bluuebunny/crossref_metadata_2025 huggingface dataset:
Review / Sythèse Nonlinear acoustic applications for material characterization: A review
Authors: Zheng Y , Maev R Gr , Solodov I Yu
Published: April 2011

The nonlinear acoustic applications for material characterization are reviewed. The general theoretical analysis of the effects of nonlinearity, dissipation, dispersion, and diffraction on intense acoustic-wave propagation is given. Acoustic nonlinear parameters and their determination methods are introduced. The investigations of nonlinear acoustic applications for solid material evaluation are discussed for different levels of disruption, from asymmetry of lattice structure and dislocation in crystals to disbonds and cracks in engineering materials. The experimental methods involved in these investigations are also considered. The techniques used for nonlinear acoustic imaging are divided into two categories, concerned with resolution improvement by using higher harmonics, and nonlinear parametric imaging. The nonlinear acoustic applications in biomedical imaging, acoustic microscopy, and nonlinear nondestructive evaluation are presented. Finally, the issues that need further investigations in this area are discussed.

PACS Nos.: 43.25, 62.65, 62.20M
The motion of rotating cylinders sliding on pebbled ice
Authors: Shegelski MRA , Reid M , Niebergall R
Published: April 2011

We consider the motion of a cylinder with the same mass and sizeas a curling rock, but with a very different contact geometry.Whereas the contact area of a curling rock is a thin annulus havinga radius of 6.25 cm and width of about 4 mm, the contact area of the cylinderinvestigated takes the form of several linear segments regularly spacedaround the outer edge of the cylinder, directed radially outward from the center,with length 2 cm and width 4 mm. We consider the motion of this cylinderas it rotates and slides over ice having the nature of the ice surfaceused in the sport of curling. We have previously presented a physicalmodel that accounts for the motion of curling rocks; we extend this modelto explain the motion of the cylinder under investigation. In particular,we focus on slow rotation, i.e., the rotational speed of the contact areasof the cylinder about the center of mass is small compared to thetranslational speed of the center of mass.The principal features of the model are (i) that the kineticfriction induces melting of the ice, with the consequence that thereexists a thin film of liquid water lying between the contact areasof the cylinder and the ice; (ii) that the radial segmentsdrag some of the thin liquid film around the cylinder as it rotates,with the consequence that the relative velocity between the cylinderand the thin liquid film is significantly different than the relativevelocity between the cylinder and the underlying solid ice surface.Since it is the former relative velocity that dictates the nature of themotion of the cylinder, our model predicts, and observations confirm, thatsuch a slowly rotating cylinder stops rotating well before translationalmotion ceases. This is in sharp contrast to the usual case of most slowlyrotating cylinders, where both rotational and translational motion ceaseat the same instant. We have verified this prediction of our model bycareful comparison to the actual motion of a cylinder having a contactarea as described.PACS Nos.: 46.00, 01.80+b
Qualitative analysis of the existence of bound states and resonances of dipositronium
Authors: Bao C G , Shi T Y
Published: April 2011

Symmetry has imposed very strong constraints on the structure and stability of the internal wave functions of dipositronium. Based on symmetry considerations, the existence of a number of bound excited states and resonances has been suggested. More specifically, evidence for the existence of four bound states has been provided.PACS Nos.: 36.10Dr, 02.20-a
Detection of the Na+-translocating NADH-quinone reductase in marine bacteria using a PCR technique
Authors: Kato Sanae , Yumoto Isao
Published: April 2011

To examine the distribution of the Na+-translocating NADH-quinone reductase (Na+-NQR) among marine bacteria, we developed a simple screening method for the detection of this enzyme. By reference to the homologous sequences of the Na+-NQR operons from Vibrio alginolyticus and Haemophilus influenzae, a pair of primers was designed for amplification of a part of the sixth ORF (nqr6) of the Na+-NQR operon. When PCR was performed using genomic DNA from 13 marine bacteria, a 0.9-kbp fragment corresponding to nqr6 was amplified in 10 strains. Although there were three PCR-negative strains phylogenetically, based on the sequence of the 16S rRNA, these were placed far from the PCR-positive strains. No product was observed in the case of nonmarine bacteria. The nucleotide and predicted amino acid sequences of nqr6 were highly conserved among the PCR-positive marine bacteria. A phylogenetic analysis of marine bacteria, based on nqr6 sequencing, was performed.Key words: Na+-translocating, NADH-quinone reductase, marine bacteria, PCR.
Overproduction in Escherichia coli of the pectin methylesterase A from Erwinia chrysanthemi 3937: One-step purification, biochemical characterization, and production of polyclonal antibodies
Authors: Laurent Franck , Kotoujansky Alain , Bertheau Yves
Published: April 2011

Pectin methylesterase A (EC 3.1.1.11), one of the pathogenicity factors of Erwinia chrysanthemi strain 3937, was purified to homogeneity using one-step chromatography on cross-linked pectate. The purified protein showed maximum activity at pH 8-9, 50°C, 50-100 mM monovalent cations or 5-10 mM divalent cations, and on a 50% esterified pectin. A particular effect of Ca2+ and Zn2+ on PMEA activity, due to the formation of a pectin gel, was observed. A Km value of 0.03% and 0.051% was determined at pH 6 and 7.6, respectively, using the same substrate. Polyclonal antibodies raised against the PMEA from E. chrysanthemi strain 3937 were produced. It recognized PMEs from Erwinia species, but did not cross-react with PME of fungal or plant origin, and will therefore be a useful tool to immunolocalize the protein during plant-pathogen interactions.Key words: soft rot disease, pectinase, affinity chromatography, polyclonal antibody.
Deletions of mob and tra pJP4 transfer functions after mating of Ralstonia eutropha JMP134 (pJP4) with Escherichia coli harboring F'::Tn10
Authors: Clément Pascale , Springael Dirk , González Bernardo
Published: April 2011

