bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid identification of Medicago nodulating strains by using two oligonucleotide probes complementary to 16S rDNA sequences
Authors: Rome Sophie , Cleyet-Marel Jean-Claude , Materon Luis A. , Normand Philippe , Brunel Brigitte
Published: February 2010

Symbiotic bacteria associated with the Medicago genus are separated into two closely related species named Sinorhizobium meliloti and Sinorhizobium medicae. To discriminate rapidly between these two bacterial species, two 15-base DNA probes, 16Smfs and 16Smed, were designed from the alignment of 16S rDNA sequences to differentiate S. meliloti from S. medicae. Their specificities were evaluated by dot-blot hybridization experiments on 25 reference strains representing 13 species of Rhizobium and Sinorhizobium, and by comparison with all 16S rDNA sequences available in the GenBank data base. No cross-reaction was found with 16Smed, which was thus considered species specific for S. medicae. By contrast, as expected according to the 16S rDNA sequence alignment, the labeled 16Smfs probe cross-hybridized with the DNAs of S. meliloti, Sinorhizobium fredii, and Sinorhizobium saheli but not with the DNA of S. medicae. Since S. saheli and S. fredii do not nodulate Medicago, 16Smed and 16Smfs can be routinely used to characterize the two Sinorhizobium species nodulating Medicago from pure cultures or from Medicago root nodules. Fifty strains isolated from eight annual Medicago species were then characterized by using colony hybridizations. Sinorhizobium meliloti was more frequently obtained (>80% isolates) than was S. medicae. Both Sinorhizobium species seemed to be trapped by annual Medicago and no plant-host specificity was detected.Key words: Sinorhizobium meliloti, Sinorhizobium medicae, Medicago, oligonucleotide probe, 16S rDNA gene.
Effect of nitrogen compounds on nitrogenase activity inHerbaspirillum seropedicaeSMR1
Authors: Klassen G. , Pedrosa F. O. , Souza E. M. , Funayama S. , Rigo L. U.
Published: February 2010

The effect of nitrogen compounds on growth and nitrogenase activity of Herbaspirillum seropedicae SMR1 was determined. L-Glutamate or L-glutamine as sole nitrogen sources supported growth, and nitrogenase activity was observed only after exhaustion of L-glutamate or L-glutamine from the culture medium. L-Serine, L-alanine, or ammonium chloride supported growth but not acetylene reduction activity. No growth was observed with L-histidine, L-lysine, L-arginine, or with the amines methylammonium chloride, tetramethylammonium chloride, or ethylenediamine chloride. All the compounds promoted the switch off of nitrogenase activity except L-histidine, L-lysine, or L-arginine, which were not taken up. The results showed that H. seropedicae cannot utilize exogenously added L-histidine, L-arginine, L-lysine, methylammonium chloride, tetramethylammonium chloride, or ethylediamine as the sole N source for growth. The inability of the positively charged amino acids to promote nitrogenase switch off might be a result of the lack of transport systems and the eventual further metabolism of these compounds.Key words: Herbaspirillum seropedicae, nitrogenase inactivation, amino compounds uptake.
Bacterial endophytes in agricultural crops
Authors: Hallmann J. , Quadt-Hallmann A. , Mahaffee W. F. , Kloepper J. W.
Published: February 2010

Endophytic bacteria are ubiquitous in most plant species, residing latently or actively colonizing plant tissues locally as well as systemically. Several definitions have been proposed for endophytic bacteria; in this review endophytes will be defined as those bacteria that can be isolated from surface-disinfested plant tissue or extracted from within the plant, and that do not visibly harm the plant. While this definition does not include nonextractable endophytic bacteria, it is a practical definition based on experimental limitations and is inclusive of bacterial symbionts, as well as internal plant-colonizing nonpathogenic bacteria with no known beneficial or detrimental effects on colonized plants. Historically, endophytic bacteria have been thought to be weakly virulent plant pathogens but have recently been discovered to have several beneficial effects on host plants, such as plant growth promotion and increased resistance against plant pathogens and parasites. In general, endophytic bacteria originate from the epiphytic bacterial communities of the rhizosphere and phylloplane, as well as from endophyte-infested seeds or planting materials. Besides gaining entrance to plants through natural openings or wounds, endophytic bacteria appear to actively penetrate plant tissues using hydrolytic enzymes like cellulase and pectinase. Since these enzymes are also produced by pathogens, more knowledge on their regulation and expression is needed to distinguish endophytic bacteria from plant pathogens. In general, endophytic bacteria occur at lower population densities than pathogens, and at least some of them do not induce a hypersensitive response in the plant, indicating that they are not recognized by the plant as pathogens. Evolutionarily, endophytes appear to be intermediate between saprophytic bacteria and plant pathogens, but it can only be speculated as to whether they are saprophytes evolving toward pathogens, or are more highly evolved than plant pathogens and conserve protective shelter and nutrient supplies by not killing their host. Overall, the endophytic microfloral community is of dynamic structure and is influenced by biotic and abiotic factors, with the plant itself constituting one of the major influencing factors. Since endophytic bacteria rely on the nutritional supply offered by the plant, any parameter affecting the nutritional status of the plant could consequently affect the endophytic community. This review summarizes part of the work being done on endophytic bacteria, including their methodology, colonization, and establishment in the host plant, as well as their role in plant–microbe interactions. In addition, speculative conclusions are raised on some points to stimulate thought and research on endophytic bacteria.Key words: endophytic bacteria, methods, localization, diversity, biological control.
Alternative respiratory system and formamide hydro-lyase activity as the key components of the cyanide-resistance mechanism inFusarium oxysporum
Authors: Pereira Pablo Tavares , Carvalho Margarida Monteiro de , Amaral-Collaço M. T. , Roseiro J. Carlos , Arrabaça João Daniel
Published: February 2010

