bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete sequence of the IncP‐9 TOL plasmid pWW0 from Pseudomonas putida
Authors: Greated Alicia , Lambertsen Lotte , Williams Peter A. , Thomas Christopher M. 
Published: March 2003

SummaryThe TOL plasmid pWW0 (117 kb) is the best studied catabolic plasmid and the archetype of the IncP‐9 plasmid incompatibility group from Pseudomonas. It carries the degradative (xyl) genes for toluenes and xylenes within catabolic transposons Tn4651 and Tn4653. Analysis of the complete pWW0 nucleotide sequence revealed 148 putative open reading frames. Of these, 77 showed similarity to published sequences in the available databases predicting functions for: plasmid replication, stable maintenance and transfer; phenotypic determinants; gene regulation and expression; and transposition. All identifiable transposition functions lay within the boundaries of the 70 kb transposon Tn4653, leaving a 46 kb sector containing all the IncP‐9 core functions. The replicon and stable inheritance region was very similar to the mini‐replicon from IncP‐9 antibiotic resistance plasmid pM3, with their Rep proteins forming a novel group of initiation proteins. pWW0 transfer functions exist as two blocks encoding putative DNA processing and mating pair formation genes, with organizational and sequence similarity to IncW plasmids. In addition to the known Tn4651 and IS1246 elements, two additional transposable elements were identified as well as several putative transposition functions, which are probably genetic remnants from previous transposition events. Genes likely to be responsible for known resistance to ultraviolet light and free radicals were identified. Other putative phenotypic functions identified included resistance to mercury and other metal ions, as well as to quaternary ammonium compounds. The complexity and size of pWW0 is largely the result of the mosaic organization of the transposable elements that it carries, rather than the backbone functions of IncP‐9 plasmids.
Global features of the Pseudomonas putida KT2440 genome sequence
Authors: Weinel Christian , Nelson Karen E. , Tümmler Burkhard 
Published: March 2003

SummaryThe compositional bias of the G+C, di‐ and tetranucleotide contents in the 6 181 862 bp Pseudomonas putida KT2440genome was analysed in sliding windows of 4000 bp in steps of 1000 bp. The genome has a low GC skew (mean 0.066) between the leading and lagging strand. The values of GC contents (mean 61.6%) and of dinucleotide relative abundance exhibit skewed Gaussian distributions. The variance of tetranucleotide frequencies, which increases linearly with increasing GC content, shows two overlapping Gaussian distributions of genome sections with low (minor fraction) or high variance (major fraction). Eighty per cent of the chromosome shares similar GC contents and oligonucleotide bias, but 105 islands of 4000 bp or more show atypical GC contents and/or oligonucleotide signature. Almost all islands provide added value to the metabolic proficiency of P. putida as a saprophytic omnivore. Major features are the uptake and degradation of organic chemicals, ion transport and the synthesis and secretion of secondary metabolites. Other islands endow P. putida with determinants of resistance and defenceor with constituents and appendages of the cell wall. A total of 29 islands carry the signature of mobile elements such as phage, transposons, insertion sequence (IS) elements and group II introns, indicating recent acquisition by horizontal gene transfer. The largest gene carries the most unusual sequence that encodes a multirepeat threonine‐rich surface adhesion protein. Among the housekeeping genes, only genes of the translational apparatus were located in segments with an atypical signature, suggesting that the synthesis of ribosomal proteins is uncoupled from the rapidly changing translational demands of the cell by the separate utilization of tRNA pools.
Perchlorate reduction by a novel chemolithoautotrophic, hydrogen‐oxidizing bacterium
Authors: Zhang Husen , Bruns Mary Ann , Logan Bruce E. 
Published: March 2003