One-tenth of Escherichia coli transconjugants resulting from the transfer of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 to E. coli XL1Blue, contained pJP4 derivatives with deletions (~15-30 kb). The occurrence of these deletions is probably associated with the presence of Tn10 in the recipient. DNA endonuclease restriction analysis of the pJP4 deletion derivatives showed the absence of SphI and EcoRI fragments previously reported to hybridize with IncP Tra DNA probes. Moreover, these pJP4 deletion derivatives are not able to self-transfer, nor are they able to be mobilized. Accordingly, these pJP4 deletion derivatives lack transfer functions.Key words: pJP4, mobilization functions, deletion.
Segregation following interspecific transfer of isolated nuclei between Phytophthora parasitica and P. capsici
Authors: Gu Y H , Ko W H
Published: April 2011

Nuclei isolated from metalaxyl-resistant (MR) protoplasts of Phytophthora parasitica were transferred into chloroneb-resistant (CnR) protoplasts of Phytophthora capsici and vice versa, with an average success rate of 2.6 × 10-4 (protoplasts with donor nuclei/regenerated protoplasts), using a selective medium containing only the fungicide tolerated by the nuclear donor. No colonies appeared when self-fusion products of donor nuclei or recipient protoplasts were exposed to the selective medium. Colonies produced by the nuclear transfer formed sectors commonly, and differed from the parental types in appearance. All the zoospores produced by the nuclear hybrids were of normal size, and one-fifth of them contained both MR and CnR genes. Since zoospores are mostly uninucleate, these results indicated the occurrence of chromosome re-assortment or mitotic crossing-over following the production of transitory tetraploids, followed by diploidization during zoosporogenesis, thus suggesting the completion of events leading to a parasexual cycle. Hyphal fragment cultures from a nuclear hybrid tested showed considerable variation in growth rate, mycelial morphology, and level of resistance to metalaxyl, indicating uneven distribution and continuous segregation of different types of nuclei in mycelia during vegetative growth.Key words: interspecific nuclear transfer, parasexual cycle, karyogamy, Phytophthora parasitica,Phytophthora capsici.
Thatch biodegradation and antifungal activities of two lignocellulolyticStreptomycesstrains in laboratory cultures and in golf green turfgrass
Authors: Chamberlain Karen , Crawford Don L
Published: April 2011

The use of lignocellulolytic Streptomyces spp. as biological agents, to enhance thatch degradation in turf and to slow its rate of accumulation while controlling fungal growth in the thatch layer, was studied. In flask scale studies, two lignocellulolytic Streptomyces violaceusniger (= hygroscopicus) strains (YCED9 and WYE53) decomposed thatch (>30% dry weight) over a 12-week incubation period. Biodegradation was accompanied by production of extracellular cellulases, xylanases, and peroxidases. The accumulation of the polymeric, water-soluble lignin degradation intermediate acid, precipitable polymeric lignin (APPL), was also observed. Residual thatch from 12-week-old cultures had an increased lignin-to-carbohydrate ratio, an indication that although lignin was metabolized, carbohydrates were preferential carbon sources for these actinomycetes. A spore-containing soluble dry powder formulation was used as an inoculum in an in situ field experiment. This formulation was maintained in storage at 4°C for over two years without viability loss. Results from the golf green experiment showed that although treated thatch layers in established greens were not appreciably reduced over the course of one summer, the Streptomyces were active and maintained their populations within the thatch, while fungal growth was suppressed as compared to controls. The results show that treatment of turfgrass with these Streptomyces may be useful for the long-term control of fungal populations within the thatch. Longer field studies are required to assess the long-term potential for also controlling thatch build-up and fungal pathogens.Key words: biocontrol, biodegradation, fungi, Streptomyces, thatch.
Cometabolic biotransformation of nitrobenzene by 3-nitrophenol degradingPseudomonas putida2NP8
Authors: Zhao Jian-Shen , Ward Owen P
Published: April 2011

A strain of Pseudomonas putida (2NP8) capable of growing on both 2-nitrophenol and 3-nitrophenol, but not on nitrobenzene (NB), was isolated from municipal activated sludge. 2-Nitrophenol was degraded by this strain with production of nitrite. Degradation of 3-nitrophenol resulted in the formation of ammonia. Cells grown on 2-nitrophenol did not degrade nitrobenzene. A specific nitrobenzene degradation activity was induced by 3-nitrophenol. Ammonia, nitrosobenzene, and hydroxylaminobenzene have been detected as metabolites of nitrobenzene degradation by cells grown in the presence of 3-nitrophenol. These results indicated a NB cometabolism mediated by 3-nitrophenol nitroreductase.Key words: biodegradation, nitrobenzene, nitrophenol, Pseudomonas putida, cometabolism, nitroreductase.
Purification and characterization of a common soil component which inhibits the polymerase chain reaction
Authors: Watson R J , Blackwell B
Published: April 2011

