bluuebunny/crossref_metadata_2025 huggingface dataset:
A microstructural approach to flaw size dependence of strength in engineering ceramics
Authors: Hoshide  , Hiramatsu
Published: March 2003

In this work, microstructural effects on the flaw size dependence of ceramic strength were investigated from aspects of stress analysis in the grain just ahead of the crack tip and also R‐curve behaviour. In the analysis, it was assumed that the stress averaged in one grain just ahead of the crack tip, in ceramics, might control the fracture from a flaw. A microstructurally modified fracture criterion using the averaged stress was established by introducing the R‐curve due to the grain bridging effect for longer cracks. A new R‐curve of an exponential type was proposed for the fracture criterion. The criterion could adequately express the central trend in the dispersal of experimental results in the strength versus flaw size relation. To explain the scatter of results, the size distribution and the crystallographic anisotropy of the grain ahead of the crack tip were examined as dominant factors. The lower bound of strength scatter was estimated from the largest grain size, and the strength dispersion was reduced by decreasing the range of grain size variation. In FEM simulations, each element was regarded as one grain with a different crystallographic orientation, which was randomly selected by using a series of quasi‐uniform random numbers. It was revealed that the scatter of strength due to crystallographic variations was smaller than the strength dispersion caused by a distributed grain size.
Standing contact fatigue testing of a ductile material: surface and subsurface cracks
Authors: Alfredsson  , Olsson
Published: March 2003

During standing contact fatigue testing of case hardened steel plates, four different fatigue crack types are found: ring/cone; lateral; radial; and median cracks. Fatigue results are presented as load versus cycle number, with endurance limits and initiation laws for the ring/cone and lateral cracks. The behaviour of the radial surface strain outside the contact is altered by the presence of cracks. In particular this makes in situ crack detection possible for the lateral crack.

The ductility of the tested material is found to be important for fatigue crack initiation. Numerical elastoplastic computations are used to derive the stress cycles responsible for each crack type. Stress cycles at different locations and in different directions are compared in order to explain why a particular crack type initiates. It is noted that cracks are produced normal to principal stresses of sufficient range, which are tensile sometime during the load cycle. Implications for spalling are discussed.
Finite element analysis of non‐local effects in ductile fracture
Authors: Howard I. C. , Li Z. H.
Published: March 2003

The paper introduces a weight function for the nonlocal analysis of ductile damage that has the potential to provide approximately uniform averaged field variables over a limited region. When this region is identified with the underlying microstructural length scale of the material, the method is consistent with the view that, once damage is significant, a damaging cell behaves as a uniform entity. The analyses through which these effects have been studied concerned a unit cell idealizing a periodic array of large voids, connected by material that is capable of nucleating smaller‐scale porosity.
Cyclic modelling of the mechanical state produced by shot‐peening
Authors: Lillamand I. , Barrallier L. , Lalanne B. , Castex L.
Published: March 2003

During low cycle fatigue of shot‐peened parts, the competition between the compressive residual stresses and the hardening damage, both of which are produced by cumulated plastic strains, is of major importance for lifetime improvement. In order to take into account these effects in life prediction, the shot‐peening treatment must be considered as a first step in the service life of the studied part. The predicted residual stresses provided by the existing shot‐peening models are not sufficient when taking account of the induced mechanical state. The proposed methodology in this paper describes the shot‐peening process by a new cyclic approach where the Chaboche constitutive equations, commonly used in the aircraft industry, show the best promise. A reversed method is employed to quantify, after shot‐peening, the complete mechanical state in line with commonly used life‐prediction algorithms. Computations are carried out for a shot‐peened TiAl6V4 titanium alloy as used in the low pressure stage compressor of turbo‐engine discs.
Stress intensity factors and weight functions for deep semi‐elliptical surface cracks in finite‐thickness plates
Authors: Wang X.
Published: March 2003

ABSTRACT Three‐dimensional finite element analyses have been conducted to calculate the stress intensity factors for deep semi‐elliptical cracks in flat plates. The stress intensity factors are presented for the deepest and surface points on semi‐elliptic cracks with a/t‐values of 0.9 and 0.95 and aspect ratios (a/c) from 0.05 to 2. Uniform, linear, parabolic or cubic stress distributions were applied to the crack face. The results for uniform and linear stress distributions were combined with corresponding results for surface cracks with a/t= 0.6 and 0.8 to derive weight functions over the range

0.05 ≤ a/c ≤ 2.0 and 0.6 ≤ a/t ≤ 0.95. The weight functions were then verified against finite element data for parabolic or cubic stress distributions. Excellent agreements are achieved for both the deepest and surface points. The present results complement stress intensity factors and weight functions for surface cracks in finite thickness plate developed previously.
Combining virtual simulation and physical vehicle test data to optimize durability testing
Authors: FERRY W. B. , FRISE P. R. , ANDREWS G. T. , MALIK M. A.
Published: March 2003

