bluuebunny/crossref_metadata_2025 huggingface dataset:
Restricted Least-Squares Estimates of Age Composition from Length Composition
Authors: Clark W. G.
Published: October 2009

An exploited stock's length distribution over a set of fixed length intervals can be represented as the product of its age distribution vector and a matrix whose columns are the length distributions of the various age-groups. This matrix should be reasonably stable over time, so it can be estimated from age–length sampling done at any time. Then, so long as the number of length intervals exceeds the number of age-groups, a restricted least-squares estimate of the age distribution underlying any sample length distribution can be found with certainty by quadratic programming. For practical work, the advantages of this method over numerical and closed-form alternatives are that the estimates are reproducible and never contain any negative values. A general statistical treatment is impossible owing to the exclusion of negative values and the presence of sampling error in the matrix of estimated age-specific length distributions, but simulation trials show that in commercial fishery assessments least-squares estimates can be obtained that are unbiased and nearly as precise as maximum-likelihood estimates.Key words: age composition, age–length key, linear regression, restricted least-squares, quadratic programming, simulation
Evidence of an Adaptive Basis for Geographic Variation in Body Morphology and Time of Downstream Migration of Juvenile Atlantic Salmon (Salmo salar)
Authors: Riddell Brian E. , Leggett William C.
Published: October 2009

Differences in growth rate, proximate composition, body morphology, and time of downstream migration between two populations inhabiting tributaries of the Miramichi River, New Brunswick, that differed in distance from the head of tide, temperature, and flow velocity were studied. Rocky Brook, located 132.6 km above the head of tide, had lower temperatures and higher average flow velocities than Sabbies River, located 42.5 km above tide. Growth rate and proximate composition were similar between populations, but body morphology and time of downstream migration differed significantly between populations. Individuals from Rocky Brook had more fusiform bodies and larger paired fins than their counterparts in Sabbies River. Rocky Brook fish also left the tributary in the fall rather than in the spring as was the case in Sabbies River. The generality of the flow regime–body morphology relationship observed was tested and confirmed by predicting differences in morphology of juvenile salmon in other rivers based on a knowledge of their flow regimes. It is suggested that early migration by the Rocky Brook fish is related to the higher energetic costs of overwintering in that stream. We hypothesize that the phenotypic similarity in growth rate and proximate composition and geographic variation in body morphology and timing of migration have an adaptive basis.Key words: geographic variation, polygenic traits, population biology, Atlantic salmon, morphology, migration, proximate composition, growth, adaptation
A Model for Responses of Vertebral Numbers in Fish to Environmental Influences During Development
Authors: Lindsey C. C. , Arnason A. N.
Published: October 2009

A model is proposed in which the number of vertebrae formed in an embryo is determined by two independent processes each building up with time. The processes may possibly but not necessarily represent growth and differentiation. Final number is fixed by the level that one process has attained when it is suddenly terminated by arrival of the second process at a critical level. Varying the temperature or other environmental conditions during development can differentially affect the time courses of the two processes and hence alter the numerical outcome. The model, termed "atroposic," is shown to encompass a welter of apparently conflicting published data on vertebral responses of many fish species to different constant temperatures or to single or double temperature changes. It suggests how vertebral numbers may respond strongly and in either direction to temperature perturbations, and how the responses may be extralimitary, and how large responses may be produced by quite brief temperature pulses. Concepts of several temperature-sensitive periods and of shock effects are abandoned. The model is shown to be capable of computerized fit to almost all published data on variation in vertebrae, but to only some on variation in fin-ray number. The atroposic model seems to approximate reality, but the present mathematical form may be only a special case of a more general form yet to be developed.Key words: environmental conditions, meristics, models, temperature responses, vertebrae counts, Salmo trutta, Oryzias latipes, Plecoglossus altivelis
Drug Immobilization of Walrus (Odobenus rosmarus)
Authors: DeMaster Douglas P. , Faro James B. , Estes James A. , Taggart James , Zabel Cindy
Published: October 2009

Five out of nine walrus (Odobenus rosmarus) were successfully immobilized at Round Island, Alaska, in May of 1978 by combinations of phencyclidine hydrochloride and acepromazine hydrochloride. A crossbow was an effective delivery technique. Walruses that had recently hauled out were more suitable for immobilization than well-rested animals. Care was taken to prevent walruses from overheating or suffocating.Key words: walrus, Odobenus rosmarus; immobilization, marine mammal
Estimation of Potential Catches of an Unexploited Stock of Soft-Shell Clam (Mya arenaria) from Length Composition Data
Authors: Brêthes Jean-Claude F. , Desrosiers Gaston
Published: October 2009

We describe a technique, derived from the von Bertalanffy growth curve and from the mortality equation, which allows the estimation of potential catches from an unexploited stock of mollusca on the basis of the population's length composition data. Comparison with results obtained from age composition data shows that both methods give similar values for mortality rates and yields. That technique could be very useful when it is difficult or impossible to obtain systematic age readings.Key words: Mya arenaria, growth, mortality, yield
Metabolic Changes during the Reproductive Migration of Two Sympatric Coregonines,Coregonus artediiandCoregonus clupeaformis
Authors: Guderley Helga , Blier Pierre , Richard Lorraine
Published: October 2009