SummaryWater treatment technologies are needed that can remove perchlorate from drinking water without introducing organic chemicals that stimulate bacterial growth in water distribution systems. Hydrogen is an ideal energy source for bacterial degradation of perchlorate as it leaves no organic residue and is sparingly soluble. We describe here the isolation of a perchlorate‐respiring, hydrogen‐oxidizing bacterium (Dechloromonas sp. strain HZ) that grows with carbon dioxide as sole carbon source. Strain HZ is a Gram‐negative, rod‐shaped facultative anaerobe that was isolated from a gas‐phase anaerobic packed‐bed biofilm reactor treating perchlorate‐contaminated groundwater. The ability of strain HZ to grow autotrophically with carbon dioxide as the sole carbon source was confirmed by demonstrating that biomass carbon (100.9%) was derived from CO2. Chemolithotrophic growth with hydrogen was coupled with complete reduction of perchlorate (10 mM) to chloride with a maximum doubling time of 8.9 h. Strain HZ also grew using acetate as the electron donor and chlorate, nitrate, or oxygen (but not sulphate) as an electron acceptor. Phylogenetic analysis of the 16S rRNA sequence placed strain HZ in the genus Dechloromonas within the β subgroup of the Proteobacteria. The study of this and other novel perchlorate‐reducing bacteria may lead to new, safe technologies for removing perchlorate and other chemical pollutants from drinking water.
The frequency and characteristics of highly thermophilic bacteria in cool soil environments
Authors: Marchant Roger , Banat Ibrahim M. , Rahman Thahira J. , Berzano Marco 
Published: March 2003

SummaryFollowing enrichment at 70°C and 80°C, five highly thermophilic aerobic eubacteria have been isolated from cool soil environments. These organisms show a temperature range for growth of 40–80°C and have optimal and very high growth rates around 70°C with generation times less than 30 min. All isolates are narrow rods, which stain Gram‐negative, but have a Gram‐positive cell wall structure and only one of five isolates is a spore former. All cultures contain a small proportion of previously unreported extremely long flexuous rods, which can be seen to divide eventually. Biochemical testing of five strains reveals a significant ability to utilize alkanes and some aromatic hydrocarbons. Using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of 16S rDNA the five strains were differentiated into three categories, which paralleled the biochemical results. 16S rDNA sequences showed high similarity with thermophilic Bacillus species now reclassified as Geobacillus. These bacteria are present in high numbers in apparently all soils and the question is raised of how these organisms, which are apparently unable to grow at the temperatures experienced in these cool soils, are so prominent.
Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation‐independent surveys
Authors: Sait Michelle , Hugenholtz Philip , Janssen Peter H. 
Published: March 2003

SummaryThe culturability of microorganisms in a 10 cm core of an Australian pasture soil was investigated using a minimal agar medium with xylan as the growth substrate. Culturability decreased with increasing depth, from a maximum of 19% of the total microscopically countable cells in the 0–2 cm section to 2.4% in the 8–10 cm section. Seventy‐one isolates from the core were identified by comparative 16S rRNA gene sequence analysis. Many of these isolates belong to groups of globally distributed soil bacteria, including well‐characterized families of the classes Alphaproteobacteria and Betaproteobacteria, and of the subclass Actinobacteridae. Other isolates belong to groups with few or no cultivated representatives: 10 isolates in two subdivisions of the phylum Acidobacteria, five isolates in a new order and nine isolates in a new family of the class Alphaproteobacteria, two isolates in a new order of the class Gammaproteobacteria, three isolates in two new families of the subclass Actinobacteridae, and two isolates in the subclass Rubrobacteridae. These new isolates represent the first laboratory cultures able to be assigned to some of these groups and greatly increase the number of cultivated strains known for others. This demonstrates that a minimal change in cultivation strategy (using a polymeric growth substrate and longer incubation times) can result in the isolation of globally distributed but previously uncultured phylogenetically novel soil bacteria.
Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns
Authors: Fromin N. , Hamelin J. , Tarnawski S. , Roesti D. , Jourdain‐Miserez K. , Forestier N. , Teyssier‐Cuvelle S. , Gillet F. , Aragno M. , Rossi P. 
Published: March 2003

