bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial diversity in marine hydrocarbon seep sediments
Authors: LaMontagne Michael G. , Leifer Ira , Bergmann Sandra , Van De Werfhorst Laurie C. , Holden Patricia A. 
Published: July 2004

SummaryMarine seeps introduce significant amounts of hydrocarbons into oceans and create unusual habitats for microfauna and ‐flora. In the vicinity of chronic seeps, microbes likely exert control on carbon quality entering the marine food chain and, in turn, hydrocarbons could influence microbial community composition and diversity. To determine the effects of seep oil on marine sediment bacterial communities, we collected sediment piston cores within an active marine hydrocarbon seep zone in the Coal Oil Point Seep Field, at a depth of 22 m in the Santa Barbara Channel, California. Cores were taken adjacent to an active seep vent in a hydrocarbon volcano, on the edge of the volcano, and at the periphery of the area of active seepage. Bacterial community profiles were determined by terminal restriction fragment length polymorphisms (TRFLPs) of 16S ribosomal genes that were polymerase chain reaction (PCR)‐amplified with eubacterial primers. Sediment carbon content and C/N ratio increased with oil content. Terminal restriction fragment length polymorphisms suggested that bacterial communities varied both with depth into sediments and with oil concentration. Whereas the apparent abundance of several peaks correlated positively with hydrocarbon content, overall bacterial diversity and richness decreased with increasing sediment hydrocarbon content. Sequence analysis of a clone library generated from sediments collected at the periphery of the seep suggested that oil‐sensitive species belong to the γ Proteobacteria and Holophaga groups. These sequences were closely related to sequences previously recovered from uncontaminated marine sediments. Our results suggest that seep hydrocarbons exert a strong selective pressure on bacterial communities in marine sediments. This selective pressure could, in turn, control the effects of oil on other biota in the vicinity of marine hydrocarbon seeps.
Analysis and glycosyl composition of the exopolysaccharide isolated from the floc‐forming wastewater bacterium Thauera sp. MZ1T
Authors: Allen Michael S. , Welch Karen T. , Prebyl Benjamin S. , Baker David C. , Meyers Arthur J. , Sayler Gary S. 
Published: July 2004

SummaryConditions were developed for the reproducible production, isolation and characterization of a novel microbial extracellular polysaccharide believed to be involved in transient viscous bulking at an industrial wastewater treatment plant. The exopolysaccharide was extracted from cell‐free culture supernatants of Thauera sp. strain MZ1T grown on a minimal medium with succinate. The purified polymer was found to be approximately 260 kDa in size by gel‐permeation chromatography. The GC–MS analysis of the alditol acetate and per‐O‐trimethylsilyl methyl glycoside derivatives revealed that the exopolysaccharide was composed of four monosaccharides including: rhamnose, galacturonic acid, N‐acetylglucosamine and N‐acetylfucosamine. Glucose, which also appeared at low levels, is most likely from a co‐eluting glucan. The FTIR and NMR spectroscopic analyses further revealed the presence of esterified component groups on the polymer. These results represent the first published description of a polysaccharide from a member of the genus Thauera, and lay the foundation for a deeper understanding of the factors potentially involved in zoogloeal cluster formation and viscous bulking.
Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing
Authors: Leclerc Marion , Delgènes Jean‐Philippe , Godon Jean‐Jacques 
Published: July 2004