DNA prepared from soil usually contains a brown-tinted inhibitor of the polymerase chain reaction (PCR) which limits the sensitivity of this technique for specific detection of microorganisms. To localize the inhibitor, soil fractions were tested for their inhibitory effect on the PCR reaction. A highly inhibitory activity, sufficient to account for the inhibition typically exhibited by soil DNA, was found to be tightly associated with the soil microorganism fraction. After cell breakage, the inhibitory material became soluble, and was not separable from DNA by standard purification procedures. A method was derived by which most of the inhibitory material could be selectively solubilized from the microorganism fraction without cell breakage, using successive washes with buffers differing in EDTA concentration. This technique was used to isolate a substance with characteristics suggesting that it is the major PCR inhibitor contaminating DNA purified from soil. It was found to be an organic, water-soluble compound of high molecular weight, and was present in a variety of soil types from different locations. It was found to be distinctly different in its solubility properties from humic and fulvic acids, and also in its FT-IR and NMR spectra. It forms a complex with protein and may inhibit the PCR reaction by an interaction with Taq DNA polymerase.Key words: fulvic acid, humic acid, PCR inhibitor, soil DNA, soil microorganisms.
Effects of experimental conditions on mycorrhizal relationships between Pinus sylvestris and Lactarius deliciosus and unprecedented fruit-body formation of the Saffron milk cap under controlled soilless conditions
Authors: Guerin-Laguette Alexis , Plassard Claude , Mousain Daniel
Published: April 2011

The mycorrhizal relationships between pines and two edible species of Lactarius sect. Dapetes were investigated by optimizing the experimental conditions of mycelial growth and of mycorrhizal colonization of pine seedlings. In vitro mycelial growth of Lactarius deliciosus and L. sanguifluus was improved on a buffered medium containing glucose, amino acids, and vitamins. Two methods of mycorrhization of pines with Lactarius deliciosus were tested. The mycorrhizal colonization was rapid and intense under non-aseptic conditions with a low nutrient supply and without exogenous glucose. A positive influence of mycorrhizal colonization on Pinus sylvestris growth was subsequently observed. Under axenic conditions and with a high nutrient supply, mycorrhization was stimulated at 10 g/L of exogenous glucose, irrespective of the phosphorus concentration. At high phosphorus level (1 mM) and 0.1, 1.0, or 10.0 g/L glucose, growth of Pinus sylvestris was reduced by inoculation. Stability and development of Pinus spp./Lactarius deliciosus symbioses were assayed in a climatic chamber using containers filled with a synthetic substrate. Over a 2-year culture period, the root systems of the pine seedlings were heavily colonized by Lactarius deliciosus. One year following inoculation, Lactarius deliciosus fruit-body primordia appeared associated with Pinus sylvestris seedlings. Six months later, two mature basidiomata were obtained. This is the first report of soilless fruit-body formation of this edible mushroom.Key words: ectomycorrhiza, inoculation, Lactarius deliciosus, Lactarius sanguifluus, Pinus, wild edible mushrooms.
Stoichiometry of diauxic growth of a xylanase-producingBacillusstrain
Authors: Schneider Gerhard , Taillandier Patricia , Strehaiano Pierre
Published: April 2011

In this work, the establishment of material balances and stoichiometry of the growth of Bacillus sp. was undertaken. This strain produces high quantities of a xylanase suitable for use as bleach boost agent in chlorine-free bleaching sequences of paper pulp. As carbon dioxide plays an important role as a growth factor, bacterial growth in two fermentations, one fed with air and another fed with carbon-dioxide-enriched air, were compared. For this purpose, a method permitting the determination of the consumption of the two carbon sources, xylan and peptone, was proposed. The material balances revealed that in both cases, the bacteria first use peptone as their carbon source, and then xylan in the second part of the growth phase. The aerated culture showed diauxic growth on these two substrates, whereas carbon-dioxide-enriched air caused disappearance of the metabolic adaptation phase, and rendered biomass production more economic. The fermentation fed with air needed 30% more xylan than the fermentation fed with carbon-dioxide-enriched air for the same quantity of biomass produced.Key words: Bacillus sp., carbon dioxide, material balances, diauxic growth.
High-frequency interconversion of turbid and clear plaque strains of bacteriophage f1 and associated host cell death
Authors: Kuo Mei-Yin , Yang Mei-Kwei , Chen Wen-Ping , Kuo Tsong-Teh
Published: April 2011

Under normal cultivation conditions, a mixture of turbid and clear plaques is often apparent in cultures of bacterial cells infected with filamentous bacteriophages. Beginning with a culture of wild-type filamentous phage f1, which itself produces turbid plaques, a clear plaque strain (c1) was isolated. From c1, the turbid plaque strain t1 was isolated; from t1, the clear plaque strain c2 was isolated; and from c2, the turbid plaque strain t2 was isolated. Each of these strains was generated with a frequency of approximately 1 × 10-4. Although filamentous phages have been thought not to induce host cell death, both turbid and clear plaque strains of f1 killed host bacteria. Plating of bacterial cells 1 h after infection revealed that colonies produced by cells infected with either wild-type f1 or strain c2 were smaller than those derived from uninfected cells, and that colony formation by infected cells was reduced by 15% and 38%, respectively. The time course of bacterial growth revealed that, at 4 h after infection, the number of CFU per milliliter of culture of cells infected with wild-type f1 or with strain c2 was reduced by 27% and 95%, respectively, compared with that for uninfected cells. Microculture analysis also revealed that the percentages of nondividing cells in f1 or c2 infected were 19% and 52%, respectively, 4 h after infection with wild-type f1 or with strain c2; no such cells were detected in cultures of uninfected cells. Negative staining and electron microscopy showed that 20% and 61% of cells infected with wild-type f1 or with strain c2 were dead 4 h postinfection. Finally, although the rates of DNA synthesis were similar for infected and uninfected cells, the rates of RNA and protein synthesis were markedly reduced in infected cells.Key words: Escherichia coli, bacteriophages, turbid plaque, clear plaque.
Purification of the NADP+: F420oxidoreductase ofMethanosphaera stadtmanae
Authors: Elias Dwayne A , Juck David F , Berry Karin A , Sparling Richard
Published: April 2011