SummaryTechnical developments in molecular biology have found extensive applications in the field of microbial ecology. Among these techniques, fingerprinting methods such as denaturing gel electrophoresis (DGE, including the three options: DGGE, TGGE and TTGE) has been applied to environmental samples over this last decade. Microbial ecologists took advantage of this technique, originally developed for the detection of single mutations, for the analysis of whole bacterial communities. However, until recently, the results of these high quality fingerprinting patterns were restricted to a visual interpretation, neglecting the analytical potential of the method in terms of statistical significance and ecological interpretation. A brief recall is presented here about the principles and limitations of DGE fingerprinting analysis, with an emphasis on the need of standardization of the whole analytical process. The main content focuses on statistical strategies for analysing the gel patterns, from single band examination to the analysis of whole fingerprinting profiles. Applying statistical method make the DGE fingerprinting technique a promising tool. Numerous samples can be analysed simultaneously, permitting the monitoring of microbial communities or simply bacterial groups for which occurrence and relative frequency are affected by any environmental parameter. As previously applied in the fields of plant and animal ecology, the use of statistics provides a significant advantage for the non‐ambiguous interpretation of the spatial and temporal functioning of microbial communities.
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
Authors: Nelson K. E. , Weinel C. , Paulsen I. T. , Dodson R. J. , Hilbert H. , Martins dos Santos V. A. P. , Fouts D. E. , Gill S. R. , Pop M. , Holmes M. , Brinkac L. , Beanan M. , DeBoy R. T. , Daugherty S. , Kolonay J. , Madupu R. , Nelson W. , White O. , Peterson J. , Khouri H. , Hance I. , Lee P. Chris , Holtzapple E. , Scanlan D. , Tran K. , Moazzez A. , Utterback T. , Rizzo M. , Lee K. , Kosack D. , Moestl D. , Wedler H. , Lauber J. , Stjepandic D. , Hoheisel J. , Straetz M. , Heim S. , Kiewitz C. , Eisen J. , Timmis K. N. , Düsterhöft A. , Tümmler B. , Fraser C. M. 
Published: March 2003

Summary Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non‐pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.
Persistence and cell culturability of biocontrol strain Pseudomonas fluorescens CHA0 under plough pan conditions in soil and influence of the anaerobic regulator gene anr
Authors: Mascher Fabio , Schnider‐Keel Ursula , Haas Dieter , Défago Geneviève , Moënne‐Loccoz Yvan 
Published: March 2003

SummaryCertain fluorescent pseudomonads can protect plants from soil‐borne pathogens, and it is important to understand how these biocontrol agents survive in soil. The persistence of the biocontrol strain Pseudomonas fluorescens CHA0‐Rif under plough pan conditions was assessed in non‐sterile soil microcosms by counting total cells (immunofluorescence microscopy), intact cells (BacLight membrane permeability test), viable cells (Kogure's substrate‐responsiveness test) and culturable cells (colony counts on selective plates) of the inoculant. Viable but non‐culturable cells of CHA0‐Rif (106 cells g−1 soil) were found in flooded microcosms amended with fermentable organic matter, in which the soil redox potential was low (plough pan conditions), in agreement with previous observations of plough pan samples from a field inoculated with CHA0‐Rif. However, viable but non‐culturable cells were not found in unamended flooded, amended unflooded or unamended unflooded (i.e. control) microcosms, suggesting that such cells resulted from exposure of CHA0‐Rif to a combination of low redox potential and oxygen limitation in soil. CHA0‐Rif is strictly aerobic. Its anaerobic regulator ANR is activated by low oxygen concentrations and it controls production of the biocontrol metabolite hydrogen cyanide under microaerophilic conditions. Under plough pan conditions, an anr‐deficient mutant of CHA0‐Rif and its complemented derivative displayed the same persistence pattern as CHA0‐Rif, indicating that anr was not implicated in the formation of viable but non‐culturable cells of this strain at the plough pan.
The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil
Authors: Nicol Graeme W. , Glover L. Anne , Prosser James I. 
Published: March 2003

