bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan
Authors: MacGregor Barbara J. , Van Mooy Benjamin , Baker Brett J. , Mellon Mark , Moisander Pia H. , Paerl Hans W. , Zehr Jonathan , Hollander David , Stahl David A. 
Published: March 2003

We have used a combination of microbiological, molecular biological and stable isotope methods to relate specific microbial populations to elemental cycling at an offshore site in Lake Michigan. Several lines of evidence suggest that atmospheric N2 may be a significant source of nitrogen to the lake. Particulate organic nitrogen (PON) at ≈ 10–15 m depth in July and October had a δ15N of 0.5–1.5‰. These values closely reflect the 15N composition of atmospheric N2, suggesting biological nitrogen fixation. Historical data show a developing late‐summer N:P minimum at ≈ 15 m; low abundance of inorganic nitrogen relative to phosphorus favours species able to acquire atmospheric nitrogen. Microscopic examination of October water samples revealed abundant heterocystous cyanobacteria, including Nodularia sp. Potentially nitrogen‐fixing Anabaena spp. have been found in Lake Michigan before but, to our knowledge, this is the first report of Nodularia. Finally, we have amplified both cyanobacterial and non‐cyanobacterial nifH sequences (encoding the nitrogenase iron protein) from lakewater samples, evidence for the presence of bacteria capable of nitrogen fixation. The surface waters of Lake Michigan are considered to be phosphate limited in the stratified season and, under these conditions, energetically expensive nitrogen fixation is expected to be uncompetitive with assimilation of combined nitrogen. Our results suggest that, from both microbiological and biogeochemical perspectives, this may be an oversimplification.
Oxygen tension and nutrient starvation are major signals that regulate agfD promoter activity and expression of the multicellular morphotype in Salmonella typhimurium
Authors: Gerstel Ulrich , Römling Ute 
Published: March 2003

SummaryExpression of multicellular behaviour (rdar morphotype) is a characteristic of wild‐type Salmonella typhimurium strains. The key target for the regulation of rdar morphotype expression is the agfD promoter. The regulation of two rdar morphotypes, regulated and semi‐constitutive (the latter differs from the former by the insertion of A after position −17), by various environmental conditions was studied using transcriptional fusions to the regulated and semi‐constitutive agfD promoters by Western blot analysis and phenotypic analysis of the rdar morphotype. AgfD promoter activities were strongly dependent on oxygen tension. Expression maxima were observed in rich medium under microaerophilic conditions and in minimal medium under aerobic conditions. The regulated rdar morphotype was only expressed under conditions of maximal promoter activity. Glucose did not influence rdar morphotype expression, and the two promoters showed no consistent response to pH. In the stationary phase of growth, nitrogen and phosphate depletion were found to be signals that switch on the agfD promoters. In the logarithmic phase of growth, ethanol was the stress signal that enhanced rdar morphotype expression. The results indicate that, although the regulated and semi‐constitutive agfD promoters are key factors in the grade of expression of the multicellular behaviour, common signals such as oxygen tension, depletion of nutrients and ethanol vary their levels of expression significantly.
Bioaugmentation of soils by increasing microbial richness: missing links
Authors: Dejonghe Winnie , Boon Nico , Seghers Dave , Top Eva M. , Verstraete Willy 
Published: March 2003

SummaryIt is generally assumed that increased microbial diversity corresponds to increased catabolic potential and, hence, to better removal of metabolites and pollutants. Yet, microbial diversity, more specifically richness of species in environmental samples and sites, is difficult to assess. It is proposed to interpret this diversity more in the framework of Pareto's law, i.e. 20% of the species govern 80% of the energy flux of the ecosystem. Ecological studies should attempt to delineate the main energy fluxes and that group of species playing quantitative key roles in the system. Consequently, bioaugmentation should aim at the rearrangement of the group of organisms dominantly involved in the overall energy flux, so that specific catabolic traits necessary for the clean up of pollutants are part of that active group. For soil ecosystems, the capacity of plant roots as creators of physical and chemical discontinuity should be used more strategically to bring about such rearrangements. Overall, this paper identifies a number of ecological concepts, such as the Pareto law, the Gompertz model and plant community‐induced microbial competence, which may, given careful underpinning, open new perspectives for microbial ecology and biodegradation.
Toxicity and synergism in transgenic Escherichia coli expressing four genes from Bacillus thuringiensis subsp. israelensis
Authors: Khasdan Vadim , Ben‐Dov Eitan , Manasherob Robert , Boussiba Sammy , Zaritsky Arieh 
Published: March 2003