A strain of Fusarium oxysporum, isolated from an industrial effluent containing a high cyanide concentration, detoxifies cyanide via formamide hydro-lyase (FHL). The importance of the coexistence of the alternative (cyanide insensitive) respiratory system and the synthesis of FHL was assessed. This enzyme, induced by cyanide, converts this compound to formamide and is partially responsible for the tolerance of F. oxysporum to high cyanide concentration. The FHL induction for cyanide detoxification depends on the alternative respiratory system when the terminal oxidase of the electron transport chain is blocked by cyanide used during the induction process. The respiratory metabolism of a F. oxysporum strain was studied. Whole cells exhibited a cyanide-sensitive respiration but developed a partially cyanide-resistant respiration under certain physiological conditions, namely, in the stationary phase of growth, in the presence of chloramphenicol in the growth medium, or upon aeration in the absence of nutrients (starvation conditions). Cycloheximide prevented the appearance of cyanide-insensitive respiration when the cells were aerated under starvation conditions. This fact suggested some form of induction involving de novo protein synthesis.Key words: cyanide tolerance, cyanide-resistant respiration, formamide hydro-lyase, Fusarium oxysporum.
Anaerobic treatment of a municipal landfill leachate
Authors: Frigon Jean-Claude , Bisaillon Jean-Guy , Paquette Gilles , Beaudet Réjean
Published: February 2010

Leachate from a municipal landfill site was treated in a laboratory using fixed-film cultures under anaerobic conditions. Serum-bottle cultures were used for optimization of the growth parameters. The reduction of the chemical oxygen demand (COD) of the leachate was faster at 29 °C compared with lower temperatures. Gradual acclimation of the microbial population to temperatures as low as 4 °C considerably increased the rate of COD removal at these temperatures. Addition of supplements to the leachate was not needed and it was not necessary to adjust the pH (5.9) for optimal COD reduction. Continuously fed reactors were also used to treat the leachate. The maximum organic loading rate of the reactor at 22 °C to obtain 85% COD removal was 2.1 kg COD∙m−3∙day−1, which corresponded to an hydraulic retention time of 1.5 days. After treatment under these conditions, the toxicity (Microtox method) of the leachate was completely eliminated and the required quality standards were met for iron, oil and grease, and phenols. The fermentative microorganisms in the biofilm of the reactor were evaluated to 4.6 × 107cells∙cm−2and identified as Streptococcus gallinarum, Clostridium glycolicum, Clostridium bifermentans or sadallii, Citrobacter amalonaticus, Bacteroides capillosus, and Eubacterium sp.Key words: anaerobic treatment, landfill, leachate, growth parameters, fixed-film reactor, microbiology.
Colocalization of microtubules and mitochondria in the yeastSchizosaccharomyces japonicusvar.versatilis
Authors: Svoboda Augustin , Slaninová Iva
Published: February 2010

Both living and fixed cells of Schizosaccharomyces japonicus var. versatilis showed thread-like mitochondria when studied by phase-contrast and fluorescence microscopy. In the interphase cells, mitochondria extended from pole to pole and converged towards the growing tips. The mitochondrial threads did not disrupt but persisted during mitosis and, subsequently, their bundle was split between the two daughter cells by a concentrically growing septum. Mitochondria in the interphase cells were accompanied by cytoplasmic microtubules. These disappeared during mitosis and, instead, spindle microtubules were formed in the nucleus. The cytoplasmic microtubules reappeared after anaphase B, again in coaligment with mitochondria. Protoplasting as well as the action of microtubule inhibitors methyl-1-(butylcarbamoyl)-2-benzimidazolecarbamate (benomyl) and 2-methylbenzimidazole (MBC) resulted in rapid disintegration of microtubules and, suprisingly, also in disruption of mitochondria into small bodies. Removal of the inhibitors or a short regeneration of protoplasts allowed both the cytoplasmic microtubules and the thread-like mitochondria to reaggregate into the original pattern. Cytochalasin D treatment caused a complete disintegration of actin filaments, while the cytoplasmic microtubules and mitochondria remained intact. These findings of a transient close association of mitochondria and microtubules and their relative independence of the arrangement of actin filaments suggest that microtubules, but not actin cables, form supports for positioning or movement of mitochondria along the cylindrical cells. The persistence of mitochondria in the cell centre during mitosis may be accounted for by the fact that disrupted microtubules fail to provide support for mitochondrial movement towards the cell poles.Key words: microtubules, mitochondria, yeast, actin, microtubular drugs, cell cycle, Schizosaccharomyces japonicus var. versatilis.
New identification of the strain Rhizopus microsporus var. oligosporus spT3 as Rhizopus microsporus var. chinensis
Authors: Schwertz A. , Villaume C. , Mejean L. , Decaris B. , Percebois G.
Published: February 2010