The reproductive migration from James Bay to the Eastmain River leads to more marked changes in the metabolic organization of the swimming muscle of Coregonus artedii than Coregonus clupeaformis. The glycolytic potential of both red and white muscle decreased significantly during the migration while the aerobic potential increased significantly at the end of the migration in white muscle of C. artedii. This increase in aerobic potential could facilitate the upstream migration of this species. In contrast, C. clupeaformis generally maintained its glycolytic capacity in both red and white muscle and did not increase the aerobic potential of its white muscle at the end of the migration. In both species, hepatic enzyme activities were variable. In liver of C. artedii the gluconeogenic potential, as judged by the ratio of fructose 1,6-bisphosphatase to phosphofructokinase 1 activity, and the transaminases glutamate-pyruvate aminotransferase and glutamate-oxaloacetate aminotransferase, increased during the spawning migration. ¡n C. clupeaformis liver, most enzymes decreased significantly during the migration.
Environmental Factors Regulating the Seaward Migration of European Silver Eels (Anguilla anguilla)
Authors: Vøllestad L. A. , Jonsson B. , Hvidsten N. A. , Næsje T. F. , Haraldstad Ø. , Ruud-Hansen J.
Published: October 2009

We examined the connection between descent of European silver eels (Anguilla anguilla) and water discharge, water temperature, turbidity, photoperiod, light intensity, and moon phase based on 10 yr of field data and field experiments. The eel migration takes place between August and December, and mean water temperature for July–August and mean water discharge for August–October explained 91% of the total variation in the start of the yearly silver eel run. Low mean water temperatures during July–August and high mean water discharge during August–October resulted in an early start of the yearly silver eel run, whereas high mean water temperature and low water discharge gave the opposite effect. There was no significant correlation between the duration of the entire yearly silver eel run and the environmental variables investigated. But the duration of a part of the run, e.g. number of days from 5 to 25% cumulative eel descent, was significantly correlated with mean water temperature and increase in water discharge for the period in question (R2 = 0.84). Maximum silver eel descent was at a water temperature of 9 °C. Few silver eels descended at temperatures below 4 °C or above 18 °C. The migration speed of transplanted silver eels in the River Imsa was correlated with water discharge and water temperature (R2 = 0.88). Water discharge alone explained 85% of the total variation in migration speeds. The recapture rate of silver eels transplanted within the River Imsa was highest at 9 °C and decreased at higher and lower temperatures (R2 = 0.95). Illumination of 20 lx upon the river reduced the descent of silver eels.
Biomass and Production of Fishes in Natural and Channelized Streams
Authors: Portt Cameron B. , Balon Eugene K. , Noakes David L. G.
Published: October 2009

Fish biomass and production were estimated at two channelized and two unchannelized stream sections. Biomass and total and available production were much lower in the channelized sections than in the natural sections. Regressions of the log of production versus the log of initial biomass had slopes significantly different from 1. This is apparently due to changes in age structure which occurred concurrently with changes in biomass. The physical homogeneity of channelized streams provides opportunities for manipulative research.
Habitat Utilization and Behavioral Interaction of Juvenile Atlantic Salmon (Salmo salar) and Rainbow Trout (S. gairdneri) in Tributaries of the White River of Vermont
Authors: Hearn William E. , Kynard Boyd E.
Published: October 2009

Competition for space between stocked juvenile Atlantic salmon, Salmo salar, and wild juvenile rainbow trout, S. gairdneri, was examined in stream channel experiments, a field experiment, and in field habitat surveys. In stream channels providing riffle and pool habitats, species differed in their distribution both as underyearlings (0+) and as yearlings (1+). Yearling salmon occurred more often in stream channel riffles during trials with 1+ rainbow trout than during trials testing only salmon; trout distributions in the channels were unaffected by salmon. In a field experiment conducted to determine if the stocking of 0+ Atlantic salmon causes the displacement of resident 0+ rainbow trout, salmon fry were stocked at a density of 85 per 100 m2. Emigration from the stocked zone and an unstocked control zone were then monitored daily with four weirs. The 0+ salmon had no apparent effect on the rate of movement of resident rainbow trout fry. During summer and fall field surveys, 0+ salmon occupied deeper and swifter water than 0+ rainbow trout; as yearlings these species occupied similar habitats. In late fall, segregation by habitat occurred: Atlantic salmon were primarily in riffles; rainbow trout were primarily in pools. We found no evidence of competition between cohorts of underyearlings; however, the niche shift by 1+ salmon in the stream channels suggested that, at times, juveniles of these species will compete for space.
Retardation and Recovery of Growth in Brook Trout Fry (Salvelinus fontinalis) Exposed for Various Durations to Acidified Water
Authors: Tam W. H. , Payson P. D. , Roy R. J. J.
Published: October 2009

Brook trout fry (Salvelinus fontinalis) were exposed to pH 4.66 for various durations up to 141 d and then returned to neutral water. Growth of test fish was in general significantly lower than that of control fish for exposures up to days 45–78. In four of six groups of acid-treated fish, growth eventually recovered and the growth rates were not different from that of control fish. The results suggested that growth inhibition was induced early in the exposure to sublethally low pH and that recovery in the latter phase of the experiment occurred whether pH remained acidic or was readjusted to neutral.
Nucleotide sequence and transcriptional analysis of the celD β-glucanase gene from Ruminococcus flavefaciens FD-1
Authors: Vercoe Philip E. , Spight Donn H. , White Bryan A.
Published: October 2009