The genes cyt1Aa and p20, encoding, respectively, cytolytic and accessory proteins of Bacillus thuringiensis subsp. israelensis, were introduced into previously constructed clones expressing cry4Aa and cry11Aa in Escherichia coli (Ben‐Dov et al., 1995). Fifteen clones with all possible combinations of the four genes were obtained and found to express the genes included. Two new combinations, pVE4‐ADRC and pVE4‐ARC, expressing cyt1Aa, p20 and cry4Aa, with or without cry11Aa, respectively, were more toxic than their counterparts without cyt1Aa. They displayed the highest toxicity against Aedes aegypti larvae ever reached in transgenic bacteria. Five out of the six clones (except pVE4‐DC) containing cry4Aa or cry11Aa (with or without p20) displayed varying levels of synergism with cyt1Aa: they are 1.5‐to 34‐fold more toxic than the respective clones without cyt1Aa against exposed larvae. Their lethal times also decreased (they kill larvae quicker), more so at higher cell concentrations. These clones are anticipated to dramatically reduce the likelihood of resistant development in the target organisms (Wirth et al., 1997).
Rhizobial position as a main determinant in the problem of competition for nodulation in soybean
Authors: López‐García Silvina L. , Vázquez Tirso E. E. , Favelukes Gabriel , Lodeiro Aníbal R. 
Published: March 2003

SummarySelected Bradyrhizobium japonicum strains inoculated on soybean seeds often fail to occupy a significant proportion of nodules when a competitor rhizobial population is established in the soil. This competition problem could result from a genetic/ physiological advantage of the adapted soil population over the introduced inoculant or from a positional advantage, as the soil population already occupies the soil profile where the roots will penetrate, whereas the inoculant remains concentrated around the seeds. Here, we have assessed the contribution of these factors with a laboratory model in which a rhizobial population is established in sterile vermiculite. We observed that the wild‐type strain B. japonicum LP 3004 was able to grow in pots with N‐free plant nutrient solution‐watered vermiculite for six or seven generations with a duplication rate of at least 0.7 day−1. In addition, the rhizobial population persisted for 3 months with 106–107 colony‐forming units ml−1 of the vermiculite‐retained solution. N‐starved, young rhizobial cultures are more efficient in performing several steps along their early association with soybean roots. However, N starvation during growth of rhizobia used for seed inoculation did not enhance their competitiveness against a 1 month vermiculite‐established rhizobial population, which occupied more than 72% of the nodules. When a similarly established rhizobial population was recovered from the vermiculite and homogeneously suspended in plant nutrient solution, these cells were significantly less competitive (29% of nodules occupied) than rhizobia obtained from a fresh, logarithmic culture in a N‐poor minimal medium, thus indicating that cell position rather than intrinsic competitiveness was the determinant for nodule occupation.
Genetic variability of Tuber uncinatum and its relatedness to other black truffles
Authors: Mello Antonietta , Cantisani Annamaria , Vizzini Alfredo , Bonfante Paola 
Published: March 2003