The wild Rhizopus strain spT3 extracted from tempeh of Bali, Indonesia (Institute of Microbial Resources, Taichung, Taiwan) had first been identified as Rhizopus microspores var. oligosporus spT3. This strain is used to ferment soybeans, to detoxify them and improve their nutritional value. Analysis of fermented seeds showed that this strain strongly degrades numerous noxious antinutritional factors, which is unusual for R. microsporus var. oligosporus. The activity of strain spT3 on carbohydrates, compared with that of R. microsporus var. oligosporus NRRL 2710 (= CBS 338.62 = ATCC 22959 = IMI 174457 = IFO 8631 = Scholer's M140), presented differences suggesting that strain spT3 was not a R. microsporus var. oligosporus. As a matter of fact, strain spT3 hydrolyzed sucrose and raffinose, whereas R. microsporus var. oligosporus NRRL 2710 did not. A taxonomic study including morphology, growth temperature, and mating showed that the strain spT3 was similar to R. microsporus var. chinensis CBS 261.28 (= Scholer's M213).Key words: Rhizopus microsporus var. oligosporus, Rhizopus microsporus var. chinensis, Rhizopus microsporus var. rhizopodiformis, mating, carbohydrate utilization, taxonomy, scanning electron microscopy.
Functional analysis of sigma-70 consensus promoters in Pseudomonas aeruginosa and Escherichia coli
Authors: McLean Bradley W. , Wiseman Shari L. , Kropinski Andrew M.
Published: February 2010

A series of synthetic promoters, based upon the Escherichia coli σ70 consensus promoter sequence, was constructed upstream of the lacZ reporter gene in the modified broad-host-range vector pQF52. The role of the intervening spacer region in gene expression in Pseudomonas aeruginosa and E. coli was studied by insertions and deletions within this region. In P. aeruginosa and E. coli the patterns of gene expression were identical with maximum β-galactosidase activity being measured from promoters possessing 19 bp in their intervening regions, presumably as a result of impeded promoter clearance with the consensus 17-bp promoter. In P. aeruginosa a second occurrence of enhanced activity, which could not be attributed to the involvement of the alternative sigma factor RpoN (σ54), was evident with the promoter having a 16-bp spacer.Key words: Pseudomonas aeruginosa, promoter, RpoD, RpoN, transcription.
Evidence for interspecies communication and its potential role in pathogen suppression in a naturally occurring disease suppressive soil
Authors: Becker Donna M. , Kinkel Linda L. , Schottel Janet L.
Published: February 2010

Streptomyces strains isolated from potato scab suppressive (n = 9) and conducive (n = 5) soils were screened for their ability to produce diffusible chemicals that trigger antibiotic production in the pathogen-suppressive Streptomyces diastatochromogenes PonSSII. Using an Agrobacterium detection system, the strains were tested for the ability to produce homoserine lactone autoinducers. In addition, suppressive strain PonSSII was screened for production of an autoinducer for antibiotic production in a chemically defined liquid medium. Interspecies communication was investigated by growing suppressive and pathogenic strains individually in liquid medium and determining whether broth from these strains could induce antibiotic production in PonSSII. No evidence was found for production of homoserine lactones by any of the Streptomyces strains nor for the production of autoinducers by PonSSII. However, addition of conditioned broth from Streptomyces strains to cultures of PonSSII stimulated, suppressed, or had no effect on antibiotic production. Conditioned broth from suppressive strain 23 and pathogenic strain RB4 triggered antibiotic production by PonSSII at earlier times during culture growth and also enhanced antibiotic production levels compared with the control. The results suggest that interspecies communication between these Streptomyces species is occurring and may contribute to pathogen inhibition in the naturally occurring disease suppressive soil.Key words: Streptomyces, suppressive soil, interspecies communication, potato scab, autoinducers.
Production and purification of an extracellular β-galactosidase from the Dutch elm disease fungusOphiostoma novo-ulmi
Authors: Binz Thomas , Gremaud Colette , Canevascini Giorgio
Published: February 2010

The causal agents of Dutch elm disease, Ophiostoma ulmi (isolate H200) and Ophiostoma novo-ulmi (isolate CKT-11), secreted similar amounts of β-galactosidase in liquid shake cultures when grown on galacturonic acid or sodium pectate (1.45 ± 0.16 and 1.03 ± 0.24 nkat∙mL−1for O. ulmi, respectively, and 1.30 ± 0.08 and 1.28 ± 0.26 nkat∙mL−1for O. novo-ulmi, respectively). Rhamnose and pectin also stimulated secretion but to a lesser extent, whereas on glucose, enzyme activity was barely detectable (≤0.01 nkat∙mL−1). Ophiostoma novo-ulmi was shown by Q-Sepharose chromatography to form two β-galactosidases, named β-galactosidases I and II. In cultures grown on galacturonic acid β-galactosidase I accounted for approximately 75% of the total activity in the culture filtrate. β-Galactosidase I was further purified to apparent electrophoretic homogeneity by means of Sephacryl gel filtration chromatography, chromatofocusing, and Superdex75 gel filtration. The molecular mass of the enzyme was 135 kDa by SDS–PAGE and 123 kDa by gel filtration. Its isoelectric point, determined by chromatofocusing, was 4.9. The optimal pH for enzyme activity was 5.8 and the optimal temperature was 50 °C. The Kmvalues for p-nitrophenyl β-D-galactopyranoside and lactose were 7.52 and 14.23 mM, respectively, and the maximum velocities for these substrates were 1733 and 355 nkat∙mg protein−1, respectively. The Kivalue for D(−)-galactonic acid γ-lactone was 2.29 mM.Key words: Dutch elm disease, β-galactosidase, Ophiostoma ulmi, Ophiostoma novo-ulmi.
Bacterial colonization patterns of intactPinus sylvestrismycorrhizospheres in dry pine forest soil: an electron microscopy study
Authors: Nurmiaho-Lassila E. -L. , Timonen S. , Haahtela K. , Sen R.
Published: February 2010