SummaryThe diversity of Archaea in anaerobic digesters was characterized by strand conformation polymorphism (SSCP) analysis and the sequencing of 16S rDNA genes. The 44 digesters sampled, located in eight different countries, treated effluents from agriculture, the food processing and petro‐chemical industries, pulp and paper plant, breweries, slaughterhouses and municipal waste. All the existing processes were represented among the samples (fixed‐film, fluidized bed, stirred‐tank, UASB, sequential batch reactor, lagoon). Single strand conformation polymorphism analysis targeting the V3 region of 16S rDNA revealed between four to six distinct archaeal peaks per digester. The diversity of dominant Archaea in the 44 digesters was estimated as 23 different 16S rDNA sequences. Cloning of archaeal 16S rRNA genes from 11 distinct total genomic DNA, screening of clones by SSCP and the sequencing of 170 of them made it possible to characterize these SSCP peaks. All the sequences retrieved were members of the Euryarchaeaota subdomain. Furthermore, most of the sequences retrieved were very close to already known and cultivated strains or to environmental clones. The most frequent archaeal sequences were close to Methanosaeta concilii and to a 16S rDNA clone vadinDC06 located in the Methanobacterium clade (84% and 73% of digesters respectively). The other sequences were members of the Methanobacteriales and the Methanomicrobiales families. Only one sequence was far from any sequence of the database and it could be grouped with several sequences of environmental clones. Each digester harboured between two to nine archaeal sequences with only one of them corresponding to a putative acetate‐utilizing species. Furthermore, the process in the digesters appeared to play a part in the distribution of archaeal diversity.
Abundance of active and inactive microcystin genotypes in populations of the toxic cyanobacterium Planktothrix spp.
Authors: Kurmayer Rainer , Christiansen Guntram , Fastner Jutta , Börner Thomas 
Published: July 2004

SummaryTo investigate the abundance of active and inactive microcystin genotypes in populations of the filamentous cyanobacterium Planktothrix spp., individual filaments were grown as clonal strains in the laboratory and analysed for microcystin synthetase (mcy) genes and microcystin. Twenty‐three green‐pigmented strains of P. agardhii originating mostly from shallow water bodies fell into two groups, those possessing mcyA and those lacking mcyA. In contrast, all of the 49 strains that were assigned to the red‐pigmented P. rubescens contained mcyA. One strain of P. agardhii and eight strains of P. rubescens contained the total microcystin synthetase gene cluster but were found inactive in microcystin synthesis. To investigate the natural abundance of inactive mcy genotypes in P. rubescens individual filaments sampled from Lake Irrsee and Lake Mondsee (Austria) were analysed directly for the presence of mcyA and microcystin by matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry. All filaments assigned to P. rubescens contained mcyA. The proportion of inactive microcystin genotypes in populations with a low (Irrsee) or high density (Mondsee) of P. rubescens was 5% and 21%, each. The results of this study demonstrate that P. rubescens typically contain mcy genes whereas P. agardhii have a patchy distribution of mcy genes. In both species microcystin producers co‐occur with non‐microcystin producers due to the absence/inactivation of mcy genes.
Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil
Authors: Nicol Graeme W. , Webster Gordon , Glover L. Anne , Prosser James I. 
Published: July 2004

SummaryGrassland management regimens influence the structure of archaeal communities in upland pasture soils, which appear to be dominated by as yet uncultivated non‐thermophilic Crenarchaeota. In an attempt to determine which grassland management factors select for particular crenarchaeal community structures, soil microcosm experiments were performed examining the effect of increased pH, application of inorganic fertilizer (ammonium nitrate) and sheep urine deposition on both archaeal and bacterial communities in unmanaged grassland soil. As grassland management typically increases pH, a further experiment examined the effect of a reduction in pH, to that typical of unimproved grassland soils, on archaeal and bacterial communities. The RT‐PCR amplification of 16S rRNA followed by denaturing gradient gel electrophoresis analysis demonstrated a distinct and reproducible effect on bacterial communities after incubation for 28 or 30 days. In contrast, none of the treatments had a significant effect on the structure of the crenarchaeal community, indicating that these factors are not major drivers of crenarchaeal community structures in grassland soils.
From PCBs to highly toxic metabolites by the biphenyl pathway
Authors: Cámara Beatriz , Herrera Cristina , González Myriam , Couve Eduardo , Hofer Bernd , Seeger Michael 
Published: July 2004