SummaryGenetic variability is one of the major survival strategies developed by symbiotic fungi. We focused on the ectomycorrhizal fungus Tuber uncinatum Chatin that produces edible ascomata. In order to understand the degree of its variability and its relatedness to another morphologically‐similar truffle, T. aestivum Vittad., ascomata of T. uncinatum were collected from a single natural truffle‐ground located in the north of Italy and compared with samples from other Italian sites, as well as with T. aestivum ascomata from other European regions.We used multi‐locus approaches, such as microsatellite‐primed PCR (polymerase chain reaction), and single locus markers, such as mitochondrial and nuclear ribosomal DNA on 30 samples. The results demonstrate that the level of genetic polymorphism among isolates of T. uncinatum was higher than in other Tuber species, like T. melanosporum. Neighbour‐joining analyses were carried out on a binary data matrix on 12 ascomata of T. uncinatum and T. aestivum, and on 15 internal transcribed spacer (ITS) sequences of these species and 5 from other Tuber species. Taken together, they clustered T. uncinatum and T. aestivum in two separate groups. The mitochondrial rDNA primers, NMS1 and NMS2, were not able to differentiate morphologically related and unrelated truffles. Moreover, a pair of primers, intentionally designed to differentiate isolates of T. aestivum and T. uncinatum from other Tuber species, successfully amplified DNA from all the samples of T. aestivum and T. uncinatum considered in our analysis. In conclusion, different molecular approaches separate T. aestivum and T. uncinatum according to their spore reticulum and their taste and smell.
Approaches to prokaryotic biodiversity: a population genetics perspective
Authors: Rodríguez‐Valera Francisco 
Published: March 2003

SummaryThe study of prokaryotic diversity has blossomed during the last 10–15 years as a result of the introduction of molecular identification, mostly based on direct 16S rRNA gene polymerase chain reaction (PCR) amplification and sequencing from natural samples. A large amount of information exists about the diversity of this specific gene. However, data from the field of bacterial population genetics and genomics make questionable the value of information regarding just one gene. Even if we accept 16S rRNA genes as useful for species identification, intraspecific variation in bacteria is so high that species catalogues are often of little value. The gene pools represented by an operational species are yet impossible to predict. On the other hand, adaptive features in prokaryotes are often coded in gene clusters (genomic islands) that can be cloned directly from the environment, sequenced and even expressed in a surrogate host. Thus, the study of the environmental genome or metagenome appears as an alternative that could eventually lead to a more realistic understanding of prokaryotic biodiversity, provide biotechnology with new tools and maybe even contribute to develop a model of prokaryotic evolution.
Adaptation to nickel spiking of bacterial communities in neocaledonian soils
Authors: Héry Marina , Nazaret Sylvie , Jaffré Tanguy , Normand Philippe , Navarro Elisabeth 
Published: March 2003

SummaryAdaptation to nickel of bacterial communities of two extreme neocaledonian soils (an ultramafic soil and an acidic soil) was investigated by nickel spiking and compared with adaptation in a non‐neocaledonian soil used as reference. Soil microcosms were amended with nickel chloride (NiCl2), and bacterial community structure was analysed with the ribosomal intergenic spacer analysis (RISA) technique. Then, bacterial populations that respond to nickel stress were identified by cloning and sequencing. In the ultramafic soil, a shift occurred on day zero on the assay profiles and consisted of the emergence of a bacterial group closely related to the Ralstonia/Oxalobacter/Burkholderia group. It is hypothesized that NiCl2 had a physico‐chemical impact on soil structure. Fourteen days after nickel spiking, another shift occurred in the two soils that concerned a bacterial group belonging to the Actinomycete group. Only a few changes occurred in the bacterial community structure of the neocaledonian soils compared with those of the reference soil, which is more affected by nickel spiking. These results suggest that neocaledonian soil bacteria are particularly well adapted to nickel.
Isolation and phylogenetic characterization of bacteria capable of inducing differentiation in the green alga Monostroma oxyspermum
Authors: Matsuo Yoshihide , Suzuki Makoto , Kasai Hiroaki , Shizuri Yoshikazu , Harayama Shigeaki 
Published: March 2003

SummaryMany green algae cannot develop normally when they are grown under axenic conditions. Monostroma oxyspermum, for example, proliferates unicellularly in an aseptic culture, but develops into a normal foliaceous gametophyte in the presence of some marine bacteria. More than 1000 bacterial strains were isolated from marine algae and sponges and assayed for their ability to induce the morphogenesis of unicellular M. oxyspermum. Fifty bacterial strains exhibiting morphogenesis‐inducing activity against unicellular M. oxyspermum were isolated. The partial gyrB (≈ 1.2 kbp) and 16S rDNA (≈ 1.4 kbp) sequences of about 40 active strains were determined, and their phylogenetic relationships were analysed. All these strains were located within the Cytophaga–Flavobacterium–Bacteroides (CFB) complex, and most of these strains were clustered in a clade comprising Zobellia uliginosa. On the other hand, these bacteria also exhibited morphogenetic activity against germ‐free spores of Ulva pertusa, Ulva conglobata and Enteromorpha intestinalis. Moreover, these bacteria induced the release of spores from the leafy young gametophyte of M. oxyspermum. These results indicate that strains belonging to several groups in the CFB complex play an important role in the normal development of green algae in the marine coastal environment.
Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil
Authors: Anderson Ian C. , Campbell Colin D. , Prosser James I. 
Published: March 2003