The bacterial populations associated with different plant and fungal habitats of intact Pinus sylvestris – Suillus bovinus or Pinus sylvestris – Paxillus involutus ectomycorrhizospheres grown in natural forest soil were examined by scanning and transmission electron microscopy. Surfaces of nonmycorrhizal Pinus sylvestris roots hosted large numbers of morphologically distinct bacteria. Bacteria were detected on the mantle surfaces and at inter- and intra-cellular locations in the mantle and Hartig net of Suillus bovinus mycorrhizas. The fungal strands were colonized by only a few bacteria unlike the outermost external fine hyphae on which extensive monolayers of bacteria were attached. The mycorrhizas of Paxillus involutus were mostly devoid of bacteria, but the intact external mycelium supported both bacterial colonies and solitary bacteria. Intracellular bacteria were not present in Paxillus involutus hyphae. In both mycorrhizal systems, bacterial aggregation and attachment to hyphae were mediated with electron-dense or -translucent material. Our study shows that the Pinus sylvestris mycorrhizospheres formed by two different ectomycorrhizal fungi are clearly dissimilar habitats for mycorrhizosphere-associated bacteria. Additionally, the spatially and physiologically defined mycorrhizosphere habitats were shown to host distinct populations of bacteria.Key words: ectomycorrhiza, intracellular bacteria, Paxillus involutus, soil bacteria, Suillus bovinus.
Control of polygalacturonase synthesis inFusarium oxyspotumf.sp.radicis lycopersici
Authors: Patiño Belén , Posada Martha Lucía , Vázquez Covadonga , González-Jaén María Teresa , Pozo Álvaro Martínez del
Published: February 2010

Genetic control of polygalacturonase (PG) activity from Fusarium oxysporum f.sp. radicis lycopersici was analyzed on pectin and glucose cultures. One exopolygalacturonase from F. oxysporum f.sp. radicis lycopersici was strongly induced, in stationary culture, when the fungus was grown on apple pectin, while on glucose no extracellular PG activity could be detected. Although SDS–PAGE detected the presence of a putative PG band (66 kDa) in both conditions, specific antibodies obtained against the purified PG only detected it in PG-inducing conditions, that is to say, when apple pectin was used as the carbon source. Northern blot analysis of RNA of two isolates of F. oxysporum f.sp. radicis lycopersici (r6and r2) confirmed that this regulation of PG synthesis was exerted at the transcriptional level. Only one single mRNA species of around 1400 nucleotides was detected on the cultures containing pectin and was absent in glucose-grown cultures. Southern blot analysis of genomic DNA indicated that pg gene seems to be present in a single copy in the genomes of F. oxysporum f.sp. radicis lycopersici r6and r2and Fusarium oxysporum f.sp. lycopersici, showing similar hybridization patterns in all species. The partial sequence of this pg gene from F. oxysporum f.sp. radicis lycopersici r6, which is also reported, showed high similarity to diverse PGs already reported. Exopolygalacturonase of F. oxysporum f.sp. radicis lycopersici r6is heavily glycosylated; its deglycosylated form had a molecular mass of 50 kDa.Key words: polygalacturonase, Fusarium oxysporum f.sp. radicis lycopersici, regulation.
Isolation and characterization of glycerol-fermenting bacteria from the rumen of red deer
Authors: Jarvis Graeme N. , Thiele Jürgen H. , Strömpl Carsten , Moore Edward R. B.
Published: February 2010

The rumen contents of juvenile red deer (Cervus elaphus) were used as a source for the enrichment of obligately anaerobic glycerol-fermenting bacteria. Three bacterial strains were isolated from the 10−4 dilution (isolates DR6A and DR6B) and 10−9 dilution (isolate DR7) of the deer rumen contents. The isolates DR6A, DR6B, and DR7 produced ethanol (42 mM) and acetate (5 mM), propionate (31 mM) and acetate (42 mM), and formate (25 mM) and ethanol (38 mM), respectively, as the major glycerol fermentation products. Interestingly, acetate, propionate, and formate were observed to be the major glycerol fermentation products in mixed cultures obtained from the deer rumen. The three isolates were all shown to be related phylogenetically to the ruminal species Clostridium clostridiiforme, Clostridium celerecrescens, and Clostridium aerotolerans within the clostridial taxonomic cluster XIVa, on the basis of 16S rRNA gene sequence comparisons. But, because of phenotypic differences, each isolate is considered to be a new species within the genus Clostridium, which has not been previously described or isolated from the rumen ecosystem.Key words: red deer, ecology, glycerol fermentation, Clostridium, rumen, 16S rRNA.
Bacteriophage infection and multiplication occur inPseudomonas aeruginosastarved for 5 years
Authors: Schrader Holly S. , Schrader John O. , Walker Jeremy J. , Wolf Thomas A. , Nickerson Kenneth W. , Kokjohn Tyler A.
Published: February 2010