SummaryThe degradation of polychlorobiphenyls (PCBs) by diverse bacteria, including Burkholderia sp. LB400, is incomplete with a concomitant accumulation of metabolic intermediates. In this study, the toxicity of diverse (chloro)biphenyls and of their biotransformation into the first two metabolic intermediates of the biphenyl pathway, were determined for the model bacterium Escherichia coli. Recombinant E. coli strains expressing different subsets of bph genes of strain LB400 accumulated metabolic intermediates from (chloro)biphenyls. During biotransformation of these compounds into metabolic intermediates, the viability and metabolic kinetics were determined. The toxicity of biotransformation of (chloro)biphenyls into different metabolic intermediates of (chloro)biphenyls varied. Dihydrodiols and dihydroxybiphenyls are very toxic metabolites for bacteria even after short incubation times, affecting the cell viability much more than (chloro)biphenyls. When bacteria transformed 2‐CB into dihydrodiol or dihydroxybiphenyl, a great decrease of intact cells and abundant cell lysis was observed by transmission electronic microscopy. Cell viability of Burkholderia sp. LB400 and of E. coli exposed directly to 2,3‐dihydroxybiphenyl decreased also drastically. The toxicity of metabolites generated during oxidation of PCBs may partly explain the recalcitrance to biodegradation of these pollutants. Conversion of less toxic compounds into products with increased toxicity resembles the bioactivation of xenobiotics in higher organisms.
Salmonella diversity associated with wild reptiles and amphibians in Spain
Authors: Briones Víctor , Téllez Sonia , Goyache Joaquín , Ballesteros Cristina , Del Pilar Lanzarot María , Domínguez Lucas , Fernández‐Garayzábal José F. 
Published: July 2004

SummaryDuring the spring and summer of 2001, faeces from 166 wild reptiles (94 individuals) and amphibians (72 individuals) from 21 different species found in central Spain were examined for the presence of Salmonella. Thirty‐nine reptiles (41.5%) yielded 48 Salmonella isolates, whereas all the amphibians examined were negative. Subspecies Salmonella enterica enterica (I) accounted for up to 50% of isolates. Fourteen isolates (29.2%) belonged to subspecies diarizonae (IIIb), six isolates (12.5%) to subspecies salamae (II), and four isolates (8.3%) to subspecies arizonae (IIIa). Twenty‐seven different serotypes were identified. Serotypes Anatum (12.5%), Herzliya (8.3%), Abony, 18:l,v:z, 9,12:z29:1,5 and 38:z10:z53 (6.2%/each) were the most frequently isolated. A high percentage (39.6%) of isolates belonged to serotypes previously associated with environmental sources. Also, 37.5% of isolates belonged to serotypes which had been related to human cases of salmonellosis. From these data, it is concluded that wild reptiles, but apparently not amphibians, may represent an important reservoir of Salmonella in nature and have potential implications for public health.
Mechanism of chromate reduction by the Escherichia coli protein, NfsA, and the role of different chromate reductases in minimizing oxidative stress during chromate reduction
Authors: Ackerley D. F. , Gonzalez C. F. , Keyhan M. , Blake R. , Matin A. 
Published: July 2004

SummaryChromate [Cr(VI)] is a serious environmental pollutant, which is amenable to bacterial bioremediation. NfsA, the major oxygen‐insensitive nitroreductase of Escherichia coli, is a flavoprotein that is able to reduce chromate to less soluble and less toxic Cr(III). We show that this process involves single‐electron transfer, giving rise to a flavin semiquinone form of NfsA and Cr(V) as intermediates, which redox cycle, generating more reactive oxygen species (ROS) than a divalent chromate reducer, YieF. However, NfsA generates less ROS than a known one‐electron chromate reducer, lipoyl dehydrogenase (LpDH), suggesting that NfsA employs a mixture of uni‐ and di‐valent electron transfer steps. The presence of YieF, ChrR (another chromate reductase we previously characterized), or NfsA in an LpDH‐catalysed chromate reduction reaction decreased ROS generation by c. 65, 40, or 20%, respectively, suggesting that these enzymes can pre‐empt ROS generation by LpDH. We previously showed that ChrR protects Pseudomonas putida against chromate toxicity; here we show that NfsA or YieF overproduction can also increase the tolerance of E. coli to this compound.
Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques
Authors: Anderson Ian C. , Cairney John W. G. 
Published: July 2004