This paper describes an ongoing project to model a vehicle on a computer with a multibody dynamics simulation software package and to merge that work with physical proving ground and laboratory tests in order to shorten vehicle development time. The intention is to mirror as closely as possible the behaviour of a physical vehicle in order to assist in determining its durability characteristics under varying road conditions. This modelling work is important because, if done with sufficient fidelity, it can be used in order to assess vehicle responses by using different suspension components or payloads. Also, potential issues associated with vehicle structure, suspension components or payload positioning can be observed on a computer prior to performing physical tests. The process has the potential to reduce vehicle development cost and time. The virtual dynamic vehicle model has been created by using Automatic dynamic analysis of mechanical systems (ADAMS) software package. The calculated outputs from the model are being compared to force and displacement data collected from actual vehicle on‐road testing or a servo‐hydraulic road test simulator (RTS). The virtual model can be adjusted until the calculated responses are in close agreement with those of the physical vehicle, thus linking the virtual and real‐world results.
Material damping in 6061‐T6511 aluminium to assess fatigue damage
Authors: COLAKOGLU M. , JERINA K. L.
Published: March 2003

Studies in fatigue can be summarized into two stages, fatigue crack initiation and crack propagation. Fatigue damage may increase the risk of failure under cyclic load. Energy dissipation, termed damping, occurs in engineering metals and is a function of the cyclic loading history. Damping behaviour of materials has been estimated using many different experimental techniques, and parameters i.e. the loss factor vs. strain amplitude, frequency range, etc. However, micro‐structural changes in the form of fatigue damage are also contributors to damping in engineering materials. In order to measure energy dissipation, a damping monitoring method has been used. Under a constant cyclic load up to the point of fatigue crack initiation, the effects of fatigue on damping factor were studied for 6061‐T6511 aluminium alloy. In the experiments, the stress levels were below yield point, 50% and 70% of ultimate strength. Experimental results showed that the damping factor changes with the number of fatigue cycles. Percentage increase in damping energy was calculated using experimental data.
Testing for latitudinal and other body‐size gradients
Authors: Manly
Published: March 2003

Testing for a relationship between the body size of animals and a gradient such as latitude is complicated by the fact that typically there is a single average size for each species, and each species occurs at several sample stations over the gradient. This results in standard tests for statistical significance being invalid. This problem can be overcome by using a randomization test. A more difficult problem, however, is determining whether the relationship between size and latitude is the same for two subfamilies of species. In this paper a general method for relating body size to latitude and subfamily differences is proposed, with the significance of effects determined by randomization. A simulation study suggests that this procedure has good properties. This approach to data analysis has promise both for the particular situation considered and for other related problems in biogeography.
No‐take areas for sustainability of harvested species and a conservation invariant for marine reserves
Authors: Mangel
Published: March 2003

Various kinds of no‐take areas (refuges, reserves) are gaining attention as conservation tools. The efficacy of reserves can be considered from the perspectives of providing baseline data sets, protecting the stock, maximizing yield to the fishery, or some combination of these. Regardless of the measure of effectiveness of a reserve, practical application requires the development of techniques for settling operational and policy questions such as how large a reserve should be. A simple model, involving population growth and harvest, is used to explore how the fraction of habitat assigned to a reserve affects the sustainability of a take and to frame the trade‐off between control of harvest outside of the reserve and the size of the reserve. This exploration also leads to the discovery of a robust conservation invariant for reserves.
Spatial variability in forest soil CO2 efflux assessed with a calibrated soda lime technique
Authors: Janssens  , Ceulemans
Published: March 2003

Accurate estimates of soil CO2 efflux are important in the current discussion on the carbon balance of forests, and can be used to validate models and remotely sensed data. Due to the typically large spatial variability, large sample numbers are required to estimate mean forest soil CO2 efflux with reasonable confidence intervals. Most infrared gas analysis (IRGA) systems are not well suited to simultaneously produce daily means and handle this spatial variability problem. The soda lime technique gives daily means and allows the required large sample numbers, but is less accurate than the IRGA systems. Using an elaborate cross‐calibration, we tried to combine the accuracy of an IRGA method with the spatial integration potential of the soda lime technique. This paper reports on the calibration technique used to improve the accuracy of the soda lime technique and confirms the spatial variability in soil CO2 efflux in a heterogeneous forest.
Disturbance, resource supply, and food‐web architecture in streams
Authors: Townsend  , Thompson  , McIntosh  , Kilroy  , Edwards  , Scarsbrook
Published: March 2003

We studied food webs comprising fish, macroinvertebrates, and algae (identified to species or morphospecies) in small streams using a consistent methodology at the same spatial and temporal scales. Our aim was to test a priori hypotheses derived from dynamic‐demographic and energetics models concerning the effects of disturbance and resource availability on food‐web attributes. The regime of bed disturbance affecting the organisms in the webs was measured in 10 streams. We also derived measures of the supply of resources for animals in the webs in terms of algal primary productivity and detritus standing crop. Both web size and number of links per species were significantly negatively related to mean intensity of bed disturbance. Mean chain length had a significant positive relationship with algal primary productivity but not disturbance. No food‐web attribute was related to detritus standing crop.
On the influence of food quality in consumer–resource interactions
Authors: Huxel
Published: March 2003