The nucleotide sequence of the celD gene, which encodes endoglucanase and xylanase activity, from Ruminococcus flavefaciens FD-1 was determined. The DNA sequence of celD contains an open reading frame of 1215 nucleotides that encodes a polypeptide of 405 amino acids with a molecular mass of 44 631 Da. The primary amino acid sequence of CelD was screened against the GenBank data base for similar polypeptide sequences and the analysis indicated that CelD has common features with endoglucanases from the family E cellulases. Both hydrophobic cluster and BESTFIT (Genetics Computer Group (University of Wisconsin) package) analyses confirmed this relationship. Pairwise alignments using BESTFIT revealed that CelD was most closely related to endE4 from Thermomonospora fusca over a 160 amino acid window. The histidine, aspartate, and glutamate residues identified as being essential for catalytic activity in family E cellulases are conserved in CelD. A Shine–Dalgamo-like sequence was present 5 base pairs (bp) upstream of the translation start site. Primer extension analysis indicated that different transcription initiation sites are used to initiate transcription of celD in Escherichia coli and R. flavefaciens. In the case of R. flavefaciens the transcription initiation site is at a T residue (nucleotide 273) 16 bp upstream from the translational start site. A region resembling a σ70-like −10 promoter sequence is present upstream from the transcription initiation site but there is no apparent −35 region. In contrast, transcription in E. coli is initiated at a C residue 258 bp upstream from the translational start site and a sequence resembling a σ70-like −10 region is present 5 bp upstream of this residue. Assuming 17 bp is the optimal distance between −10 and −35 sites for σ70 consensus sequences, the −35 region for celD transcription initiation in E. coli would be outside the boundaries of the cloned R. flavefaciens DNA.Key words: endoglucanase, xylanase, DNA sequencing, family E cellulase.
Endophytic bacteria in grapevine
Authors: Bell C. R. , Dickie G. A. , Harvey W. L. G. , Chan J. W. Y. F.
Published: October 2009

The nonfastidious, xylem-inhabiting bacteria from a selection of grape cultivars in Nova Scotia have been examined. The size of this population varied with the method of extraction: 2.65 × 102 to 3.46 × 103/mL xylem sap with vacuum extraction, 3.83 × 103 to 1.31 × 104/g xylem tissue with homogenization, 3.33 × 104 to 9.89 × 104/mL xylem sap with Acridine Orange direct counts. These figures suggest that many endophytic bacteria may be attached to vessel walls and that the majority are fastidious. There was no significant difference in the number of endophytic bacteria found in two grape varieties, Michurinetz and Marechal Foch. There was a significant difference between vineyards. The frequency distribution followed a log normal model. Seventy-eight percent of isolates were Gram negative, with Pseudomonas and Enterobacter being the predominant genera. Only six strains were identified as potential phytopathogens. A comparison of eight hydrolytic exo–enzymes in a subset of endophytic bacteria to those in a random sample of rhizosphere bacteria revealed that the two populations were distinct and that the former possessed less hydrolytic enzyme capacity than the latter. It therefore seems unlikely that this endophytic population gains entry to the xylem symplastically (intracellularly).Key words: endophytic bacteria, grapevine, xylem-inhabiting.
Biotransformation of di-n-butyl phthalate by a psychrotrophicPseudomonas fluoresceins(BGW) isolated from subsurface environment
Authors: Chauret Christian , Mayfield Colin I. , Inniss William E.
Published: October 2009

A psychrotrophic denitrifying Pseudomonas fluorescens was isolated from an unamended subsurface microcosm incubated at 10 °C for 43 days. This pseudomonad transformed di-n-butyl phthalate at 10 °C in a chemically defined medium under both aerobic and anaerobic conditions using NO3−as the terminal electron acceptor. Biotransformation of di-n-butyl phthalate by the pseudomonad appeared to take place only in the stationary and decline phases of growth and was correlated to the amount of biomass. Studies with growth inhibitors and outer membrane permeabilizers suggested that the outer membrane of the cells in the stationary and decline phases was possibly made more permeable to di-n-butyl phthalate, which would explain the biotransformation pattern. Butanol was produced and utilized by cells that transformed di-n-butyl phthalate, implying that the side chains were hydrolyzed by means of an esterase. An esterase was detected by staining after isolation by gel electrophoresis. The esterase was not induced by di-n-butyl phthalate and was present at various stages of growth. The isolated pseudomonad did not grow with phthalic acid as the sole source of carbon, indicating that di-n-butyl phthalate was not mineralized by this bacterium.Key words: biotransformation, di-n-butyl phthalate, psychrotroph, pseudomonad.
Taxonomy and protein fingerprinting of halophilic Vibrio isolates from bivalves of the Ebre delta
Authors: Montilla R. , Viñas M. , Palomar J. , Fusté M. C.
Published: October 2009

A total of 380 isolates of halophilic Vibrio and related bacteria isolated from shellfish bred in the Ebre delta (in northeastern Spain) were studied by biochemical characterization; this allowed the use of numerical taxonomy programs. All but 25 isolates fell into 12 phena. The analysis of whole-cell electrophoretic fingerprints of 100 isolates confirmed the numerical analysis of biochemical and morphological traits.Key words: halophilic Vibrio, aquaculture, protein fingerprint, bivalves.
A comparison of the efficacy of six media for isolating wood-decaying Hymenomycetes
Authors: Johnson Gary C.
Published: October 2009