Methanosphaera stadtmanae (DSM 3091) is a methanogen that requires H2and CH3OH for methanogenesis. The organism does not possess an F420-dependent hydrogenase and only low levels of F420. It does however possess NADP+:F420oxidoreductase activity. The NADP+:F420oxidoreductase, the enzyme which catalyses the electron transfer between NADP+and F420in this organism, was purified and characterized. NAD+, NADH, FMN, and FAD could not be used as electron acceptors. Optimal pH for F420reduction was 6.0, and 8.5 for NADP+reduction. During the purification process, it was noted that precipitation with (NH4)2SO4increased total activity 16-fold but reduced the stability of the enzyme. However, recombination of cell-free extracts with resuspended 65-90% (NH4)2SO4pellet returned activity to near cell-free extract levels. Neither high salt or protease inhibitors were effective in stabilizing the activity of the partially purified enzyme. The purified enzyme from M. stadtmanae possessed a molecular weight of 148 kDa as determined by gel filtration chromatography and native-PAGE, consisting of α, β, and γ subunits of 60, 50, and 45 kDa, respectively, using SDS-PAGE. The Kmvalues were 370 µM for NADP+, 142 µM for NADPH, 62.5 µM for F420, and 7.7 µM for F420H2. These values were different from the Kmvalues observed in the cell-free extract.Key words: methanogen, NADP:F420oxidoreductase, NADP reductase, F420, NADP+.
Use of lycorine and DAPI staining inSaccharomyces cerevisiaeto differentiate betweenrho0andrho-cells in acce1/Δcce1 nuclear background
Authors: Massardo Domenica Rita , Zweifel Stephan G , Gunge Norio , Miyakawa Isamu , Sando Nobundo , Giudice Angelica Del , Wolf Klaus , Giudice Luigi Del
Published: April 2011

In the yeast Saccharomyces cerevisiae, mutants are viable with large deletions (rho-), or even complete loss of the mitochondrial genome (rho0). One class of rho-mutants, which is called hypersuppressive, is characterised by a high transmission of the mutated mitochondrial genome to the diploid progeny when mated to a wild-type (rho+) haploid. The nuclear gene CCE1 encodes a cruciform cutting endonuclease, which is located in the mitochondrion and is responsible for the highly biased transmission of the hypersuppressive rho-genome. CCE1 is a Holliday junction specific endonuclease that resolves recombination intermediates in mitochondrial DNA. The cleavage activity shows a strong preference for cutting after a 5'-CT dinucleotide. In the absence of the CCE1 gene product, the mitochondrial genomes remain interconnected and have difficulty segregating to the daughter cells. As a consequence, there is an increase in the fraction of daughter cells that are rho0. In this paper we demonstrate the usefulness of lycorine, together with staining by 4',6-diamidino-2-phenylindole (DAPI), to assay for the mitotic stability of a variety of mitochondrial genomes. We have found that rho+and rho-strains that contain CT sequences produce a large fraction of rho0progeny in the absence of CCE1 activity. Only those rho-mitochondrial genomes lacking the CT recognition sequence are unaffected by the cce1 allele.Key words: yeast, mitochondria, hypersuppressive, Saccharomyces cerevisiae, lycorine.
Construction of a multiframe vector to express coding sequences inEscherichia coli
Authors: Domínguez-Martínez Verónica , Guarneros-Peña Gabriel , Segura-Nieto Magdalena , Curiel-Quesada Everardo
Published: April 2011

Cloning of foreign DNA fragments for coding sequence analysis in Escherichia coli usually involves sets of three vectors. To simplify this, we constructed an expression vector named pMFV7 containing three ATG codons in different frames downstream of a Shine-Dalgarno sequence, assuming that the ribosome can use any of the three start codons in an alternative manner. Translation beginning at either of the start codons would drive the expression of any coding fragment cloned downstream. To test the feasibility of this proposal, we cloned DNA fragments of the lacZ gene in each of the possible reading frames downstream from pMFV7 start codons. Sequence analysis of the N-terminus regions around the fusion sites indicates that ribosomes indeed initiate translation at each of the three initiation codons. In one case, levels of β-galactosidase activity depended largely on the N-terminus of the translation products. We conclude that pMFV7 may be useful for expressing coding sequences regardless of their reading frame.Key words: translation initiation, in-frame gene cloning, expression vectors.
Ultrastructure of interaction in alginate beads between the microalgaChlorella vulgariswith its natural associative bacteriumPhyllobacterium myrsinacearumand with the plant growth-promoting bacteriumAzospirillum brasilense
Authors: Lebsky Vladimir K , Gonzalez-Bashan Luz E , Bashan Yoav
Published: April 2011