While nutrients are an important regulating factor in food webs, no theoretical studies have examined limits to consumer growth imposed by nutrient concentrations (i.e. food quality) of their prey. Empirical studies have suggested that nutrients may play a role in limiting assimilation efficiencies of herbivores. Using a simple food chain model, I find that prey nutrient concentration does directly influence the growth rate of consumers and potentially increase the stability of consumer–resource interactions. This suggests that the strength of trophic cascades and the relative importance of top–down versus bottom–up control in food webs is significantly influenced by nutrient availability in food resources of consumers. Additionally, the results imply that increases in resource input may cause a change in which resource is limiting and thereby negate any potential “paradox of enrichment”.
Bacterial ecology, antibiotics and selection for virulence
Authors: Wilkinson
Published: March 2003

The evolution of antibiotic resistance in bacteria is well known. Here I describe possible mechanisms by which an increased rate of re‐colonization of vertebrate guts by microbes caused by antibiotic use could lead to selection for increased virulence in currently mutualistic or benign microbes. The importance of understanding both the source and the frequency of colonization in such mutualisms is stressed and the possible importance of pseudo‐vertical transmission in the evolution of these systems is discussed. A number of areas requiring experimental investigation are identified.
Stability and species richness in complex communities
Authors: Ives A.R. , Klug J.L. , Gross K.
Published: March 2003

Using both numerical simulations and analytical methods, we investigate how the stability of ecological communities depends on the number of species they contain. To investigate complex communities, we construct communities from modular “subcommunities” that can have arbitrary community structure; e.g. subcommunities could consist of pairs of predator and prey species, trios of prey, specialist predator and generalist predator, or any collection of interacting species. By building entire communities from subcommunities, we can change the number of species in the community without changing community structure. We further suppose that species sharing the same ecological role in different subcommunities act additively on the per capita population growth rates of other species. Under these assumptions, the inter‐actions between species from different subcommunities have no effect on community‐level stability, measured by the variability in the combined densities of species sharing the same ecological role in different subcommunities. Furthermore, increasing species richness (i.e. the number of subcommunities comprising the community) increases community‐level stability only when it introduces species that respond differently to environmental fluctuations. Therefore, our results support the “insurance hypothesis” that species richness increases community‐level stability by insuring that some species in a community are tolerant of different environmental fluctuations.
An alternative explanation for the post‐disturbance NO3– flush in some forest ecosystems
Authors: Bradley Robert L.
Published: March 2003

The appearance of soil NO3– after forest disturbance is commonly ascribed to a higher availability of NH4+ to autotrophic nitrifiers, or to a reduction in available‐C resulting in lower microbial assimilation of NO3–. Alternatively, it has been proposed that increasing NH4+ pools following disturbance could increase net nitrification by reducing microbial assimilation of NO3–. Forest floor material was collected from shelterwood harvest plots which displayed both low available‐C and low NH4+ pools, and where previous experiments had suggested the prevalence of heterotrophic nitrification. Subsamples were amended with incremental rates of glucose‐C or NH4+, and gross NO3– transformation rates were measured by isotope dilution. Glucose‐C additions had little effect on the net difference between gross NO3– production and consumption rates. On the other hand, NH4+ additions caused gross NO3– consumption processes to decrease sharply, while gross NO3– production processes remained constant. The results suggest that NH4+ can have an immediate positive effect on net nitrification rates by suppressing NO3– assimilation and uptake systems.
Dispersal, vaccination and regression of immune defence organs
Authors: Møller Anders Pape , Erritzøe Johannes
Published: March 2003

The thymus in vertebrates and the bursa of Fabricius in birds regress before reproduction, while the immunological information of these organs is maintained as cell memory. Regression at a certain age presupposes that individuals have achieved exposure to a large fraction of parasites in the environment. Here we present a new scenario for regression of immune defence organs, based on optimality reasoning. This scenario links early involution of immune defence organs with (1) effects of exposure to parasites on adaptive immune responses to these parasites, (2) exposure to local parasite communities during natal dispersal and migration as a means of “vaccination” against local parasites, and (3) the function of visits to future breeding sites by juveniles as a means of exposure to local parasites. This scenario provides explanations for why natal dispersal is longer than breeding dispersal, for sex differences in dispersal, and for why the bursa of Fabricius regresses relatively early in life among bird species with delayed start of reproduction.
Null models and spatial patterns of species richness in South American birds of prey
Authors: Diniz‐Filho José Alexandre Felizola , De Sant'Ana Carlos Eduardo Ramos , De Souza Márcia Christianne , Rangel Thiago F. L. V. B.
Published: March 2003