Six media reported to be useful for isolating Hymenomycetes from decaying wood were compared. Plates containing these media were inoculated with small segments taken from decaying wood collected in the field. Hymenomycetes and other microorganisms that grew from the segments were recorded. A malt extract – potato dextrose agar medium that incorporated benomyl, neomycin, and streptomycin was the most successful at isolating the white or brown rot fungi.Key words: isolation media, Hymenomycetes, Basidiomycotina, wood decay fungi, benomyl.
Effects of vitamin B12 concentration on chemostat cultured Synechococcus sp. strain PCC 7002
Authors: Wilhelm Steven W. , Trick Charles G.
Published: October 2009

The effects of vitamin B12 availability on the physiology of the cyanobacterium Synechococcus sp. strain PCC 7002 were examined in a continuous culture chemostat system. The availability of vitamin B12 within the system was demonstrated to control the cell density and cellular chlorophyll levels under nutrient-limiting conditions. Electron micrographs of vitamin B12 replete and vitamin B12 deficient cyanobacteria indicated that a reduction in vitamin B12 availability induced a loss of thylakoid integrity within the system. Polyacrylamide gel electrophoresis demonstrated that the expression of outer membrane proteins of 95, 70, and 34 kDa was enhanced during vitamin B12 limited growth. Cellular quotients were determined to be a minimum of 256 molecules of vitamin B12/cell to sustain a growth rate of 0.6/day. A comparison with eukaryotic plankton demonstrated that the vitamin B12 requirements of cyanobacteria may be more similar to those of chloroplasts than to those of the entire group of eukaryotic algae.Key words: chemostats, cellular quotients, cyanobacterial physiology, Synechococcus, vitamin B12.
Contractile-tailed bacteriophages adsorb toEscherichia coliO128ab lipopolysaccharide that is altered by large plasmids to provide receptors and lipopolysaccharide heterogeneity within the serogroup
Authors: Kalmokofff M. L. , Bradley D. E.
Published: October 2009

The verotoxigenic Escherichia coli strain H.I.8 (originally O128:B12, now not typeable) contained a ColB+M plasmid and two morphologically identical temperate bacteriophages (HI8A and HI8B). Both phages were O128ab specific, using the lipopolysaccharide O side chains of susceptible clinical isolates as receptors. SDS polyacrylamide gel electrophoresis with silver staining of O128ab lipopolysaccharide revealed four distinct types of ladder with different interband spacings. No specificity was found between ladder type and sensitivity to either phage. One of the numerous large plasmids present in O128ab isolates was found to modify the structure of the lipopolysaccharide O side chains to provide phage receptors.Key words: bacteriophage, plasmid, lipopolysaccharide, O antigen.
Nutrient effects on growth and armentomycin production in cultures of Streptomyces atmentosus
Authors: He Jian-Yong , Vining Leo C. , White Robert L. , Horton Katherine L. , Doull Janice L.
Published: October 2009

A high-performance liquid chromatographic method for the analysis of armentomycin (L-2-amino-4,4-dichlorobutanoic acid) in culture broths was developed and calibrated using DL-2-amino-4,4-dichlorobutanoic acid synthesized in five steps from methyl acrylate, carbon tetrachloride, and sodium azide. Armentomycin was produced optimally (5–10 mM during 8 days' fermentation) by Streptomyces armentosus in media containing starch, lysine, chloride ions, and a low concentration of phosphate. Production was markedly affected by carbon and nitrogen sources: of those tested, starch supported both the highest biomass yield and the highest armentomycin titre; lysine was the best source of nitrogen for growth and for achieving the maximal armentomycin titre. Increasing the concentration of lysine from 40 to 120 mM nitrogen increased armentomycin production, and gave no evidence of nitrogen catabolite repression. Growth and armentomycin biosynthesis increased as the initial concentration of phosphate in media was increased up to 3 mM; further additions of phosphate tended to increase biomass and decrease the armentomycin titre, but the responses were marginal. Chloride ions were absolutely required for armentomycin synthesis, and at their optimal concentration, more than 80% of the chloride ions in the medium were incorporated into the antibiotic. Excess chloride in cultures reduced armentomycin biosynthesis. Neither bromide nor iodide was incorporated; bromide interfered with the biosynthesis of armentomycin, but iodide had no effect. Analysis of fermentation parameters showed that armentomycin biosynthesis paralleled growth and suggested that secondary metabolism was derepressed by a nitrogen-related limitation of the growth rate.Key words: 2-amino-4,4-dichlorobutanoic acid, antibiotic, armentomycin, halide ions, Streptomyces armentosus, secondary metabolism.
Protection against bacteriocin 28b inSerratia matcescensis apparently not related to the expression of an immunity gene
Authors: Viejo Margarita Beatriz , Enfedaque Josefina , Guasch Joan Francesc , Ferrer Santiago , Regué Miguel
Published: October 2009