Bacteriophages specific for Pseudomonas aeruginosa and Escherichia coli were examined for their ability to multiply in stationary phase hosts. Four out of five bacteriophages tested, including E. coli bacteriophage T7M, were able to multiply in stationary phase hosts. The bacteriophage ACQ had a mean burst size of approximately 1000 in exponential phase P. aeruginosa hosts and 102 in starved hosts, with corresponding latent periods that increased from 65 to 210 min. The bacteriophage UT1 had a mean burst size of approximately 211 in exponential phase P. aeruginosa hosts and 11 in starved hosts, with latent periods that increased from a mean of 90 min in exponential phase hosts to 165 min in starved hosts. Bacteriophage multiplication occurred whether or not the hosts had entered stationary phase, either because the cultures had been incubated for 24 h or were starved. Significantly, bacteriophage multiplication occurred in P. aeruginosa, which had been starved for periods of 24 h, several weeks, or 5 years. Only one P. aeruginosa virus, BLB, was found to be incapable of multiplication in stationary phase hosts. These results reveal that starvation does not offer bacterial hosts refuge from bacteriophage infection and suggest that bacteriophages will be responsible for significant bacterial mortality in most natural ecosystems.Key words: bacteriophage multiplication, stationary phase, starvation.
Ecbl and EcbR: homologs of Luxl and LuxR affecting antibiotic and exoenzyme production byErwinia carotovorasubsp.betavasculorum
Authors: Costa José M. , Loper Joyce E.
Published: February 2010

Erwinia carotovora subsp. betavasculorum Ecb168 causes vascular necrosis and root rot of sugar beet and produces an antibiotic(s) that is antagonistic against other Erwinia spp. EcbI−mutants of Ecb168, each containing a single transposon insertion in the ecbI gene (for Erwinia carotovora subsp. betavasculorum inducer), do not produce detectable levels of extracellular protease or antibiotic(s), and express less pectate lyase activity and virulence than the wild-type strain. A plasmid containing the cloned ecbI gene complemented the EcbI−mutants for these phenotypes. Protease production by EcbI−mutants grown on agar surfaces was restored by neighboring cells of Escherichia coli containing ecbI. Production of a diffusible N-acylhomoserine lactone autoinducer by wild-type Ecb168 was detected with indicator strains of E. coli and Agrobacterium tumefaciens. EcbI−mutant strains did not produce an autoinducer detected by the indicator strains. Antibiotic production by EcbI−mutants was restored by cell-free culture supernatants of Ecb168 or E. coli containing a cloned ecbI gene. The predicted amino acid sequence of EcbI is similar to those of CarI, ExpI, and HslI, three LuxI homologs required for production of a diffusible N-acylhomoserine lactone autoinducer in Erwinia carotovora subsp. carotovora. A luxR homolog, termed ecbR (for Erwinia carotovora subsp. betavasculorum regulator), is convergently transcribed and overlaps with ecbI by 17 bp at their 3′ ends. These results are consistent with the hypothesis that a quorum-sensing system related to the prototypic luxI–luxR gene pair controls antibiotic and exoenzyme production in Erwinia carotovora subsp. betavasculorum.Key words: quorum sensing, β-lactam, gene regulation.
Limitations on the use of polymerase chain reaction – restriction fragment length polymorphism analysis of the rDNA NTS2 region for the taxonomic classification of the speciesSaccharomyces cerevisiae
Authors: Pulvirenti Andrea , Solieri Lisa , De Vero Luciana , Giudici Paolo
Published: February 2010

Different molecular techniques were tested to determine which was the most effective in the identification of Saccharomyces cerevisiae strains. In particular, polymerase chain reaction – restriction fragment length polymorphism (PCR–RFLP) analysis of the internal transcribed spacer (ITS) regions and the nontranscribed spacer 2 (NTS2) region, sequencing of the D1/D2 domain, and electrophoretic karyotyping were applied to 123 yeast strains isolated from different sourdoughs and tentatively attributed to the species S. cerevisiae. All of the strains tested showed an identical PCR–RFLP pattern for the ITS regions, an identical nucleotide sequence of the D1/D2 domain, and the typical electrophoretic karyo type of S. cerevisiae. In contrast, 14 out of the 123 strains tested showed some polymorphism with BanI restriction analysis of the NTS2 region. Our results indicate that while the sequencing of the D1/D2 domain, the PCR–RFLP analysis of the ITS regions, and the electrophoretic karyotype can be employed successfully to identify S. cere visiae strains, PCR–RFLP analysis of the NTS2 region does not allow a consistent and accurate grouping for S. cere visiae strains. The fact that the NTS2 region of a small number of strains (8.78% of the total strains tested) is different from that of the other S. cerevisiae strains confirms that molecular methods should always be tested on a great number of strains.Key words: ribosomal DNA, Saccharomyces cerevisiae, yeast identification.
Nitrification in activated sludge batch reactors is linked to protozoan grazing of the bacterial population
Authors: Petropoulos Penny , Gilbride Kimberley A
Published: February 2010

Protozoa feed upon free-swimming bacteria and suspended particles inducing flocculation and increasing the turnover rate of nutrients in complex mixed communities. In this study, the effect of protozoan grazing on nitrification was examined in activated sludge in batch cultures maintained over a 14-day period. A reduction in the protozoan grazing pressure was accomplished by using either a dilution series or the protozoan inhibitor cycloheximide. As the dilutions increased, the nitrification rate showed a decline, suggesting that a reduction in protozoan or bacterial concentration may cause a decrease in nitrification potential. In the presence of cycloheximide, where the bacterial concentration was not altered, the rates of production of ammonia, nitrite, and nitrate all were significantly lower in the absence of active protozoans. These results suggest that a reduction in the number or activity of the protozoans reduces nitrification, possibly by limiting the availability of nutrients for slow-growing ammonia and nitrite oxidizers through excretion products. Furthermore, the ability of protozoans to groom the heterotrophic bacterial population in such systems may also play a role in reducing interspecies competition for nitrification substrates and thereby augment nitrification rates.Key words: nitrification, activated sludge, protozoan grazing, ammonia-oxidizing bacteria, cycloheximide.
Partial constraint checking for context consistency in pervasive computing
Authors: Xu Chang , Cheung S. C. , Chan W. K. , Ye Chunyang
Published: February 2010