In this paper, we used geostatistical approaches to describe bi‐dimensional spatial patterns in species richness of South American birds of prey (Falconiformes and Strigiformes). They indicated strong spatial patterns both across latitude and longitude, for the two groups. These patterns were then correlated with those expected by a bi‐dimensional null model constructed to take into account South America continental edges. As considerable departures from the null model were observed, there may be other ecological or evolutionary explanations for spatial patterns in species richness. Variation seems to be related to habitat heterogeneity across the continent, especially when considering differences between habitats in the central and south‐eastern portion of the continent and in the Andean region. This supports previous conclusions that habitat type and heterogeneity affect species richness and abundance at different spatial scales.
Genetic assessment of spatiotemporal evolutionary relationships and stocking effects in grayling (Thymallus thymallus, Salmonidae)
Authors: Koskinen Mikko T. , Sundell Pekka , Piironen Jorma , Primmer Craig R.
Published: March 2003

Domestically reared introduced (or escaped) individuals can have detrimental genetic effects on the indigenous populations into which they are released. Consequently, numerous studies have attempted to estimate whether non‐native specimens have contributed to the gene pool of wild populations. So far, the key limiting factor of such studies has been their lack of appropriate baseline genetic material. Here, microsatellite DNA analyses of historical scale samples and contemporary wild and introduced populations were used to assess spatiotemporal population structure and stocking effects among endangered Lake Saimaa (eastern Finland) grayling (Thymallus thymallus, Salmonidae). Significant decreases in genetic differentiation were detected between wild and introduced populations since the commencement of stocking in 1986. Accordingly, up to 15% of the contemporary wild grayling were confidently identified to be of pure hatchery origin, and recent hybridization between the hatchery and indigenous individuals appeared likely. Despite these clear genetic imprints of stocking, the contemporary populations exhibited evolutionary relationships congruent with the sampling locations, and up to 73% of contemporary individuals were identified to be of pure indigenous origin. The use of historical baseline material should prove efficient for monitoring gene flow between domesticated and wild populations in other species also, e.g. salmonids, game animals and plants.
Adaptive mgl‐regulatory mutations and genetic diversity evolving in glucose‐limited Escherichia coli populations
Authors: Notley‐McRobb Lucinda , Ferenci Thomas
Published: March 2003

The mutational adaptation of E. coli to low glucose concentrations was studied in chemostats over 280 generations of growth. All members of six independent populations acquired increased fitness through the acquisition of mutations at the mgl locus, increasing the binding protein‐dependent transport of glucose. These mutations provided a strong fitness advantage (up to 10‐fold increase in glucose affinity) and were present in most isolates after 140 generations. mgl constitutivity in some isolates was caused by base substitution, short duplication, small deletion and IS1 insertion in the 1041 bp gene encoding the repressor of the mgl system, mglD (galS). But an unexpectedly large proportion of mutations were located in the short mgl operator sequence (mglO), and the majority of mutations were in mglO after 280 generations of selection. The adaptive mglO substitutions in several independent populations were at exactly the positions conserved in the two 8 bp half‐sites of the mgl operator, with the nature of the base changes also completely symmetrical. Either mutations were directed to the operator or the particular operator mutations had a selective advantage under glucose limitation. Indeed, isolates carrying mglO mutations showed greater rates of transport for glucose and galactose at low concentrations than those carrying mglD null mutations. mglO mutations avoid cross‐talk by members of the GalR–LacI repressor family, reducing transporter expression and providing a competitive advantage in a glucose‐limited environment. Another interesting aspect of these results was that each adapted population acquired multiple mgl alleles, with several populations containing at least six different mgl‐regulatory mutations co‐existing after 200 generations. The diversity of mutations in the mglO/mglD region, generally in combination with mutations at other loci regulating glucose uptake (malT, mlc, ptsG), provided evidence for multiple clones in each population. Increased fitness was accompanied by the generation of genetic diversity and not the evolution of a single winner clone, as predicted by the periodic selection model of bacterial populations.
An evaluation of terminal‐restriction fragment length polymorphism (T‐RFLP) analysis for the study of microbial community structure and dynamics
Authors: Osborn A. Mark , Moore Edward R. B. , Timmis Kenneth N.
Published: March 2003

A systematic evaluation of the value and potential of terminal‐restriction fragment length polymorphism (T‐RFLP) analysis for the study of microbial community structure has been undertaken. The reproducibility and robustness of the method has been assessed using environmental DNA samples isolated directly from PCB‐polluted or pristine soil, and subsequent polymerase chain reaction (PCR) amplification of total community 16S rDNA. An initial investigation to assess the variability both within and between different polyacrylamide gel electrophoresis (PAGE) runs showed that almost identical community profiles were consistently produced from the same sample. Similarly, very little variability was observed as a result of variation between replicate restriction digestions, PCR amplifications or between replicate DNA isolations. Decreasing concentrations of template DNA produced a decline in both the complexity and the intensity of fragments present in the community profile, with no additional fragments detected in the higher dilutions that were not already present when more original template DNA was used. Reducing the number of cycles of PCR produced similar results. The greatest variation between profiles generated from the same DNA sample was produced using different Taq DNA polymerases, while lower levels of variability were found between PCR products that had been produced using different annealing temperatures. Incomplete digestion by the restriction enzyme may, as a result of the generation of partially digested fragments, lead to an overestimation of the overall diversity within a community. The results obtained indicate that, once standardized, T‐RFLP analysis is a highly reproducible and robust technique that yields high‐quality fingerprints consisting of fragments of precise sizes, which, in principle, could be phylogenetically assigned, once an appropriate database is constructed.
Modification of the aggregation behaviour of the environmental Ralstonia eutropha‐like strain AE815 is reflected by both surface hydrophobicity and amplified fragment length polymorphism (AFLP) patterns
Authors: Bossier Peter , Top Eva M. , Huys Geert , Kersters Karel , Boonaert Christophe J. P. , Rouxhet Paul G. , Verstraete Willy
Published: March 2003