Chlorella vulgaris, a microalga often used in wastewater treatment, was coimmobilized and coincubated either with the plant growth-promoting bacterium Azospirillum brasilense, or with its natural associative bacterium Phyllobacterium myrsinacearum, in alginate beads designed for advanced wastewater treatment. Interactions between the microalga and each of the bacterial species were followed using transmission electron microscopy for 10 days. Initially, most of the small cavities within the beads were colonized by microcolonies of only one microorganism, regardless of the bacterial species cocultured with the microalga. Subsequently, the bacterial and microalgal microcolonies merged to form large, mixed colonies within the cavities. At this stage, the effect of bacterial association with the microalga differed depending on the bacterium present. Though the microalga entered a senescence phase in the presence of P. myrsinacearum, it remained in a growth phase in the presence of A. brasilense. This study suggests that there are commensal interactions between the microalga and the two plant associative bacteria, and that with time the bacterial species determined whether the outcome for the microalga is senescence or continuous multiplication.Key words: Azospirillum, Chlorella, Phyllobacterium, wastewater treatment, water bioremediation.
Chemostat modeling ofEscherichia colipersistence in conventionalized mono-associated and streptomycin-treated mice
Authors: Rang Camilla , Midtvedt Tore , Molin Søren , Chao Lin
Published: April 2011

We have previously shown that Escherichia coli BJ4 has similar doubling time in mice that are mono-associated (having only the inoculated E. coli BJ4) or streptomycin-treated (having mainly gram-positive bacteria plus the inoculated E. coli BJ4). We also showed that when the mice were conventionalized (fed cecum homogenate from conventional mice or ones with a complete microbial flora), the introduction of complete flora in both cases increased the in vivo doubling time, while decreasing the colony counts in fecal samples. To determine whether the increase in doubling time could explain the decrease in colony counts, we analyzed our previous results by a chemostat model. The analysis shows that the increasing doubling time alone is sufficient to explain the decrease in colony counts in mono-associated mice, but not in the streptomycin-treated mice. The observed decreasing rate in colony counts in streptomycin-treated mice is slower than predicted. Furthermore, whereas the model predicted a decrease to extinction in both mice, the E. coli persist at a frequency 10-80 times higher in streptomycin-treated mice than in mono-associated mice. Thus, while a chemostat model is able to explain some of the population dynamics of intestinal bacteria in mice, additional factors not included in the model are stabilizing the system. Because we find that E. coli declines more slowly and to a higher stabilization frequency in streptomycin-treated mice, which have a more diverse flora before conventionalization, we take these results to suggest that the persistence of E. coli populations is promoted by species diversity. We propose that a mechanism for the persistence may be the presence of new E. coli niches created by keystone species in the more diverse flora.Key words: intestinal ecology, intestinal colonization, chemostat, keystone species, conventionalization.
Characterization of the iron superoxide dismutase gene ofAzotobacter vinelandii:sodBmay be essential for viability
Authors: Qurollo Barbara A , Bishop Paul E , Hassan Hosni M
Published: April 2011

Azotobacter vinelandii contains two superoxide dismutases (SODs), a cytoplasmic iron-containing enzyme (FeSOD), and a periplasmic copper/zinc-containing enzyme (CuZnSOD). In this study, the FeSOD was found to be constitutive, while the activity of CuZnSOD increased as the culture entered the stationary phase. Total SOD (units/mg protein) in stationary phase cells grown under nitrogen-fixing conditions was not significantly different from those grown under non-nitrogen-fixing conditions. The gene encoding FeSOD (sodB) was isolated from an A. vinelandii cosmid library. A 1-kb fragment containing the coding region and 400 base pairs of upstream sequence was cloned and sequenced. The nucleotide sequence and the deduced amino acid sequence had a high degree of homology with other bacterial FeSODs, particularly with P. aeruginosa. Attempts to construct a sodB mutant by recombination of a sodB::kan insertion mutation into the multicopy chromosome of A. vinelandii were unsuccessful even in the presence of SOD mimics or nutritional supplements. These results suggest that FeSOD may be essential for the growth and survival of A. vinelandii, and that the periplasmic CuZnSOD cannot replace the function of FeSOD.
Determination of 1-aminocycopropane-1-carboxylic acid (ACC) to assess the effects of ACC deaminase-containing bacteria on roots of canola seedlings
Authors: Penrose Donna M , Moffatt Barbara A , Glick Bernard R
Published: April 2011

Previously, it was proposed that plant growth-promoting bacteria that possess the enzyme, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, can reduce the amount of ethylene produced by a plant and thereby promote root elongation. To test this model, canola seeds were imbibed in the presence of the chemical ethylene inhibitor, 2-aminoethoxyvinyl glycine (AVG), various strains of plant growth-promoting bacteria, and a psychrophilic bacterium containing an ACC deaminase gene on a broad host range plasmid. The extent of root elongation and levels of ACC, the immediate precursor of ethylene, were measured in the canola seedling roots. A modification of the Waters AccQ*Tag Amino Acid Analysis Method(tm) was used to quantify ACC in the root extracts. It was found that, in the presence of the ethylene inhibitor, AVG, or any one of several ACC deaminase-containing strains of bacteria, the growth of canola seedling roots was enhanced and the ACC levels in these roots were lowered.
Removal of indicator bacteria, human enteric viruses, Giardia cysts, and Cryptosporidium oocysts at a large wastewater primary treatment facility
Authors: Payment Pierre , Plante Robert , Cejka Patrick
Published: April 2011