Pervasive computing environments typically change frequently in terms of available resources and their properties. Applications in pervasive computing use contexts to capture these changes and adapt their behaviors accordingly. However, contexts available to these applications may be abnormal or imprecise due to environmental noises. This may result in context inconsistencies, which imply that contexts conflict with each other. The inconsistencies may set such an application into a wrong state or lead the application to misadjust its behavior. It is thus desirable to detect and resolve the context inconsistencies in a timely way. One popular approach is to detect context inconsistencies when contexts breach certain consistency constraints. Existing constraint checking techniques recheck the entire expression of each affected consistency constraint upon context changes. When a changed context affects only a constraint's subexpression, rechecking the entire expression can adversely delay the detection of other context inconsistencies. This article proposes a rigorous approach to identifying the parts of previous checking results that are reusable without entire rechecking. We evaluated our work on the Cabot middleware through both simulation experiments and a case study. The experimental results reported that our approach achieved over a fifteenfold performance improvement on context inconsistency detection than conventional approaches.
Free software, economic 'realities', and information justice
Authors: Chopra S. , Dexter S.
Published: February 2010

Free and open source software (FOSS) is taking an increasingly significant role in our software infrastructure. Yet many questions still exist about whether a software economy based on FOSS would be viable. We argue that contemporary trends definitively demonstrate this viability. Claiming that an economy must be evaluated as much by the ends it brings about as by its size or vigor, we draw on widely accepted notions of redistributive justice to show the ethical superiority of a software economy based on FOSS.
What should we share?
Authors: Wong Pak-Hang
Published: February 2010

The aim of Intercultural Information Ethics (IIE), as Ess aptly puts, is to "(a) address both local and global issues evoked by ICTs / CMC, etc., (b) in a ways that both sustain local traditions / values / preference, etc. and (c) provide shared, (quasi-) universal responses to central ethical problems? (Ess 2007a, 102). This formulation of the aim of IIE, however, is not unambiguous. In this paper, I will discuss two different understandings of the aim of IIE, one of which advocates "shared norms, different interpretations" and another proposes "shared norms, different justifications". I shall argue that the first understanding is untenable, and the second understanding is acceptable only with qualification. Finally, I shall briefly suggest an alternative way to understand the aim of IIE.
I do declare
Authors: Alvaro Peter , Condie Tyson , Conway Neil , Hellerstein Joseph M. , Sears Russell
Published: February 2010

The Paxos consensus protocol can be specified concisely, but is notoriously difficult to implement in practice. We recount our experience building Paxos in Overlog, a distributed declarative programming language. We found that the Paxos algorithm is easily translated to declarative logic, in large part because the primitives used in consensus protocol specifications map directly to simple Overlog constructs such as aggregation and selection. We discuss the programming idioms that appear frequently in our implementation, and the applicability of declarative programming to related application domains.
Checking process-oriented operating system behaviour using CSP and refinement
Authors: Barnes Frederick R.M. , Ritson Carl G.
Published: February 2010

Process orientation is an approach to concurrency that uses concepts of processes and message-passing communication, with whole systems constructed from layered and dynamically evolving networks of communicating processes. The work described in this paper relates to the automatic model generation and verification of systems developed in processoriented languages. We discuss some early applications of this technique to our experimental operating system, RMoX, as a means to giving a guarantee of correct system behaviour at a range of levels.
Overview of the ROADS'09 workshop
Authors: Dabbous Walid , Ott Maximilian
Published: February 2010

This report presents a brief overview of the organization and the program of the fourth Real Overlays and Distributed Systems Workshop ROADS'09 co-located with the 22nd SOSP conference at Big Sky, Montana.
NEPI
Authors: Lacage Mathieu , Ferrari Martin , Hansen Mads , Turletti Thierry , Dabbous Walid
Published: February 2010

Evaluating new network protocols, applications, and architectures uses many kinds of experimentation environments: simulators, emulators, testbeds, and sometimes, combinations of these. As the functionality and complexity of these tools increases, mastering and efficiently using each of them is becoming increasingly difficult.

In this paper, we consider how to make it easier to use multiple tools separately and together to improve the productivity of network researchers. We show how a single object model which encompasses every aspect of a typical experimentation workow can be used to completely describe experiments to be run within very different experimentation environments.

Although Nepi is still in early design and prototyping stage, we expect that its ability to describe and automate easily complex mixed experiments will enable further experimentation with heterogenous networks.
Towards a cost-effective networking testbed
Authors: Knežević Nikola , Schubert Simon , Kostić Dejan
Published: February 2010

The Internet is suffering from ossification. There has been substantial research on improving current protocols, but the vendors are reluctant to deploy new ones. We believe that this is in part due to the difficulty of evaluating protocols under realistic conditions. Recent wide-area testbeds can help alleviate this problem, but they require substantial resources (equipment, bandwidth) from each participant, and they have difficulty in providing repeatability and full control over the experiments. Existing in-house networking testbeds are capable of running controlled, repeatable experiments, but are typically small-scale (due to various overheads), limited in features, or expensive.