After inoculation of the plasmid‐free non‐aggregative Ralstonia eutropha‐like strain AE815 in activated sludge, followed by reisolation on a selective medium, a mutant strain A3 was obtained, which was characterized by an autoaggregative behaviour. Strain A3 had also acquired an IncP1 plasmid, pLME1, co‐aggregated with yeast cells when co‐cultured, and stained better with Congo red than did the AE815 strain. Contact angle measurements showed that the mutant strain was considerably more hydrophobic than the parent strain AE815, and scanning electron microscopy (SEM) revealed the production of an extracellular substance. A similar hydrophobic mutant (AE176R) could be isolated from the AE815‐isogenic R. eutropha‐like strain AE176. With the DNA fingerprinting technique repetitive extragenic palindromic‐polymerase chain reaction (REP‐PCR), no differences between these four strains, AE815, A3, AE176 and AE176R, could be revealed. However, using the amplified fragment length polymorphism (AFLP) DNA fingerprinting technique with three different primer combinations, small but clear reproducible differences between the banding patterns of the autoaggregative mutants and their non‐autoaggregative parent strains were observed for each primer set. These studies demonstrate that, upon introduction of a strain in an activated sludge microbial community, minor genetic changes readily occur, which can nevertheless have major consequences for the phenotype of the strain and its aggregation behaviour.
Horizontal transfer of an exopolymer complex from one bacterial species to another
Authors: Osterreicher‐Ravid D. , Ron E. Z. , Rosenberg E.
Published: March 2003

Alasan, the exocellular polymeric emulsifier produced by Acinetobacter radioresistens KA53 was shown to bind to the surface of Sphingomonas paucimobilis EPA505 and Acinetobacter calcoaceticus RAG‐1. The presence of alasan on the surface of S. paucimobilis EPA505 and A. calcoaceticus RAG‐1 caused a decrease in their cell‐surface hydrophobicities. Binding was proportional to the concentration of recipient cells and input alasan. At the highest concentration of A. calcoaceticus RAG‐1 (4 × 109 ml−1) and alasan (20 µg ml−1) tested, 75% of the alasan was cell bound. Alasan binding was measured by the loss of emulsifying activity and alasan protein and polysaccharide from the aqueous phase after incubation of alasan with the recipient cells. In addition, alasan was visualized on the surface of the recipient cells by staining with anti‐alasan antibodies and rhodamine‐labelled secondary antibodies. Moreover, when the alasan‐producing A. radioresistens KA53 was grown together with A. calcoaceticus RAG‐1, alasan was released from the producing strain and became bound to the recipient RAG‐1 cells, as demonstrated by fluorescence microscopy. This horizontal transfer of exopolymers from one bacterial species to another has significant implications in natural microbial communities, coaggregation and biofilms.
Isolation and characterization of a chromium‐reducing bacterium from a chromated copper arsenate‐contaminated site
Authors: McLean Jeff S. , Beveridge Terry J. , Phipps David
Published: March 2003

A Gram‐negative bacterium (CRB5) was isolated from a chromium‐contaminated site that was capable of reducing hexavalent chromium to an insoluble precipitate, thereby removing this toxic chromium species from solution. Analysis of the 16S rRNA from the isolate revealed that it was a pseudomonad with high similarity to Pseudomaonas synxantha. CRB5 was tolerant to high concentrations of chromate (500 mg l−1) and can reduce Cr(VI) under aerobic and anaerobic conditions. It also exhibited a broad range of reduction efficiencies under minimal nutrient conditions at temperatures between 4°C and 37°C and at pH levels from 4 to 9. As reduction increased, so did total cellular protein, indicating that cell growth was a requirement for reduction. Under low nutrient conditions with CRB5 or when using non‐sterile contaminated groundwater from the site, reduction of Cr(VI) was followed by a increase in solution turbidity as a result of the formation of fine‐grained Cr(III) precipitates, most probably chromium hydroxide mineral phases such as Cr(OH)3. Chromium adsorption and precipitation, as observed by transmission electron microscopy coupled with energy dispersive X‐ray spectroscopy (TEM/EDS), revealed that the surfaces of the cells were uniformly stained with bound Cr(III) and amorphous precipitates (as determined by selected area electron diffraction; SAED). A mass balance of chromium in a batch bioreactor revealed that up to 30% of the total Cr was as settable precipitates or bound to cells.
Nitrogenase activity in cyanobacteria measured by the acetylene reduction assay: a comparison between batch incubation and on‐line monitoring
Authors: Staal Marc , Lintel‐Hekkert Sacco te , Harren Frans , Stal Lucas
Published: March 2003