SummaryFour fungal 18S rDNA and internal transcribed spacer (ITS) polymerase chain reaction (PCR) primer pairs were tested for their specificity towards target fungal DNA in soil DNA extracts, and their ability to assess the diversity of fungal communities in a natural grassland soil was compared. Amplified PCR products were cloned, and ≈ 50 clones from each library were sequenced. Phylogenetic analysis and database searches indicated that each of the sequenced cloned DNA fragments was of fungal origin for each primer pair, with the exception of the sequences generated using the 18S rDNA primers nu‐SSU‐0817 and nu‐SSU‐1196, where 35 of the 50 sequenced clones represented soil invertebrates. Although some of the primers have previously been suggested to be biased towards certain fungal taxonomic groups, the ratio of sequences representing each of the four main fungal phyla, Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota, was similar for each of the primer pairs, suggesting that primer bias may be less significant than previously thought. Collector's curves were plotted to estimate the coverage obtained for each of the clone libraries after clustering the sequences into operational taxonomic units at a level of 99% sequence similarity. The curves indicated that good coverage of diversity was achieved, with the exception of the clone library constructed using primers nu‐SSU‐0817 and nu‐SSU‐1196, on account of the high number of non‐fungal sequences obtained. The work demonstrates the usefulness of 18S rDNA and ITS PCR primers for assessing fungal diversity in environmental samples, and it also highlights some potential limitations of the approach with respect to PCR primer specificity and bias.
Attenuating CV risk factors in patients with diabetes: clinical evidence to clinical practice
Authors: Garber Alan J. 
Published: March 2003

AbstractIndividuals with diabetes are at high risk of cardiovascular (CV) disease, a risk that is significantly greater in the presence of traditional CV risk factors (hyperlipidaemia, hypertension, prothrombotic state). Glucose control and management of these risk factors decreases but does not eliminate CV events, reflecting the complexity of atherosclerosis. Novel risk factors (C‐reactive protein, lipoprotein a, homocysteine, and endothelial dysfunction) have been proposed and are potentially modifiable. However, clinical trials data are not yet available to guide therapy. At this time, no single agent can achieve adequate risk reduction in patients with diabetes. Even with the use of multiple agents and classes of agents to manage CV risk, 75% of patients with diabetes are expected to die from CV causes. Despite the recent advances in primary and secondary prevention of CV events, new approaches are needed. Data from the Heart Outcomes Prevention Evaluation (HOPE) trial demonstrated that CV risk can be further reduced by the addition of the ACE inhibitor ramipril to the existing treatment regimen of high‐risk patients with diabetes.
Positive cost effectiveness of early diagnosis of colorectal cancer
Authors: Bolin  , Korman  , Stanton  , Talley  , Newstead  , Donnelly  , Hall  , Ho  , Lapsley  
Published: March 2003