The gene encoding bacteriocin 28b from Serratia marcescens N28b (bss gene) has been cloned in Escherichia coli and its nucleotide sequence has been determined. The genetic determinants coding for other well-characterized bacteriocins from enterobacteria (colicins) are located in plasmids and they have always been shown to contain a gene responsible for immunity located downstream from the bacteriocin structural gene. In some cases there is another gene located downstream from the immunity gene, which is responsible for bacteriocin release. Analysis of bacteriocin 28b release and the sensitivity to this bacteriocin of E. coli strains harbouring recombinant plasmids containing the bss gene showed that bacteriocin 28b is not released from the cell in these strains and that their phenotypic insensitivity is not associated with any region close to the structural gene. The nucleotide sequence of the region downstream from the bss gene contains two putative open reading frames transcribed in the opposite direction to the bss gene. These open reading frames apparently encode proteins that seem not to be involved in bacteriocin immunity or release. Moreover, a S. marcescens N28b genomic library was screened and no immunity gene was found. Therefore, bacteriocin 28b differs greatly from the bacteriocins from other enterobacteria, and in the following senses it is unique: firstly, the gene encoding bacteriocin 28b seems to be located on the chromosome, and secondly, insensitivity to this bacteriocin in S. marcescens N28b is not associated with the expression of an immunity gene.Key words: bacteriocin, pore-forming colicins, immunity, Serratia marcescens.
Effect of ionophores on denitrification inFlexibacter canadensis
Authors: Wu Qitu , Knowles Roger , Niven Donald F.
Published: October 2009

Denitrification by Flexibacter canadensis was investigated by measuring the production and (or) consumption of nitrite, nitric oxide (NO), and nitrous oxide (N2O) under anaerobic conditions. Carbonyl cyanide m-chlorophenylhydrazone (CCCP), carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP), 2,4-dinitrophenol, and nigericin, but not valinomycin-K+inhibited the production of nitrite and N2O from nitrate by intact cells. However, CCCP, FCCP, 2,4-dinitrophenol, nigericin, and valinomycin-K+did not affect nitrite production from nitrate by cell-free extracts. These results suggest that nitrate transport was dependent on the transmembrane pH gradient but not on the membrane potential. CCCP, FCCP, and nigericin but not 2,4-dinitrophenol and valinomycin-K+caused NO accumulation during the reduction of nitrite, and also inhibited NO consumption and N2O production from nitrite by intact cells. These results preclude an explanation for NO accumulation based on the collapse of the proton motive force by ionophores, and imply that CCCP, FCCP, and nigericin perhaps dissociated a nitrite reductase–nitric oxide reductase complex, and (or) inhibited nitric oxide reductase specifically. 2,4-Dinitrophenol and CCCP did not inhibit the reduction of N2O to dinitrogen. Addition of ≤ 1.16 μM dissolved NO did not affect the production of nitrite from nitrate, or the disappearance of nitrite or N2O. The rate of NO consumption was linear with concentrations of dissolved NO up to 67 nM. Above 67 nM NO, NO consumption was inhibited, suggesting that NO is toxic to nitric oxide reductase.Key words: ionophores, denitrification, nitric oxide, Flexibacter canadensis.
Biocontrol of postharvest diseases of apple usingBacillusspp. isolated from stored apples
Authors: Sholberg P. L. , Marchi A. , Bechard J.
Published: October 2009

Ninety-five bacterial isolates were recovered from 38 of 77 apples that had been stored at 1 °C for 6–7 months. The highest number of bacteria were recovered in nutrient, dextrose, and V8 juice broths, respectively. The bacteria were screened as biocontrol agents on cultivar Red Delicious apples primarily for control of blue mold caused by Penicillium expansum. Three bacteria effective against P. expansum were also tested against Botrytis cinerea for control of gray mold. Ten, four, and five isolates significantly reduced blue mold decay when apples were stored at 5, 10, and 20 °C. Two isolates tested against gray mold decay significantly reduced decay at 5 and 10 °C and one isolate was effective at 20 °C. Thirty-six isolates that had been selected for identification by the Biolog Microstation™ System were Gram positive and contained endospores, and 30 of these were positively identified as Bacillus spp. Further testing of 15 isolates that were effective biocontrol agents identified 7 as Bacillus subtilis on the basis of 15 microbiological tests used for determining species within the genus Bacillus.Key words: endophytic, bacteria, biocontrol, postharvest.
Pattern of polar extension of the cell wall in the fission yeast Schizosaccharomyces pombe
Authors: May J. W. , Mitchison J. M.
Published: October 2009

The indirect fluorescent-antibody technique has been used to establish the pattern of polar extension in the fission yeast Schizosaccharomyces pombe 160 over a complete cell cycle in liquid medium, thus avoiding the possibility of perturbations being introduced by growth on an agar pad, which is the technique used in most other investigations. Nearly all of the cells (about 98%) showed more growth at the old end than at the new end that was formed by cleavage of the septum at the previous division. Importantly, there was no evidence of the abnormal growth pattern (i.e., the significant contribution of new ends to extension) in cells of S. pombe growing on agar pads reported by Miyata et al. (H. Miyata, M. Miyata, and B.F. Johnson. 1986. Can. J. Microbiol. 32: 528–530 and 1990. Can. J. Microbiol. 36: 390–394). In addition, extension over the cycle was inversely related to birth length (cells shorter than the mean at birth tended to produce daughter cells longer than themselves and vice versa), there was a small but significant asymmetry in the position of the septum, and the time of initiation of extension at the new end was estimated at about 0.24 of the cycle.Key words: Schizosaccharomyces pombe, fission yeast, cell-wall extension, end growth, cell cycle.
The effect of light and phosphate concentrations on phosphatase activities of the photosynthetic bacteriumChlorobiumspp.
Authors: Wynne D. , Ben-Dan T. Bergstein
Published: October 2009