Pathogens and fecal indicator bacteria occurrence and removal were studied for a period of 6 months at the Montreal Urban Community wastewater treatment facility. With a capacity of about 7.6 million cubic metres per day (two billion U.S. gallons per day), it is the largest primary physico-chemical treatment plant in America. The plant discharges a nondisinfected effluent containing about 20 mg/L of suspended matter and 0.5 mg/L of total phosphorus on the basis of average annual concentrations. BDO5 (annual mean) is 75 mg/L before treatment and 32 mg/L after treatment. Samples were collected for a period of 6 months, and they demonstrated that the plant was not efficient at removing indicator bacteria and the pathogens tested. Fecal coliforms were the most numerous of the indicator bacteria and their removal averaged 25%. Fecal streptococci removal was 29%, while Escherichia coli removal was 12%. In untreated sewage, fecal coliforms, E. coli, and human enteric viruses were more numerous in summer and early autumn. Fecal streptococci counts remained relatively similar throughout the period. Clostridium perfringens removal averaged 51%. Giardia cysts levels were not markedly different throughout the study period, and 76% of the cysts were removed by treatment. Cryptosporidium oocyst counts were erratic, probably due to the methods, and removal was 27%. Human enteric viruses were detected in all samples of raw and treated wastewater with no removal observed (0%). Overall, the plant did not perform well for the removal of fecal indicator bacteria, human enteric viruses, or parasite cysts. Supplementary treatment and disinfection were recommended to protect public health. Various alternatives are being evaluated.
Variability and interactions between endophytic bacteria and fungi isolated from leaf tissues of citrus rootstocks
Authors: Araújo Welington L , Maccheroni Jr. Walter , Aguilar-Vildoso Carlos I , Barroso Paulo AV , Saridakis Halha O , Azevedo João Lúcio
Published: April 2011

Fungi and bacteria were isolated from surface disinfected leaf tissues of several citrus rootstocks. The principal bacterial species isolated were Alcaligenes sp., Bacillus spp. (including B. cereus, B. lentus, B. megaterium, B. pumilus, and B. subtilis), Burkholderia cepacia, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium extorquens, and Pantoea agglomerans, with P. agglomerans and B. pumilus being the most frequently isolated species. The most abundant fungal species were Colletotrichum gloeosporioides, Guignardia citricarpa, and Cladosporium sp. Genetic variability between 36 endophytic bacterial isolates was analysed by the random amplified polymorphic DNA (RAPD) technique, which indicated that B. pumilus isolates were more diverse than P. agglomerans isolates, although genetic diversity was not related to the host plants. In vitro interaction studies between G. citricarpa isolates and the most frequently isolated endophytic bacteria showed that metabolites secreted by G. citricarpa have an inhibitory growth effect on some Bacillus species, and a stimulatory growth effect on P. agglomerans.Key words: endophytes, citrus, fungal-bacterial interaction, RAPD, diversity, Pantoea agglomerans, Bacillus pumilus, Guignardia citricarpa.
Selective isolation and distribution of the genus Planomonospora in soils
Authors: Suzuki Shin-ichi , Okuda Toru , Komatsubara Saburo
Published: April 2011

For the screening of bioactive compounds and study of global distribution, a selective isolation method for Planomonospora strains by centrifugation from soil is examined. Planomonospora strains produced characteristic sporangia on the humic acid-trace salts gellan gum medium (pH 9.0) so that this genus was readily recognized on the isolation plate. High yields of motile spores were obtained by using a flooding solution containing 0.1% skim milk in 5 mM N-cyclohexyl-2-amino-ethanesulfonic acid (pH 9.0) followed by incubating the preparation at 32°C for 90 min, centrifuging it at 1000 × g for 10 min, and further incubation at 32°C for 60 min after centrifugation. By combining the techniques described above, we isolated 246 Planomonospora strains from 137 of the 1200 soil samples examined. Ninety-four percent of these strains were recovered from neutral to slightly alkaline soils (pH 7.0 to 9.0). Strains of P. venezuelensis group were obtained from 13 soil samples (1.1%), which were collected in Bolivia, Cyprus, Egypt, Greece, India, Japan, New Caledonia, and Turkey. Strains of this group appear widely distributed in the soil of tropical to temperate regions. To our knowledge, this is the first record that strains of this group have been isolated from a location other than Venezuela.Key words: Planomonospora, gellan gum, selective isolation, distribution, actinomycete.
Possible involvement ofPseudomonas fluorescensand Bacillaceae in structural modifications ofTuber borchiifruit bodies
Authors: Citterio Barbara , Malatesta Manuela , Battistelli Serafina , Marcheggiani Francesco , Baffone Wally , Saltarelli Roberta , Stocchi Vilberto , Gazzanelli Giancarlo
Published: April 2011