BackgroundStudies examining interventional screening have lacked accurate data, because costs of hospital infrastructure, nursing and disinfection have not been included. We compared all costs of different strategies for screening, including colonoscopy, to provide a rational basis for decisions in early diagnosis. The costs, although based on Australian data, are probably applicable to all developed countries.MethodsComprehensive cost data from Australian private day endoscopy centres, public and private hospitals, physicians, anaesthetists and pathologists were used to assess medical and infrastructure hospital costs for various methods of screening. The data were processed using the Office of Technology Assessment colorectal cancer screening model.ResultsAnnual or triennial faecal occult blood tests (FOBT; Hemoccult®) are cost‐effective, particularly with assumed 10‐year dwell times (the time taken for an adenoma to become a cancer), the costs per year of life saved being $US 26 015 and $US 24 756, respectively. Colonoscopy at 5‐ or 10‐year intervals is also cost‐effective with similar dwell times, and colonoscopy every 10 years with a cost of $27 159 per year saved is comparable to annual or triennial FOBT. Double contrast barium enema at either 3‐ or 5‐year intervals is cost‐effective, but ideally should be combined with an annual FOBT, reducing the cost effectiveness of these options. FOBT also is ideally combined with flexible sigmoidoscopy; an annual FOBT and 5‐yearly flexible sigmoidoscopy is cost‐effective with both 5‐ and 10‐year dwell times, though less than FOBT or colonoscopy. A once‐only colonoscopy at age 50 is not cost‐effective.ConclusionsAnnual or triennial FOBT, double contrast barium enema (DCBE) 3 and 5 and colonoscopy 5 and 10 are all cost‐effective. There is less value in combining FOBT and flexible sigmoidoscopy, or flexible sigmoidoscopy alone. Physicians therefore have the option of offering individuals a range of cost‐effective screening strategies, including colonoscopy.
The effect of abdominal rectopexy with mesh on anal sphincter and bowel function in patients with complete rectal prolapse; special reference to age of patient
Authors: Aitola  , Hiltunen  , Matikainen  
Published: March 2003

Objective The main source of concern in patients with rectal prolapse is usually incontinence and constipation developing post‐operatively. It has been claimed that sphincter pressures improve only after non‐implant surgery. The aim of this study was to assess our own results after mesh rectopexy.Patients and methods We reviewed the results in 50 patients on whom posterior abdominal Marlex mesh rectopexy for complete rectal prolapse had been performed. These patients underwent pre‐ and post‐operative anal manometry. Sixteen of them also underwent colon transit time study before and after the operation. They were followed clinically for a median of 5 months.Results Twenty‐two of the 38 patients (58%) with preoperatively defective anal control regained full continence. Resting anal canal pressures improved significantly after surgery in all cases (P=0.001), including those who regained full continence (P=0.005). The change in continence in all patients correlated inversely with the preoperative (r=–0.43, P=0.003) and post‐operative (r=–0.40, P=0.005) resting anal pressures. The change in resting anal pressures after surgery was significantly better in patients under 40 years of age (mean 19 cmH2O) than in those 40 years or older (mean 4 cmH2O) (P=0.01). All four preoperatively incontinent patients regained full continence in the younger group as opposed to only 50% (17/34) in the older group. Colon transit time normalized in three of the four patients with preoperatively slow transit time and five patients with preoperatively normal transit time developed slow transit.Conclusion Internal sphincter pressures do improve after mesh rectopexy for rectal prolapse, and the change also correlates with the improvement in continence. Internal sphincter function and continence recover better in younger patients.
A randomized trial of rubber band ligation with or without injection sclerotherapy in the treatment of piles
Authors: Ackroyd  , Dicks  , Shorthouse  
Published: March 2003

Objectives Rubber band ligation (RBL) is an effective treatment for piles but may be followed by pain and bleeding. It is postulated that the addition of injection sclerotherapy (IS) may reduce these complications. This trial aims to compare the use of RBL alone with RBL + IS in the treatment of piles.Patients and methods Sixty patients with piles were randomized to RBL alone (n=30) or RBL + IS (n=30). Each patient was given a pro forma on which to record the amount of pain (on a visual analogue scale) and bleeding (none, slight or heavy) for 10 days following treatment. Patients were subsequently asked to describe the overall symptomatic outcome in the 6‐week follow‐up clinic (worse, same, slightly better, much better). Long‐term outcome was ascertained by a telephone survey.Results Symptomatic improvement was similar in both groups (median score (range)=1.5 (0–2) vs 2 (0–2); P=NS), and there was no difference in pain (median score (range)=6 (0–77) vs 6 (0–50); P=NS). However, the amount of bleeding was significantly less in the RBL + IS group (median score (range)=3.5 (0–12) vs 0 (0–10); P < 0.001). The long‐term outcome was similar in both groups.Conclusion The addition of IS to RBL does not affect procedure‐related pain or symptomatic outcome, but significantly reduces the risk of post‐bleeding.