A new on‐line method for measuring acetylene reduction is described. It consists of a gas‐flow cell connected to an electronic gas‐mixing system and an automatic sample loop in the gas chromatograph. Alternatively, ethylene can be determined by using laser‐based trace gas detection. The laser‐based trace gas detection technique achieves a detection limit that is three orders of magnitude better than gas chromatography. We have applied the on‐line method to the measurement of nitrogen fixation in a culture of the heterocystous cyanobacterium Nodularia spumigena and compared it with conventional batch‐type incubations. Incubation of N. spumigena in the gas‐flow cell resulted in very short response times with a steady‐state flux of ethylene obtained within 2 min. Nitrogenase was shown to respond immediately to changes in light and oxygen. Monitoring of nitrogenase activity could be continued for several hours without having a negative impact on nitrogen fixation rates in N. spumigena. This was not the case in batch incubations, in which changes in nitrogenase activities were recorded during incubations, probably as a result of varying oxygen concentrations. It was therefore concluded that the on‐line method is superior to batch incubations when rates of nitrogenase activity are to be measured. The method is suitable for natural samples (water or sediment).
Design and application of oligonucleotide probes for fluorescent in situ identification of the filamentous bacterial morphotype Nostocoida limicola in activated sludge
Authors: Liu Jian Rong , Seviour Robert J.
Published: March 2003

16S rRNA targeted probes, designed using sequence data from pure cultures of the three morphotypes of the filamentous bulking bacteria Nostocoida limicola I, II and III and their successful application to the in situ identification of these bacteria in activated sludge biomass samples are described here. Two probes were required to detect all the sequenced N. limicola II isolates. Results from fluorescent in situ hybridization suggest that the morphotypes N. limicola I and II contain at least two phylogenetically unrelated bacteria. The N. limicola II filaments that did not respond to the probes designed in this study fluoresced instead with the probes previously designed for the α‐Proteobacteria. The data also suggest that both N. limicola I and III can exist in activated sludge as single, paired or clumped cells and thus in a form not recognizable microscopically as this morphotype. Some N. limicola II filaments which responded to the probes designed here were much thinner than the filaments conventionally ‘identified’ as this morphotype and better fitted the descriptions often used in the literature for N. limicola I.
Upstream‐independent ribosomal RNA amplification analysis (URA): a new approach to characterizing the diversity of natural microbial communities
Authors: Yakimov Michail M. , Giuliano Laura , Timmis Kenneth N. , Golyshin Peter N.
Published: March 2003

Here, we propose an advanced method for recently developed fingerprinting strategies to analyse microbial populations by direct detection of 16S rRNA sequences occurring in natural habitats. The differential display (DD) technique, which is widely used to analyse for eukaryotic gene expression, was optimized to assess bacterial rRNA diversity in environmental samples. Double‐stranded cDNAs of rRNAs were synthesized without a forward primer digested with endonuclease and ligated with a double‐stranded adapter. The fragments obtained were then amplified using an adapter‐specific extended primer and a 16S rDNA universal reverse primer pair displayed by electrophoresis on a polyacrylamide gel. We validated this approach by characterization of a microbial community colonizing a geothermal (48°C) vent system located close to the eruption zone of the south‐east crater of the Mount Etna volcano, Sicily. Analysis of the patterns of abundant 16S rRNA revealed a considerable diversity of metabolically active bacteria phylogenetically clustering within the Crenarchaeota, Cyanobacteria, Firmicutes, Planctomycetales and Thermus divisions. Two sequence phylotypes were affiliated with uncultivated representatives of the recently described candidate division OP10 from a Yellowstone hot spring.
A review of bacterial methyl halide degradation: biochemistry, genetics and molecular ecology
Authors: McDonald I. R. , Warner K. L. , McAnulla C. , Woodall C. A. , Oremland R. S. , Murrell J. C.
Published: March 2003