SummaryFungi fulfil a range of important ecological functions, yet current understanding of fungal biodiversity in soil is limited. Direct DNA extraction from soil, coupled with polymerase chain reaction amplification and community profiling techniques, has proved successful in investigations of bacterial ecology and shows great promise for elucidating the taxonomic and functional characteristics of soil fungal communities. These community profiling techniques include denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single‐strand conformation polymorphism (SSCP), terminal restriction fragment length polymorphism (T‐RFLP), amplified rDNA restriction analysis (ARDRA), amplified ribosomal intergenic spacer analysis (ARISA) and cloning, and are generally coupled with DNA sequencing. The techniques and their potential limitations are discussed, along with recent advances that have been made possible through their application in soil fungal ecology. It is unlikely that a single approach will be universally applicable for assessing fungal diversity in all soils or circumstances. However, judicious selection of the methodology, keeping the experimental aims in mind, and the exploitation of emerging technologies will undoubtedly increase our understanding of soil fungal communities in the future.
The implementation of contextual therapy in the therapeutic community for substance abusers: a case study
Authors: Soyez Veerle , Tatrai Hilde , Broekaert Eric , Bracke Rudy 
Published: July 2004

Family therapy takes a special position in the therapeutic community for substance abusers (TC). In the early therapeutic communities, the family of origin was not considered as important for the substance abuser's recovery process, and was even labelled as part of the problem. It was only in the 1970s that the TC acknowledged the significance of family involvement in treatment. Nowadays, the contextual vision of Ivan‐Boszormenyi‐Nagy seems to have a strong impact on family counselling activities in Belgian TCs.In this article, the integration of contextual thinking in the TC is discussed. By means of a case study, it is shown that there are some clear parallels between the treatment evolutions in family counselling and the peer group community. The central position of trust both in contextual therapy and the TC treatment model is an important common ground for stimulating integration. Some obstacles that can disrupt this integration process are discussed.
Obesity, adipocytokines, and insulin resistance in breast cancer
Authors: Rose D. P. , Komninou D. , Stephenson G. D. 
Published: July 2004

SummaryThe adipocytokines are biologically active polypeptides that are produced either exclusively or substantially by the adipocytes, and act by endocrine, paracrine, and autocrine mechanisms. Most have been associated with obesity, hyperinsulinaemia, type 2 diabetes, and chronic vascular disease; in addition, six adipocytokines – vascular endothelial growth factor, hepatocyte growth factor, leptin, tumour necrosis factor‐alpha, heparin‐binding epidermal growth factor‐like growth factor, and interleukin‐6 – promote angiogenesis while one, adiponectin, is inhibitory. Obesity and insulin resistance have both been identified as risk factors for breast cancer and are associated with late‐stage disease and poor prognosis. Angiogenesis is essential for breast cancer development and progression, and so it is plausible that obesity‐related increases in adipocytokine production and a reduction in adiponectin may adversely affect breast cancer outcome by their angiogenesis‐related activities. There is also experimental evidence that some adipocytokines can act directly on breast cancer cells to stimulate their proliferation and invasive capacity. Thus, adipocytokines may provide a biological mechanism by which obesity and insulin resistance are causally associated with breast cancer risk and poor prognosis. Both experimental and clinical studies are needed to develop this concept, and particularly in oestrogen‐independent breast cancers where preventive and therapeutic options are limited.
Obesity as a disease: no lightweight matter
Authors: Conway B. , Rene A. 
Published: July 2004

SummaryThe epidemic rise in obesity has fuelled the current debate over its classification as a disease. Contrary to just being a medical condition or risk factor for other diseases, obesity is a complex disease of multifaceted aetiology, with its own disabling capacities, pathophysiologies and comorbidities. It meets the medical definition of disease in that it is a physiological dysfunction of the human organism with environmental, genetic and endocrinological aetiologies. It is a response to environmental stimuli, genetic predisposition and abnormalities, and has a characteristic set of signs and symptoms with consistent anatomical alterations. Excess adipose tissue increases the work of the heart and leads to anatomical changes in this organ. It alters pulmonary, endocrine and immunological functions, all with adverse effects on health. Some of the complications of obesity include cardiovascular disease, non‐insulin‐dependent diabetes mellitus, obstructive pulmonary disease, arthritis and cancer. Given the excess mortality, substantial morbidity and the economic toll of obesity, this is a disease that warrants serious attention by the medical community. Obesity's status and acceptance as a disease is pivotal in determining its treatment, reimbursement for treatment and the development of widespread interventions.
Rugged Plateaus and Extensive Floodplains — Modelling Landform Evolution in a Northern Australian Catchment
Authors: Boggs G.S. , Evans K.G. , Devonport C.C. 
Published: July 2004