Previous studies on Tuber borchii fruit bodies in early maturation stages suggested a role of bacteria in sporocarp structural modifications. In order to verify this hypothesis, in the present study we investigated by means of microbial and ultrastructural approaches, the bacterial population of T. borchii sporocarps from intermediate maturation phases to advanced decomposition stages, paying particular attention to chitinolytic and cellulolytic bacteria and to their relationships with ascii and ascospores. We found that Pseudomonas fluorescens and spore-forming Bacillaceae, both able to degrade cellulose and chitin, are present inside the sporocarps in all maturation stages investigated. Moreover, rod-shaped bacteria seem able to erode ascus walls and colonize the interior of ascii containing mature spores. These results suggest a possible role of these bacteria in the process of ascus opening. Moreover, the presence of P. fluorescens and Bacillaceae on isolated mature spores after decontamination suggests an intimate association between these bacteria and the ascospores.Key words: bacteria, cellulose, chitin, ectomycorrhiza.
Detection ofLegionella pneumophilain bioaerosols by polymerase chain reaction
Authors: Pascual Leonor , Pérez-Luz Sara , Amo Antonio , Moreno Carmen , Apraiz David , Catalán Vicente
Published: April 2011

Most studies focusing on detecting microorganisms in air by polymerase chain reaction (PCR) have used a liquid impinger to sample bioaerosols, mainly because a liquid sample is easy to be processed by PCR analysis. Nevertheless, the use of multiple-hole impactors for the analysis of bioaerosols by PCR has not been reported despite its great utility in culture analysis. In this study we have modified the impaction onto an agar surface sampling method to impaction onto a liquid medium using the MAS-100 air sampler (Merck) (single-stage multiple-hole impactor). To evaluate the recovery of airborne microorganisms of both sampling methods, a suspension containing Escherichia coli was artificially aerosolized and bioaerosols were collected onto Tergitol-7 agar and phosphate-buffered saline (PBS) with the MAS-100. A linear regression analysis of the results showed a strong positive correlation between both sampling methods (r = 0.99, slope 0.99, and y intercept 0.07). Afterwards, the method of impingement into a liquid medium was used to study airborne Legionella pneumophila by PCR. A total of 64 samples were taken at a wastewater treatment plant, a chemical plant, and an office building and analyzed by culture and PCR. Results showed that three samples were positive both by PCR and plate culture, and that nine samples negative by plate culture were positive by PCR, proving that L. pneumophila was present in bioaerosols from these three different environments. The results demonstrate the utility of this single-stage multiple-hole impactor for sampling bioaerosols, both by culture and by PCR.Key words: Legionella pneumophila, bioaerosols, PCR, multiple-hole impactor.
Comparison of the activity spectra against pathogens of bacterial strains producing a mutacin or a lantibiotic
Authors: Morency Hélène , Mota-Meira Marilaine , LaPointe Gisèle , Lacroix Christophe , Lavoie Marc C
Published: April 2011

The increase of drug resistance among bacterial pathogens is currently a major threat in hospital settings. New and more efficient antibiotic compounds have to be developed to fight infectious diseases. In the present work, a deferred antagonism test was used to determine the activity of different bacterial strains producing either a mutacin or a lantibiotic against bacterial pathogens. The mutacins A, B, C, D, I, K, L, M, and nisins A and Z were active against all enterococci tested. Mutacins A and B, and nisins A and Z inhibited all the staphylococci tested. Except for the strains producing mutacins P, Q, and X, all the other producing strains inhibited the streptococci tested. Mutacins A, B, I, J, T, nisins A and Z, and epidermin inhibited the two antibiotic-resistant strains of Neisseria gonorrhoeae tested. Mutacins A, B, C, D, and nisins A and Z inhibited Campylobacter jejuni and Helicobacter pylori. Thus, the wide activity spectra of nisin A and Z are confirmed. These results also indicate that many of the mutacins, especially those of groups A, B, C, D, I, J, K, L, M, and T, could be candidates for further development as useful antibiotics.Key words: mutacin, lantibiotic, bacteriocin, antibiotic.
Levels of ACC and related compounds in exudate and extracts of canola seeds treated with ACC deaminase-containing plant growth-promoting bacteria
Authors: Penrose Donna M , Glick Bernard R
Published: April 2011

It was previously proposed that plant growth-promoting bacteria that possess 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase could utilize ACC that is present in the exudate of germinating canola seeds. The uptake and cleavage of ACC by these bacteria would lower the level of ACC, and thus ethylene within the plant, and reduce the extent of its inhibition on root elongation. To test part of the above mentioned model, ACC levels were monitored in canola seed tissues and exudate during germination. Lower amounts of ACC were present in the exudate and tissues of seeds treated with the plant growth-promoting bacterium Enterobacter cloacae CAL3, than in control seeds treated with MgSO4. The ACC-related compounds, α- and γ-aminobutyric acids, both known to stimulate ethylene production, were also measured in the canola seed exudate and tissues. Approximately the same levels of α-aminobutyric acid were present in the exudates of the bacterium-treated seeds and the control seeds, but the amount of α-aminobutyric acid was lower in the tissues of the bacterium-treated seeds than in the control seeds. Smaller quantities of γ-aminobutyric acid were seen in both the exudate and tissues of the E. cloacae CAL3-treated seeds than in the control seeds.Key words: ACC ethylene, canola, seed extract, seed exudate, plant growth-promoting bacteria.
Evidence and characterization of a gene cluster required for the production of viscosin, a lipopeptide biosurfactant, by a strain ofPseudomonas fluorescens
Authors: Braun P Gordon , Hildebrand Paul D , Ells Tim C , Kobayashi Donald Y
Published: April 2011