Methyl halide‐degrading bacteria are a diverse group of organisms that are found in both terrestrial and marine environments. They potentially play an important role in mitigating ozone depletion resulting from methyl chloride and methyl bromide emissions. The first step in the pathway(s) of methyl halide degradation involves a methyltransferase and, recently, the presence of this pathway has been studied in a number of bacteria. This paper reviews the biochemistry and genetics of methyl halide utilization in the aerobic bacteria Methylobacterium chloromethanicum CM4T, Hyphomicrobium chloromethanicum CM2T, Aminobacter strain IMB‐1 and Aminobacter strain CC495. These bacteria are able to use methyl halides as a sole source of carbon and energy, are all members of the α‐Proteobacteria and were isolated from a variety of polluted and pristine terrestrial environments. An understanding of the genetics of these bacteria identified a unique gene (cmuA) involved in the degradation of methyl halides, which codes for a protein (CmuA) with unique methyltransferase and corrinoid functions. This unique functional gene, cmuA, is being used to develop molecular ecology techniques to examine the diversity and distribution of methyl halide‐utilizing bacteria in the environment and hopefully to understand their role in methyl halide degradation in different environments. These techniques will also enable the detection of potentially novel methyl halide‐degrading bacteria.
Molecular phylogenetic analyses of reverse‐transcribed bacterial rRNA obtained from deep‐sea cold seep sediments
Authors: Inagaki Fumio , Sakihama Yuri , Inoue Akira , Kato Chiaki , Horikoshi Koki
Published: March 2003

A depth profile of naturally occurring bacterial community structures associated with the deep‐sea cold seep push‐core sediment in the Japan Trench at a depth of 5343 m were evaluated using molecular phylogenetic analyses of RNA reverse transcription‐PCR (RT‐PCR) amplified 16S crDNA fragments. A total of 137 clones of bacterial crDNA (complimentary rDNA) phylotypes (phylogenetic types) obtained at three different depths (2–4, 8–10 and 14–16 cm) were identified in partial crDNA sequencings. crDNA phylotypes from the cold seep sediment were dominantly composed of δ‐ and ɛ‐Proteobacteria (36% and 42% respectively). Phylotype analysis of crDNA clone libraries and terminal restriction fragment length polymorphism (T‐RFLP) analysis revealed that the majority of bacterial components shifted from δ‐ Proteobacteria to ɛ‐Proteobacteria with increasing depth. Among the δ‐proteobacterial crDNA clones, the sequences related to the genus Desulfosarcina were dominant. Almost all sequences of crDNA belonging to ɛ‐Proteobacteria were affiliated with the same cluster (ɛ‐CSG: ɛ‐proteobacterial cold seep group), and were closely related with rDNA sequences from deep‐sea hydrothermal vent environments.
The influence of host dynamics on the clonal composition of Escherichia coli populations
Authors: Davis Stephen A. , Gordon David M.
Published: March 2003

Species, be they plant or animal, vary in their capacity for population growth or decline. Populations of the same species may also differ in their capacity for population change. A series of mathematical models were developed with the aim of determining if host population dynamics could influence the clonal composition of the Escherichia coli community in that host population. The biological assumptions
underlying the models are described in some detail. Analytical and numerical approaches
were used to investigate the behaviour of these models. The results demonstrate that
host dynamics can have a profound influence on the E. coli clonal composition of the host population. This outcome is largely independent of the nature of the assumptions underlying the models. The ways in which the predictions of these models may be tested empirically are discussed, as are the implications of these models for understanding the nature of host–bacterial pathogen dynamics.
First insight into the genome of an uncultivated crenarchaeote from soil
Authors: Quaiser Achim , Ochsenreiter Torsten , Klenk Hans‐Peter , Kletzin Arnulf , Treusch Alexander H. , Meurer Guido , Eck Jürgen , Sensen Christoph W. , Schleper Christa
Published: March 2003

Molecular phylogenetic surveys based on the characterization of 16S rRNA genes have revealed that soil is an environment particularly rich in microbial diversity. A clade of crenarchaeota (archaea) has frequently been detected among many other novel lineages of uncultivated bacteria. In this study we have initiated a genomic approach for the characterization of uncultivated microorganisms from soil. We have developed a procedure based on a two‐phase electrophoresis technique that allows the fast and reliable purification of concentrated and clonable, high molecular weight DNA. From this DNA we have constructed complex large‐insert genomic libraries. Using archaea‐specific 16S rRNA probes we have isolated a 34 kbp fragment from a 900 Mbp fosmid library of soil DNA. The clone contained a complete 16S/23S rRNA operon and 17 genes encoding putative proteins. Phylogenetic analyses of the rRNA genes and of several protein encoding genes (e.g. DNA polymerase, FixAB, glycosyl transferase) confirmed the specific affiliation of the genomic fragment with the non‐thermophilic clade of the crenarchaeota. Content and structure of the genomic fragment indicated that the archaea from soil differ significantly from their previously studied uncultivated marine relatives. The protein encoding genes gave the first insights into the physiological potential of these organisms and can serve as a basis for future genomic and functional genomic studies.
High bacterial diversity of a waste gas‐degrading community in an industrial biofilter as shown by a 16S rDNA clone library
Authors: Friedrich Udo , Prior Karola , Altendorf Karlheinz , Lipski André
Published: March 2003