SummaryThe community structure of rhizosphere soil Archaea from three grassland types, associated with different management practices, was examined at a site in the Borders region of Scotland, by analysis of 16S rRNA gene fragments amplified from 16S rDNA and from rRNA. Denaturing gradient gel electrophoresis (DGGE) and sequence analysis of amplified products indicated high relative abundance within the archaeal community of two distinct lineages of non‐thermophilic (group 1) Crenarchaeota. Grassland management practices influenced archaeal community structure, as characterized by both 16S rRNA‐ and 16S rDNA‐derived DGGE profiles. One band dominated DGGE profiles in all three grassland types examined, and reproducible differences in the presence and intensity of bands were observed between profiles from managed and natural grassland sites. Analysis of 16S rRNA‐derived amplicons from managed and natural grasslands at sites in the north of England and the north of Wales also indicated high relative abundance of non‐thermophilic crenarchaeotes within the archaeal community. The band dominating the Scottish grassland site also dominated DGGE profiles from the English and Welsh sites, and similar differences were seen between profiles derived from soils subjected to different management regimes. The study indicates that grassland archaeal communities are dominated by Crenarchaeota, with closely related members of this lineage ubiquitous in distribution in UK upland pasture, and indicate that management practices influence the nature of the crenarchaeotal community.
Quantification of cell‐specific substrate uptake by probe‐defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization
Authors: Nielsen Jeppe Lund , Christensen Dinna , Kloppenborg Marie , Nielsen Per Halkjær 
Published: March 2003

SummaryA technique based on quantitative microautoradiography (QMAR) and fluorescence in situ hybridization (FISH) was developed and evaluated in order to determine the quantitative uptake of specific substrates in probe‐defined filamentous bacteria directly in a complex system. The technique, QMAR‐FISH, has a resolution of a single cell and is based on an improved fixation protocol and the use of an internal standard of bacteria with known specific radioactivity. The method was used to study the in situ ecophysiology of the filamentous bacteria ‘Candidatus Meganema perideroedes’ and Thiothrix sp. directly in an activated sludge system. The cellular uptake rate of tritium‐labelled substrates revealed an average cell‐specific uptake rate of 4.1 ¥ 10−15 mol of acetate cell−1 h−1 and 3.1 ¥ 10−15 mol of acetate cell−1 h−1 for the two filamentous species respectively. The two filamentous species had very similar activity in all cells along each filament. Surprisingly, the filaments within both probe‐defined populations had threefold variation in activity between the different filaments, demonstrating a large variation in activity level within a single population in a complex system. The substrate affinity (Ks) for uptake of acetate of the cells within the two filamentous bacteria was determined by incubation with variable concentrations of labelled acetate. The Ks values of the ‘Candidatus Meganema perideroedes’ and the Thiothrix filamentous bacteria were determined to be 1.8 µM and 2.4 µM acetate respectively.
What should the role of ACE inhibitors be in the treatment of diabetes? Lessons from HOPE and MICRO‐HOPE
Authors: Heinig Robert E. 
Published: March 2003

SummaryExperimental and clinical evidence suggest that angiotensin converting enzyme (ACE) inhibition may reduce cardiovascular (CV) risk by directly affecting endothelial dysfunction, atherosclerosis and thrombus formation. These direct effects are in addition to effects on vascular tone or pressure. The Health Outcomes and Prevention Evaluation (HOPE) study assessed the role of an ACE inhibitor ramipril in reducing CV events in 9297 patients ≥ 55 years who were at high risk of CV events but did not have left ventricular dysfunction, heart failure, or high blood pressure at the time of study entry. In the overall HOPE population, the risk of the primary composite outcome (cardiovascular death, myocardial infarction, or stroke) was reduced by 22% (p < 0.001), and in patients with diabetes plus one other CV risk, it was reduced by 25% (p = 0.0004). Ramipril treatment achieved risk reduction in patients with mild renal insufficiency (serum creatinine ≥ 1.4 mg/dl). Ramipril treatment did not increase adverse events in patients with renal insufficiency. The Study to Evaluate Carotid Ultrasound changes in patients treated with Ramipril and Vitamin E (SECURE) demonstrated that ramipril 10 mg significantly reduced the rate of carotid intimal medial thickening, suggesting a direct effect on atherosclerotic progression.
Multiple CHD risk factors in type 2 diabetes: beyond hyperglycaemia
Authors: Reaven Gerald M. 
Published: March 2003

