section , FALSE
    Format: application/pdf
    Format: application/pdf
    Format: 35-42
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5114 | 3949 | 2011-09-29 15:21:32 | 5114 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: An article looking at the numerical distribution of bacteria in lakes, the types most commonly present and the nitrogen-cycle, in Lake Windermere. The methodology is explained, including the sampling frequency and depths, and bacteria culturing techniques. Water bodies other than Lake Windermere were also sampled and these are detailed, including a water reservoir. A summary of the work into horizontal of bacteria is given, including a table showing the number of bacteria per millilitre at different distances from inflow into Windermere. A summary of the work into vertical distribution is also given, including two figures, one showing seasonal variation during 1938-9 in numbers of bacteria at different depths in Winderemere, and the other showing the relationship between the numbers of bacteria at 10 metres depth in Windermere and the rainfull during the previous 7 days. A summary of the types of bacteria found, as well as work on the nitrogen cycle in Esthwaite Water, Lake Windermere and Blelham Tarn are given.
    Keywords: Biology ; Chemistry ; Limnology ; Nitrogen cycle ; Bacteria ; Freshwater ecology ; Limnology ; Seasonal variations ; Water column ; Water reservoirs ; Annual reports ; England ; Lake District
    Repository Name: AquaDocs
    Type: book_section , FALSE
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    Format: application/pdf
    Format: 51-57
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5168 | 3949 | 2011-09-29 15:18:43 | 5168 | Freshwater Biological Association
    Publication Date: 2021-07-08
    Description: Obtaining a reliable estimate of the bacterial population is one of the main problems facing the bacterial ecologist. The author discusses the various methods available and concludes that the observed variability in bacterial populations depends on the sampling interval used.
    Keywords: Biology ; Ecology ; Bacteria ; Biomass ; Population characteristics ; Population number ; Annual report
    Repository Name: AquaDocs
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    Freshwater Biological Association | Ambleside, UK
    In:  http://aquaticcommons.org/id/eprint/5184 | 3949 | 2011-09-29 15:17:22 | 5184 | Freshwater Biological Association
    Publication Date: 2021-07-09
    Description: Three different methods for determining bacterial growth rate in rivers are described. Two of the methods are for bacteria in suspension: a recirculating experimental channel method and a radioactive tracer technique using super(35)SO sub(4). The third method is for bacteria attached to surfaces and specifically considers the surface of the common duckweed Lemna minor).
    Keywords: Biology ; Ecology ; Bacteria ; Growth ; Nannoplankton ; Rivers ; Lemna minor ; England ; Dorset ; River Frome ; Annual report
    Repository Name: AquaDocs
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Keywords: Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository Name: Woods Hole Open Access Server
    Type: Article
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