The premise of our work is that it is possible to leverage the recent increases in computational power to improve the researchers' ability to experiment with new protocols in lab settings. We propose a cost-effective testbed, called MX, which emulates many programmable routers running over a realistic topology on multi-core commodity servers. We leverage open source implementations of programmable routers, such as Click, and modify them to allow coexistence of multiple instances in the same kernel in an effort to reduce packet forwarding overheads. Our initial results show that we outperform similar cost-effective solutions by a factor of 2. Next, we demonstrate that grouping and placing routers on to cores which share the L2 cache yields high performance.
Crowd translator
Authors: Ledlie Jonathan , Odero Billy , Minkov Einat , Kiss Imre , Polifroni Joseph
Published: February 2010

We present a method to expand the number of languages covered by simple speech recognizers. Enabling speech recognition in users' primary languages greatly extends the types of mobile-phone-based applications available to people in developing regions. We describe how we expand language corpora through user-supplied speech contributions, how we quickly evaluate each contribution, and how we pay contributors for their work.
SOSP diversity workshop
Authors: Mickens James , da Silva Dilma
Published: February 2010

In this paper, we report on the activities at the 2009 SOSP Diversity Workshop. The workshop contained a mix of technical presentations and mentoring sessions, providing traditionally underrepresented students with a unique opportunity to get advice from established researchers in academia and industry. Feedback surveys suggest that many attendees received valuable career guidance.
eNOS plays a major role in adiponectin synthesis in adipocytes
Authors: Koh Eun Hee , Kim Mina , Ranjan K. C. , Kim Hyun Sik , Park Hye-Sun , Oh Ki Sook , Park In-Sun , Lee Woo Je , Kim Min-Seon , Park Joong-Yeol , Youn Jang Hyun , Lee Ki-Up
Published: February 2010

Nitric oxide (NO) stimulates mitochondrial biogenesis. We recently reported that adiponectin synthesis is regulated by mitochondrial function in adipocytes. This study was undertaken to test the hypothesis that endothelial NO synthase (eNOS) plays an important role in adiponectin synthesis by producing NO and enhancing mitochondrial function in adipocytes. We examined the effects of eNOS knockdown on adiponectin synthesis in 3T3-L1 adipocytes and also examined plasma adiponectin levels and the mitochondria in adipose tissue of eNOS knockout (eNOS−/−) mice with and without chronic administration of a NO donor. In cultured 3T3-L1 adipocytes, eNOS siRNA decreased rosiglitazone-induced adiponectin secretion, which was associated with decreases in mitochondrial proteins and biogenesis factors. Plasma adiponectin concentrations were reduced in adult eNOS−/− mice compared with age-matched wild-type mice. Mitochondrial contents in adipose tissue were reduced in eNOS−/− mice, and this was associated with decreased expression of mitochondrial biogenesis factors, increased levels of 8-hydroxyguanosine, a biomarker of oxidative stress, and morphological abnormalities in mitochondria. Rosiglitazone-induced increases in adiponectin expression and mitochondrial content were also reduced significantly in eNOS−/− mice. Chronic administration of a NO donor reversed mitochondrial abnormalities and increased adiponectin expression in adipose tissue of eNOS−/− mice. eNOS plays an important role in adiponectin synthesis in adipocytes by increasing mitochondrial biogenesis and enhancing mitochondrial function.
A Predator‐Prey Gompertz Model with Time Delay and Impulsive Perturbations on the Prey
Authors: Jia Jianwen , Li Chunhua
Published: February 2010

We introduce and study a Gompertz model with time delay and impulsive perturbations on the prey. By using the discrete dynamical system determined by the stroboscopic map, we obtain the sufficient conditions for the existence and global attractivity of the “predator‐extinction” periodic solution. With the theory on the delay functional and impulsive differential equation, we obtain the appropriate condition for the permanence of the system.
Dynamic Modal Analysis of Vertical Machining Centre Components
Authors: Patwari Anayet U. , Faris Waleed F. , Nurul Amin A. K. M. , Loh S. K.
Published: February 2010

The paper presents a systematic procedure and details of the use of experimental and analytical modal analysis technique for structural dynamic evaluation processes of a vertical machining centre. The main results deal with assessment of the mode shape of the different components of the vertical machining centre. The simplified experimental modal analysis of different components of milling machine was carried out. This model of the different machine tool′s structure is made by design software and analyzed by finite element simulation using ABAQUS software to extract the different theoretical mode shape of the components. The model is evaluated and corrected with experimental results by modal testing of the machine components in which the natural frequencies and the shape of vibration modes are analyzed. The analysis resulted in determination of the direction of the maximal compliance of a particular machine component.
Genetic Variability and Phylogenetic Relationships withinTrypanosoma cruziI Isolated in Colombia Based on Miniexon Gene Sequences
Authors: Herrera Claudia , Guhl Felipe , Falla Alejandra , Fajardo Anabella , Montilla Marleny , Adolfo Vallejo Gustavo , Bargues M. Dolores
Published: February 2010

Phylogenetic studies ofTrypanosoma cruzihave identified the existence of two groups:T. cruziI andT. cruziII. There are aspects that still remain unknown about the genetic variability within theT. cruziI group. Given its epidemiological importance, it is necessary to have a better understanding ofT. cruzitransmission cycles. Our purpose was to corroborate the existence of haplotypes within theT. cruziI group and to describe the genetic variability and phylogenetic relationships, based on single nucleotide polymorphisms (SNPs) found in the miniexon gene intergenic region, for the isolates from different hosts and epidemiological transmission cycles in Colombian regions. 31T. cruziisolates were molecularly characterized. Phylogenetic relationships withinT. cruziI isolates showed four haplotype groups (Ia–Id), associated with their transmission cycle. In previous studies, we reported that haplotype Ia is mainly associated with the domestic cycle and domiciliatedRhodnius prolixus. Haplotype Ib is associated with the domestic cycle and peridomestic cycle, haplotype Ic is closely related with the peridomestic cycle, and haplotype Id is strongly associated with the sylvatic cycle. The phylogenetic methodologies applied in this study are tools that bolster the associations among isolates and thus shed light on Chagas disease epidemiology.
Oscillation Theorems for Second‐Order Forced Neutral Nonlinear Differential Equations with Delayed Argument
Authors: Shao Jing , Meng Fanwei
Published: February 2010