SummaryRecent evidence from the United Kingdom Prospective Diabetes Study convincingly demonstrates that good glycaemic control is difficult to achieve and, despite its positive impact on microvascular complications, is not sufficient to reduce the risk of coronary heart disease (CHD). Syndrome X—a cluster of abnormalities associated with resistance to insulin‐mediated glucose uptake that have been implicated in accelerating atherogenesis—provides a useful clinical concept to prevent CHD in patients with type 2 diabetes. Components of syndrome X can include hypertension, hyperinsulinaemia, dyslipidaemia, and a procoagulant state, changes that contribute to the development of atherosclerosis. Low‐density lipoprotein cholesterol (LDL‐C) levels are usually close to normal, but the LDL‐C is present in abnormally small and dense particles. Triglyceride levels are elevated and are associated with an increase in postprandial accumulation of atherogenic, remnant lipoprotein particles. High‐density lipoprotein cholesterol levels are typically low. This particular dyslipidaemia, along with hyperinsulinaemia, induces expression of plasminogen activator inhibitor‐1, contributing to a prothrombotic state. In addition, plaque formation may be accelerated in insulin‐resistant subjects by increased expression of adhesion molecules on endothelial cells and increased rate of monocyte adhesion to cultured endothelial cells. Syndrome X and type 2 diabetes are associated with multiple abnormalities that enhance the atherosclerotic process. The opportunities for new therapeutic approaches to reduce cardiovascular risk will undoubtedly evolve along with our understanding of the complex factors responsible for insulin resistance, compensatory hyperinsulinaemia, and CHD.
Endoanal ultrasound or magnetic resonance imaging for preoperative assessment of anal fistula: a comparative study
Authors: Gustafsson U.‐M. , Kahvecioglu B. , Åström G. , Ahlström H. , Graf W. 
Published: March 2003

ObjectiveTo compare endoanal ultrasound (EUS) with a 10‐MHz probe vs. bodycoil magnetic resonance imaging (MRI) in the preoperative evaluation of anal fistula.Subjects and methods23 patients with fistula in the anal region underwent preoperative 0.5 T bodycoil MRI and 10 MHz EUS which included probing in 6 patients. The results of the EUS and MRI were compared against the surgical findings as a reference method.ResultsIn classification of the primary tract there was agreement between EUS and surgical findings in 14 (61%) and between MRI and surgery in 11 (48%). Concerning the presence of an internal opening the corresponding figures were 17 (74%) and 10 (43%) and in judging the presence of an extension or an abscess 15 (65%) vs. 11 (48%), respectively. In three out of eight patients with nonhealing or recurrence after surgery preoperative imaging had shown an extension and/or an abscess that was not identified by the surgeon.ConclusionEUS, sometimes complemented with probing, is well comparable to bodycoil MRI in classifying and describing the topography of an anal fistula.
Circular stapled anopexy for haemorrhoidal disease: results
Authors: Lehur P.‐A. , Gravié J.‐F. , Meurette G. 
Published: March 2003

ObjectiveStapled anopexy is a new approach for haemorrhoids requiring surgical treatment. This study reviews the available information concerning the present results of this procedure.MethodsMedline and hand search of the literature was conducted to identify available information on the procedure, with a special interest for the on‐going or published randomized clinical trials.ResultsThe advantages of the stapled approach of haemorrhoids were analyzed in the different areas of concern, including postoperative pain reduction, length of hospital stay and sick‐leave, postoperative wound care and type and rate of complications. Continence status, symptom cure and patient satisfaction following stapled anopexy are also reported.ConclusionStapled anopexy is probably less painful than conventional haemorrhoidectomy. Other advantages in the short term result from this new approach. Long term efficacy of the procedure is still unknown.