Two species of photosynthetic sulphur bacteria, Chlorobium phaeobacteroides and Chlorobium limicola, found growing under different environmental conditions in the Kinneret, were cultured in the laboratory under various orthophosphate (Pi) concentrations and light intensities. Growth was followed using direct ceil counts, protein content, and pigment content. In general, the same growth pattern was shown by all three parameters and the final cell yields of both species were dependent on ambient Pi concentrations. Chlorobium limicola compensated for low light intensities by increasing pigment production. In addition, light (but not apparently the Pi concentration) influenced the lag period of these cells, with a longer lag observed at lower light intensities. Intra- and extra-cellular activities of both acid and alkaline phosphatases were generally detected in both bacterial species. As Pi levels dropped, both the intra- and extra-cellular activities of acid and alkaline phosphatases increased, suggesting that both enzymes were inducible, although the interaction of P and light limitations was often complex. At high Pi concentrations, residual activities of both acid and alkaline phophatases were detected, probably reflecting the activity of constitutive enzymes not involved in P nutrition of the cells. Extracellular acid and alkaline phophatase activities were low and approximately constant at all light levels. Intracellular activities were relatively high and influenced by light, exhibiting saturation kinetics, and suggest that alkaline phosphatase is more sensitive to light than acid phosphatase. At low Pi concentrations, intracellular phosphatase activities were high and approximately constant over the range of light intensities examined, whereas activities of the extracellular enzymes were low but increased at lower light levels.Key words: photosynthetic bacteria, Chlorobium phaeobacteroides, Chlorobium limicola, growth, phosphate concentration, phosphatases.
A full factorial analysis of nine factors influencing in vitro antagonistic screens for potential biocontrol agents
Authors: Dickie G. A. , Bell C. R.
Published: October 2009

The effect of nine factors on the outcome of classic in vitro screens testing the antagonistic action of endophytic bacterial isolates from grape vines against virulent Agrobacterium vitis has been examined. These factors were (i) the strain of A. vitis, (ii) the strain of endophyte, (iii) the growth medium of the pathogen, (iv) the growth medium of the endophyte, (v) the temperature of growth of the pathogen, (vi) the temperature of growth of the endophyte, (vii) the pH of growth of the pathogen, (viii) the pH of growth of the endophyte, and (ix) the medium of the assay plate. Analyses of variance of the full factorial design incorporating main effects and two- and three-way interactions accounted for 66% of the variance. All nine factors had a significant effect on the diameter of inhibition zones (p < 0.001). An examination of the three-way interactions revealed that generalizations were difficult to draw; each target agrobacterium had a specific response to a given antagonistic isolate. It was possible to determine that the growth history of bacterial strains, before they were administered to an assay plate to test for antagonism (especially the composition of the growth medium and the temperature of growth), had a profound effect on the outcome of the test. Generally the more chemically defined media produced less inhibition whereas the lower growth temperature of 15 °C produced more inhibition. These findings could be relevant to in situ inhibitory activity. The method used to conduct the inhibitory screen (order of strain application and the medium of the assay plate) had a profound influence on the results. These influences add to the caution necessary in the use of in vitro antagonistic screens for finding successful biocontrol agents.Key words: in vitro antagonism, endophytic bacteria, grape crown gall disease, biocontrol, screening strategy.
Characterization of the pTFI91 -family replicon of Thiobacillus ferrooxidans plasmids
Authors: Chakravarty Leena , Zupancic Thomas J. , Baker Beth , Kittle Joseph D. , Fry Ilona J. , Tuovinen Olli H.
Published: October 2009

Plasmids found in six strains of Thiobacillus ferrooxidans were mapped and compared in an effort to detect the origin of replication. Four strains yielded an identical 9.8-kb plasmid, pTFI91. Restriction mapping and Southern blot hybridization analysis were used to confirm this finding. Dissimilar plasmids found in two other strains contained a conserved 2.2-kb SacI region common to pTFI91. DNA sequence analysis of this region showed structural features common to bacterial plasmid replicons. A comparison of the pTFI91 origin with those of T. ferrooxidans pTF-FC2 and other broad host range vectors did not show significant homologous DNA sequences. To verify the replication function, a chloramphenicol acetyl transferase marker gene was ligated at the unique sites of pTFI91, and the plasmid was transformed into Escherichia coli DH5α cells but no transformants were identified. To test the replication of pTFI91 independent of DNA polymerase I in E. coli, different restriction fragments of pTFI91 were cloned into pHSG398 (Cmr, ColEI origin) and transformed into the polA1 mutant SF800, but chloramphenicol-resistant transformants were not detected. Electrotransformation of T. ferrooxidans TFI-70 and Pseudomonas putida ATCC 19151 also failed to yield transformants. The results suggested that the pTFI91 plasmid replicon does not function either in E. coli or in P. putida. Since pTFI91 contains the same origin of replication as other plasmids in several other T. ferrooxidans strains, this replicon may be commonly distributed in T. ferrooxidans.Key words: nucleotide sequence, origin of replication, plasmid DNA, replicon, Thiobacillus ferrooxidans.
An unusual rRNA gene organization in Mycoplasma fermentans (incognitus strain)
Authors: Huang Y. , Stemke G. W. , Robertson J. A.
Published: October 2009