The genetic control of viscosin production was examined in a strain of Pseudomonas fluorescens (PfA7B) that causes broccoli head rot. Viscosin is a potent lipopeptide biosurfactant that enables the bacteria to come into intimate contact with the difficult-to-wet waxy heads of broccoli. Tn5 mutagenesis completely disrupted viscosin production as shown by HPLC analysis of the mutagenized cell lysates. The Vismutants retained their pectolytic capability and were able to decay potato slices. On broccoli, however, the Vismutants caused decay of wounded florets, but the decay failed to spread to adjacent nonwounded florets as had occurred with the wild-type PfA7B. Triparental matings of the Vismutants with their corresponding wild-type clones and the helper Escherichia coli HB101 carrying the mobilization plasmid pPK2013 resulted in three stable viscosin-producing transconjugants that caused typical decay of broccoli tissue. Linkage maps of clones and protein profiles showed that a 25-kb chromosomal DNA region of PfA7B affected the production of three high molecular mass proteins required for viscosin synthesis. These proteins, approximately 218, 215, and 137 kDa in size, likely compose a synthetase complex that assembles the nine amino acid peptide of viscosin and subsequently attaches this to the hydrophobic fatty acid component of the molecule. A probe made from this DNA region hybridized with DNA fragments of other phytopathogenic pseudomonads to varying degrees.Key words: virulence factor, head rot, broccoli.
Rapid detection of Brevibacillus formosus BN53-1 in chicken feces
Authors: Nakada Yuji , Ohta Yoshiyuki
Published: April 2011

Here we describe a rapid method for detecting the hydrogen sulfide-decomposing bacterium Brevibacillus formosus BN531 in chicken feces. The method, which can be adapted to the specific detection of a variety of useful eubacteria, is based on blot hybridization and polymerase chain reaction (PCR), and makes use of the genus or species hypervariable region of eubacterial 16S rDNA. The approximate limit of detection under the conditions we tested was 1.0 × 103 cells in 10 mg of chicken feces.Key words: Brevibacillus, detection methods, PCR, blot hybridization, 16S rDNA.
Comparative strain typing ofRhizobium leguminosarumbv.viciaenatural populations
Authors: Corich Viviana , Giacomini Alessio , Carlot Milena , Simon Reinhard , Tichy Hans-Volker , Squartini Andrea , Nuti Marco P
Published: April 2011

372 natural isolates of Rhizobium leguminosarum bv. viciae, rescued from nodules of pea plants grown in an agricultural field in northern Italy, were analyzed by different methods. Three DNA-based fingerprinting techniques were lined up to compare their relative degree of resolution and possible advantages of each approach. The methods included (i) Eckhardt gel plasmid profiles, (ii) pulsed-field gel electrophoresis (PFGE) of genomic large fragment digests, and (iii) random amplified polymorphic DNA (RAPD) profiles, generated with arbitrary primers. The scheme also involved the isolation of a number of different isolates per nodule to estimate the level of intra-nodular variability. It was therefore possible to evaluate the frequency of double and multiple occupancies, and the proportion of the alternative profiles sharing the same nodule, generally resulting in a numerically dominant, main representative accompanied by a secondary one with a slightly different fingerprint. This finding revealed that the different profiles within a nodule are normally due to bacteria derived from the same single invader following genetic alterations possibly occurred during infection, e.g., by plasmid loss. The analysis of 31 nodules revealed 16 different patterns, representing the most frequently occurring nodulation-proficient isolates of the natural soil examined, five of which were found with frequencies around 15%. The sensitivity of the methods in differentiating isolates was compared. The relatedness of the different natural rhizobial isolates was investigated by densitometrical gel analysis of the fingerprints, allowing a comparison of the results. One of the most interesting conclusions was that the degree of information yielded by the plasmid gel profiling alone, carried out by simple visual inspection without software-aided analyses, was surprisingly high, as it enabled a placement of the isolates, whose accuracy, in terms of relatedness, was subsequently confirmed by each of the two genomic methods.Key words: Rhizobium, fingerprinting, DAF, PFGE, plasmid, Eckhardt gel.
Characterization of soybean bradyrhizobia for which serogroup affinities have not been identified
Authors: Berkum Peter van , Fuhrmann Jeffry J
Published: April 2011

The USDA, ARS National Rhizobium Germplasm Collection contains 143 accessions of slow-growing soybean strains among which there are 17 distinct serological groups. However, 11 strains appear to have no serological affinity with the 17 serogroups. Therefore, we determined whether these strains were diverse and examined their phylogenetic placement. Nine strains formed nitrogen-fixing symbioses with soybean indicating that these accessions were not contaminants. We concluded from results of amplified fragment length polymorphism (AFLP) analysis, using 3 selective primers with 8 strains, that they were genetically dissimilar. Nine strains were examined for their fatty acid composition using fatty acid methyl ester (FAME) derivatives. The FAME results with 5 strains and serotype strains of Bradyrhizobium elkanii were similar, while results with each of the remaining 2 pairs were either similar to the type strain of Bradyrhizobium japonicum (USDA 6) or to USDA 110. Evolutionary history of 9 strains was reconstructed from sequence divergence of a combination of the complete 16S rRNA gene, the internally transcribed spacer region, and about 400 bases of the 5' end of the 23S rRNA gene. Placement of 5 strains was nested within B. elkanii, 2 with USDA 110, and the other 2 with USDA 6. We concluded that soybean isolates that cannot be placed within one of the 17 established serogroups are phenotypically and genetically as diverse as the serotype strains.Key words: bradyrhizobium, phylogeny, soybean, Glycine max, FAME, AFLP.