The bacterial diversity of an industrial biofilter used for waste gas abatement in an animal‐rendering plant was investigated. A 16S rDNA clone library was generated and 444 clones were screened using computer‐aided amplified ribosomal DNA restriction analysis (ARDRA). Of the screened clones, 60.8% showed unique ARDRA patterns and the remaining 174 clones were clustered into 65 groups. Almost full‐length 16S rDNA sequences of 106 clones were determined and 90.5% of the clones were affiliated with the two phyla Proteobacteria and Bacteroidetes. Alpha‐, Beta‐, and Gammaproteobacteria accounted for 22.1, 17.6 and 18.6% respectively. Minor portions were affiliated with the Actinobacteria (2.0%), Firmicutes and Verrucomicrobia (both 1.0%), and the Deltaproteobacteria and Thermomicrobia (each 0.5%). Only six out of the 106 16S rDNA sequences exhibited similarities of more than 97% to classified bacterial species indicating that a substantial fraction of the clone sequences were derived from unknown taxa. It was also evaluated whether a database containing 281 computer‐simulated bacterial rDNA fragment patterns generated from published reference sequences can be used for identification purposes. The data analysis demonstrated that this was possible only for a small number of clones, which were closely related to described bacterial strains. Rarefaction analysis of ARDRA clusters demonstrated that the 444 clones screened are insufficient to describe the entire diversity of the clone library.
`Canoe closure' of loop ileostomy gives improved cosmesis compared with conventional closure
Authors: Patel  , Frost  , Bearn  , Allan
Published: March 2003

Objective

The cosmetic appearance of the abdominal scar following closure of loop ileostomy can result in puckering and tethering of the skin, together with a shallow depression. A technique to improve the cosmetic result which also facilitates an easier and more secure closure is described.

Patients and methods

A measured elliptical incision, five times greater in length than the ileostomy diameter, is marked. The skin ellipse, subcutaneous fat and ileo‐ stomy are mobilized together. The skin is removed and the ileostomy is closed with a stapler. This technique is compared with conventional techniques with regard to operative stay, complications and cosmetic appearance over an 18‐month period.

Results

The median operating time has been 50 min and post‐operative stay 5 days. There have been no major complications.

Conclusion

This technique allows better access, improves on cosmesis and has a low complication rate.
Restorative proctocolectomy for distal proctocolitis
Authors: Connolly  , Tan  , Morton  , Keighley
Published: March 2003

Background

Restorative proctocolectomy (RP) is usually the surgical treatment of choice for severe ulcerative colitis, but patients with distal disease (rectosigmoid only) are frequently denied operation on the grounds that they are not systemically ill. Nevertheless, they may continue to have high frequency, low volume diarrhoea with severe urgency and bleeding, despite medical therapy.

Objective

To report the outcome of RP in `distal disease' compared with `more extensive' disease.

Patients and methods

The results of all patients having RP for ulcerative colitis between February 1983 and February 1997 were reviewed. We excluded patients later found to have Crohn's disease.

Results

RP was used for 34 with `distal' disease compared with 134 with `more extensive' disease. Pre‐operative steroids were used in 9% of the `distal' group compared with 34% in the `more extensive' group. Anastomotic leaks and pelvic sepsis occurred in 3% and 9%, respectively, in the `distal' group compared with 13% and 17% in the `more extensive' group, but these differences were not statistically significant. Pre‐operative steroids significantly influenced anastomotic leaks 22% vs 5% (P = 0.006). Pouch‐related fistulas occurred in 12% of the `distal' group compared with 15% in the remainder. Pouchitis occurred in 44% of the `distal' group: 44% compared with 33% in the remainder. Pouch failure occurred in 3% in `distal' compared with 15% in those with `more extensive' disease.

Conclusion

These results imply that RP has a role in the treatment of intractable `distal' colitis, that morbidity is low and urgency is usually eliminated.
Aggressive initial surgery for chronic radiation enteritis: long‐term results of resection vs non‐resection in 44 consecutive cases
Authors: Perrin  , Panis  , Messing  , Matuchanski  , Valleur
Published: March 2003

Objective

One third of patients with chronic radiation enteritis will require surgery. There is, however, no consensus on the best surgical strategy. The long‐term results of intestinal resection vs a `conservative' procedure, including stoma, bypass, and/or adhesiolysis, were reviewed with special reference to reoperation rates and the ultimate need for long‐term parenteral nutrition.

Patients and methods

Forty‐four patients operated for chronic radiation enteritis were divided into two groups: Group I resection (n = 21) and Group II conservative (n = 23). Twenty patients had received preoperative total parenteral nutrition, 16 (76%) in the resection group vs four (17%) in the conservative group (P < 0.001). In the resection group, intestinal resection was combined with a stoma in six patients. In the conservative group, 10 patients underwent adhesiolysis, five a bypass procedure, and eight diverting stoma.

Results

Post‐operative mortality was similar in both groups (9.5% vs 8.5%). Mean follow up was 53 and 55 months for Group I and Group II, respectively. The reoperation rate was significantly lower in Group I: 9 (47%) vs 19 (86%), P < 0.01. Although not significant, the ultimate need for long‐term parenteral nutrition rate was lower in Group I than in Group II: 6 (32%) vs 10 (48%).

Conclusion

Resection resulted in better treatment outcomes than `conservative' surgery for chronic radiation enteritis.