The macro-restriction map of Mycoplasma fermentans (incognitus strain) was constructed and its rRNA genes were located on the map. It was found that this organism contains two sets of rRNA genes. The 16S and 23S rRNA genes were closely linked as two clusters. However, both 5S rRNA genes were separated from the 16S and 23S genes. The two 16S–23S rRNA gene clusters were arranged in an unusual tail to tail orientation.Key words: physical map, rRNA, Mycoplasma fermentans, genome, gene organization.
Persistence in soil of the plant growth promoting rhizobacterium Pseudomonas putida GR12-2 and genetically manipulated derived strains
Authors: Tang Weizhen , Pasternak J. J. , Glick Bernard R.
Published: October 2009

Transformation of the plant growth promoting rhizobacterium Pseudomonas putida GR12-2 with broad-host-range vectors can affect the growth of the bacterium, its ability to promote root elongation of canola seedlings under gnotobiotic conditions, and its persistence in soil. Plasmid transformants, and a transposon-mutagenized derivative of P. putida GR12-2, fell into two classes with respect to these three attributes: strains that were clearly diminished in these capabilities and strains that behaved like the nontransformed wild type. These differences can be accounted for by the imposition of a metabolic load that is created by some types of genetic modification that results in a physiological impairment of the modified bacterium and decreases its ability to function as a plant growth promoting rhizobacterium.Key words: plant growth promoting rhizobacteria, PGPR, bacterial fertilizer, soil bacteria, soil persistence, microcosm.
The oxidation of pyrene and benzo[a]pyrene by nonbasidiomycete soil fungi
Authors: Launen Loren , Pinto Linda , Wiebe Christine , Kiehlmann Eberhard , Moore Margo
Published: October 2009

The purpose of this study was to determine the ability of nonbasidiomycete soil fungi to oxidize pyrene (four rings) and benzo[a]pyrene (BaP) (five rings). Fungi were isolated from five different soils in which the polycyclic aromatic hydrocarbon content ranged from 0.8 to 80 μg/g dry soil. Approximately 50% of the isolates in all sites were able to oxidize pyrene. The pyrene-oxidizing species belonged to all fungal divisions except basidiomycetes. The most common were Penicillium spp. of the subgenus Furcatum and these dominated the more contaminated soils. Penicillium janthinellum and Syncephalastrum racemosum exhibited the most rapid rates of pyrene oxidation. The major pyrene metabolites were identified by proton NMR and mass spectrometry as 1-pyrenol, 1,6- and 1,8-pyrenediol, and the 1,6- and 1,8-pyrenequinones. A high correlation was found between the ability to oxidize pyrene and BaP. As with pyrene, approximately 50% of the fungal isolates tested oxidized BaP to 9-hydroxy-BaP. Eighty percent of the pyrene-oxidizing strains were also able to metabolize BaP.Key words: fungi, polycyclic aromatic hydrocarbons, biotransformation, bioremediation, cytochrome P-450.
Stress-related compounds in xylem fluid of blight-diseased citrus containingFusarium solaninaphthazarin toxins and their effects on the host
Authors: Nemec S.
Published: October 2009

Naphthazarin toxins of Fusarium solani were detected and quantified by competitive enzyme-linked immunosorbent assay (ELISA) in xylem fluid of scaffold roots from blight-diseased trees. These toxins alter plant metabolic activity; this study examined their effects on xylem health by measuring physiological components in xylem fluid. Protein concentration in fluid was positively correlated with increases in toxin concentration. In fluid containing about 100 μg∙L−1toxin, total amino acids reached levels 2.5 to 3.0 times greater than those in fluid containing no detectable toxin; asparagine, glutamic acid, proline, glycine, and arginine were the most abundant. Levels of phenylalanine ammonia-lyase, polyphenol oxidase, chlorogenic acid oxidase, and superoxide dismutase activity did not increase in xylem fluid containing toxin, which may be a reason why vascular discoloration did not occur. Xylem fluid containing about 20 μg∙L−1toxin was associated with a 9-fold increase in total phenolics and a 15-fold increase in peroxidase. Peroxidases were predominantly anionic and may function in defense. Some of these peroxidases may function as lignases, releasing phenolic and other constituents from cells and cell walls. These toxins are known to enhance membrane permeability, which may be the main reason for the accumulation of these stress metabolites in xylem fluid. These data explain the disruption of hydraulic conductivity in blight tree roots and the eventual physiological breakdown of roots on diseased trees.Key words: phytotoxins, isomarticin, ELISA, fungi, roots.
A novel procedure for rapid isolation of plant growth promoting pseudomonads
Authors: Glick Bernard R. , Karaturovíc Damir M. , Newell Peter C.
Published: October 2009