We are concerned with the oscillation of the forced second‐order neutral nonlinear differential
equations with delayed argument in the form . No restriction is imposed on the potentials p(t), qi(t), ande(t) to be nonnegative. Our methodology is somewhat different from those of previous authors.
Classes of Meromorphic Functions Defined by the Hadamard Product
Authors: Dziok J.
Published: February 2010

The object of the present paper is to introduce new classes of meromorphic functions with
varying argument of coefficients defined by means of the Hadamard product (or convolution). Several properties like the coefficients bounds, growth and distortion theorems, radii of starlikeness and convexity, and partial sums are investigated. Some consequences of the main results for well‐known classes of meromorphic functions are also pointed out.
An Analytical Multimodulus Algorithm for Blind Demodulation in a Time-Varying MIMO Channel Context
Authors: Daumont Steredenn , Le Guennec Daniel
Published: February 2010

This paper addresses the issue of blind multiple-input multiple-output (MIMO) demodulation of communication signals, with time-varying channels and in an interception context. A new adaptive-blind source separation algorithm, which is based on the implementation of the Multimodulus cost function by analytical methods, is proposed. First a batch processing analysis is performed; then an adaptive implementation of the (Analytical Multi-Modulus Algorithm) AMMA and its simplified version named (Analytical Simplified Constant Modulus Algorithm) ASCMA is detailed. These algorithms, named adaptive-AMMA and adaptive-ASCMA, respectively, are compared with the adaptive (Analytical Constant Modulus Algorithm) ACMA and the MMA (Multi-Modulus Algorithm). The adaptive-AMMA and adaptive-ASCMA achieve a lower residual intersymbol interference and bit error rate than those of the adaptive-ACMA and MMA.
Which Patients with Estrogen Receptor-Positive Early Breast Cancer Should Be Treated with Adjuvant Chemotherapy?
Authors: Chiuri Vincenzo Emanuele , Lorusso Vito
Published: February 2010

Estrogen receptor expression in breast cancer cells represents an important predictive and prognostic factor. The estrogen receptor is a target for endocrine therapy, which avoids chemotherapy especially in highly hormone-sensitive early breast cancer. Paradoxically, recent data from several clinical trials and meta-analyses have demonstrated the superiority of adjuvant chemotherapy independently of age, estrogen receptor and nodal status. For this reason, new tools are needed to better define the intrinsic characteristics of breast cancers and to establish the role of cytotoxic treatment for those tumors with potentially good outcome, such as hormone-sensitive early breast cancer.
Molecular Mechanism and Clinical Implications of Endocrine Therapy Resistance in Breast Cancer
Authors: Arpino Grazia , De Angelis Carmine , Giuliano Mario , Giordano Antonio , Falato Claudette , De Laurentiis Michele , De Placido Sabino
Published: February 2010

Endocrine therapy, the first targeted therapy in oncology, is the most successful systemic therapy in the management of estrogen receptor (ER)-positive breast cancer. Approximately 50% of patients with advanced disease do not respond to first-line treatment with tamoxifen, and many women who receive tamoxifen as adjuvant therapy experience tumor relapse and die from their disease. Aromatase inhibitors are proving superior to tamoxifen, at least in certain patient subsets. However, the response rate to these compounds is only slightly higher than that to tamoxifen in patients with advanced breast cancer, and both de novo or acquired resistance also occur, limiting the efficacy of the treatment. Advanced studies of ER biology have highlighted the role of an intimate cross talk between the ER and HER2/growth factor signaling pathways as a fundamental contributor to the development of resistance to hormone therapies. The aim of this review article is to summarize the current knowledge on mechanisms of resistance of breast cancer cells to endocrine therapies due to the cross talk between the ER and growth factor signaling pathways, and to explore newly available therapeutic strategies that could prolong duration of response and circumvent endocrine-resistant tumor growth.
The Dark Side of the Moon: The PI3K/PTEN/AKT Pathway in Colorectal Carcinoma
Authors: Silvestris Nicola , Tommasi Stefania , Petriella Daniela , Santini Daniele , Fistola Ettore , Russo Antonio , Numico Gianmauro , Tonini Giuseppe , Maiello Evaristo , Colucci Giuseppe
Published: February 2010

Wild-type KRAS status is required but not sufficient to confer sensitivity to anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (mAbs) in colorectal cancer patients. As a consequence, one of the major challenges is to identify, in non-mutant KRAS patients, other markers that can predict lack of response to this therapy. Small series have investigated the clinical effect of PIK3CA mutations on resistance to anti-EGFR mAbs and discrepant results have been observed. Furthermore, PTEN loss in metastases may be predictive of resistance to anti-EGFR mAbs, even if PTEN determination is far from an immediate clinical application. The introduction of modulators of the PI3K/AKT/mTOR pathway as potential targeted anticancer drugs is encouraging, but this attractive therapy option is still at an early stage of development.