AbstractMedium to large natural catchments are often more spatially heterogeneous than small catchments or single landforms. Attempting to model landform evolution of large areas is consequently more complex. This paper demonstrates that modelling landform evolution in medium to large catchments can be improved by calibrating the model to smaller, more geomorphologically homogenous sub‐catchments. The paper investigates landform evolution in the Ngarradj catchment in the Northern Territory of Australia (a medium scale catchment of approximately 67 km2). The catchment is complex and contains two distinct landform regions; an upland plateau region with highly dissected sandstone and shallow, sandy soils, and a lowlands region with gentle, wooded slopes and floodplains with deep, sandy soils. The SIBERIA landform evolution model is calibrated and applied to the Ngarradj catchment. The complexity of the Ngarradj catchment is incorporated into the modelling by dividing the catchment into three sub‐catchments (Swift Creek (SC), Upper Main (UM) and East Tributary (ET)) which are relatively homogeneous and for which hydrology and sediment transport data are available. A discharge‐area relationship and long‐term, sediment loss rates for the catchment are derived based on an annual series flood frequency analysis of a 20 year runoff record predicted in a previous study. Sediment transport modelling incorporates both suspended and bedload sediment loss. The denudation rates derived using these data are 37, 63 and 77 mm kyr−1 for the SC, UM and ET sub‐catchments, respectively. Model predictions indicate that the UM sub‐catchment will have the greatest mean erosion. This is balanced by the large amount of deposition that will occur in the upper Ngarradj valley of the UM sub‐catchment. Further deposition occurs on the floodplain of Ngarradj, with the area between the SC and ET/UM (up‐stream) sub‐catchments experiencing a small net accretion of sediment (15 mm kyr−1).
Wired Communities in the City: Sydney, Australia
Authors: Baum Scott , Van Gellecum Yolanda , Yigitcanlar Tan 
Published: July 2004

AbstractQuestions relating to the ability of particular groups in society to access information and communications technologies (ICTs) have become a growing part of the academic and policy literature. The issues raised in this literature have revolved around a number of themes, many of which can be subsumed under concerns about a growing digital divide whereby society is being divided into information rich and information poor sectors. This differentiation can be between particular social groups irrespective of place, or between people in particular places be these large regional areas (e.g. metropolitan versus non‐metropolitan) or localities and communities within an urban area. This paper focuses on the existence of a ‘digital divide’ across the Sydney metropolitan area. Using ABS 2001 census data the paper presents an analysis of computer and internet access and use for clusters of local communities and focuses on how usage differs across communities as differentiated by socio‐economic status, household and family status and ethnic background.
Characterizing Pareto Improvements   in an Interdependent Demand System
Authors: Kooreman Peter , Schoonbeek Lambert 
Published: July 2004

AbstractInterdependent preferences generally imply Pareto inefficiency. For a general demand system, we provide a characterization of Pareto improvements. For a prominent parametric specification, the Linear Expenditure System, we characterize in detail the welfare loss associated with interdependent preferences. Using an estimated empirical model of this kind, we calculate the compensating variation corresponding to the welfare loss.
Optimal Income Maintenance and the “Unemployable”
Authors: Leblanc Greg 
Published: July 2004

AbstractThis paper examines optimal income maintenance policy with asymmetric information about individuals' abilities. A minimum skill level is required for employment. The unemployable are those (low) ability types who find this minimum investment too costly. To guarantee some minimum income level, the government chooses between welfare, workfare, earnings subsidies, and training. Results show that the optimal scheme entails training. Moreover, though complex separating mechanisms are both feasible and encourage investments in skills, the least‐cost income maintenance scheme is quite simple: the government offers training at the lowest level consistent worth employment to all who want it.