A rapid and novel procedure for the isolation of plant growth promoting rhizobacteria (PGPR) is described. This method entails screening soil bacteria for the ability to utilize the compound 1-aminocyclopropane-1-carboxylate (ACC) as a sole N source, a trait that is a consequence of the presence of the activity of the enzyme ACC deaminase. This trait appears to be limited to soil bacteria that are also capable of stimulating plant growth. Seven different soil samples from two geographically disparate locations were found to contain pseudomonads that were able to to utilize ACC as a N source. Each of the seven strains was shown, by the ability of the bacterium to promote canola seedling root elongation under gnotobiotic conditions, to be a PGPR. The method described here may be used to replace the otherwise slow and tedious process of testing individual bacterial strains for their ability to promote plant growth, thereby significantly speeding up the process of finding new PGPR.Key words: plant growth promoting rhizobacteria, PGPR, 1-aminocyclopropane-1-carboxylate, ACC, ACC deaminase, bacterial fertilizer, soil bacteria.
Atypical oxidative stress regulation of a Xanthomonas oryzae pv. oryzae monofunctional catalase
Authors: Chamnongpol Sangpen , Vattanaviboon Paiboon , Loprasert Suvit , Mongkolsuk Skorn
Published: October 2009

Catalase is an important oxidative stress protective enzyme. We have shown in Xanthomonas oryzae pv. oryzae that catalase has atypical regulation in response to stresses and growth conditions. The superoxide generators paraquat and menadione at subinhibitory concentrations for growth were potent inducers (8.3 and 10.4 fold, respectively) of the catalase of X. oryzae pv. oryzae. In contrast, H2O2 under all conditions tested was a poor inducer of catalase. It gave a maximum induction level of 2.4 fold, while ascorbate produced an intermediate level of induction (4.5 fold). Unexpectedly, methyl methanesulphonate, a DNA methylating agent and mutagen, was a potent inducer of catalase (8 fold). Catalase induction required de novo synthesis of the enzyme and aerobic growth but it was independent of growth phase. Catalase induction by superoxide generators and methyl methanesulphonate was due to increasing synthesis of the 80 000 Da monofunctional catalase. Similar patterns of catalase induction by various agents were observed in all Xanthomonas strains tested, except that paraquat did not induce catalase in the strains with high paraquat resistance. The data illustrate novel aspects of catalase regulation in Xanthomonas strains that differ from that in other microbes. This may have important consequences for plant–microbe interactions.Key words: oxidative stress response, catalase regulation, phytopathogen.
The evolution off invasion by enteric bacteria
Authors: Ochman Howard , Groisman Eduardo A.
Published: October 2009

Despite differences in disease pathologies and host range, many enteric pathogens, including Salmonella and Shigella spp., utilize a remarkably similar machinery to secrete proteins that promote their entry into host cells. Analogous structures are required for the export of virulence proteins in other animal and plant pathogens. While the structure and organization of the gene complexes specifying these secretory pathways are broadly conserved, their phylogenetic distribution and genomic locations suggest that these sequences arose independently in divergent pathogens.Key words: pathogenesis, protein transport, bacterial evolution, Salmonella.
Characterization of monoclonal antibodies to Yersinia enterocolitica iron-regulated proteins
Authors: Kooi Cora , Sokol Pamela A.
Published: October 2009

Yersinia enterocolitica 1165 (0:8) expressed several iron-regulated proteins with molecular masses of 240, 194, 80, 79, 70, and 67 kDa. These proteins were not detected in cells grown in iron-rich conditions. Cell surface iodination indicated that the 240- and 190-kDa proteins (HMWPs) were not surface exposed, whereas the 67- and 70-kDa proteins appeared to be exposed to the cell surface. Incubation with iron protected the 67- and 70-kDa proteins from proteinase K treatment, suggesting that they may be involved in iron acquisition. Monoclonal antibodies (MAbs) were produced against the HMWPs and the 67-kDa iron-regulated protein. MAbs to the HMWPs not only recognized the 240- and 194-kDa proteins but also reacted with the 67- and 70-kDa iron-regulated proteins. Similarly, MAbs to the 67-kDa protein reacted with the 67- and 70-kDa proteins and the HMWPs, suggesting that these iron-regulated proteins are related immunologically. In addition, the MAbs recognized the 67- and 70-kDa proteins and HMWPs from other Y. enterocolitica serotypes, suggesting that the antigenic sites recognized on these iron-regulated proteins are conserved. The MAbs examined did not inhibit iron binding or iron uptake and did not provide protection against a Y. enterocolitica 1165 (0:8) infection in a systemic mouse infection model. Although these MAbs were not protective in this model, these iron-regulated proteins may play a role in iron acquisition and virulence, but the MAbs examined are probably not directed against epitopes involved in iron acquisition or virulence.Key words: Yersinia enterocolitica, monoclonal antibodies, iron-regulated proteins.
Repression of motility and flagellin production at 37 °C is stronger inListeria monocytogenesthan in the nonpathogenic speciesListeria innocua
Authors: Kathariou S. , Mizumoto C. , Kanenaka R. , Allen R. D. , Fok A. K.
Published: October 2009

Listeria monocytogenes and Listeria innocua differ markedly in virulence but are indistinguishable by classical taxonomic criteria. Both species are actively motile and produce abundant flagellin at 22 °C. We have found, however, noticeable differences between L. monocytogenes and L. innocua in motility and flagellin production at 37 °C. At this temperature, L. monocytogenes strains were virtually nonmotile and produced little or no detectable flagellin, whereas strains of L. innocua were frequently motile and produced substantial amounts of flagellin. This flagellin was recognized by a Listeria genus-specific monoclonal antibody that also recognized flagellin produced at 22 °C. These results suggest differential regulation of flagellin production between L. monocytogenes and L. innocua at 37 °C.Key words: Listeria monocytogenes, Listeria innocua, flagellin, motility, temperature, pathogenesis.