bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Statistical Approaches to Evaluate Factors Associated With Metabolic Syndrome
Authors: Fekedulegn Desta , Andrew Michael , Violanti John , Hartley Tara , Charles Luenda , Burchfiel Cecil
Published: February 2010

J Clin Hypertens (Greenwich).

In statistical analyses, metabolic syndrome as a dependent variable is often utilized in a binary form (presence/absence) where the logistic regression model is used to estimate the odds ratio as the measure of association between health‐related factors and metabolic syndrome. Since metabolic syndrome is a common outcome the interpretation of odds ratio as an approximation to prevalence or risk ratio is questionable as it may overestimate its intended target. In addition, dichotomizing a variable that could potentially be treated as discrete may lead to reduced statistical power. In this paper, the authors treat metabolic syndrome as a discrete outcome by defining it as the count of syndrome components. The goal of this study is to evaluate the usefulness of alternative generalized linear models for analysis of metabolic syndrome as a count outcome and compare the results with models that utilize the binary form. Empirical data were used to examine the association between depression and metabolic syndrome. Measures of association were calculated using two approaches; models that treat metabolic syndrome as a binary outcome (the logistic, log‐binomial, Poisson, and the modified Poisson regression) and models that utilize metabolic syndrome as discrete/count data (the Poisson and the negative binomial regression). The method that treats metabolic syndrome as a count outcome (Poisson/negative binomial regression model) appears more sensitive in that it is better able to detect associations and hence can serve as an alternative to analyze metabolic syndrome as count dependent variable and provide an interpretable measure of association.
Rearticulating the myth of human–wildlife conflict
Authors: Peterson M. Nils , Birckhead Jessie L. , Leong Kirsten , Peterson Markus J. , Peterson Tarla Rai
Published: February 2010

Human–wildlife conflict has emerged as the central vocabulary for cases requiring balance between resource demands of humans and wildlife. This phrase is problematic because, given traditional definitions of conflict, it positions wildlife as conscious human antagonists. We used content analysis of wildlife conservation publications and professional meeting presentations to explore the use of the phrase, human–wildlife conflict, and compared competing models explaining its usage. Of the 422 publications and presentations using human–wildlife conflict, only 1 reflected a traditional definition of conflict, >95% referred to reports of animal damage to entities human care about, and <4% referred to human–human conflict. Usage of human–wildlife conflict was related to species type (herbivores with human food, carnivores with human safety, meso‐mammals with property), development level of the nation where the study occurred (less developed nations with human food and more developed nations with human safety and property damage), and whether the study occurred on private lands or protected areas (protected areas with human–human conflict and other areas with property damage). We argue that the phrase, human–wildlife conflict, is detrimental to coexistence between humans and wildlife, and suggest comic reframing to facilitate a more productive interpretation of human–wildlife relationships.
Optimal conservation planning for migratory animals: integrating demographic information across seasons
Authors: Sheehy Justin , Taylor Caz M. , McCann Kevin S. , Norris D. Ryan
Published: February 2010

Conservation strategies for migratory animals are typically based on ad‐hoc or simple ranking methods and focus on a single period of the annual cycle. We use a density‐dependent population model to examine one‐time land purchase strategies for a migratory population with a breeding and wintering grounds. Under equal rates of habitat loss, we show that it is optimal to invest more, but never solely, in the habitat with the higher density dependence to habitat cost ratio. When there are two habitats that vary in quality within a season, the best strategy is to invest only in one habitat. Whether to purchase high‐ or low‐quality habitat depends on the general life history of the species and the ratio of habitat quality to habitat cost. When carry‐over effects are incorporated, it is almost always optimal to invest in high‐quality habitat during the season that produces the carry‐over effect. We apply this model to a threatened warbler population and show the optimal strategy is to purchase more breeding than wintering habitat despite the fact that breeding habitat is over ten times more expensive. Our model provides a framework for developing year‐round conservation strategies for migratory animals and has important implications for long‐term planning and management.
Signaling Stop from the Inside
Authors: Gough Nancy R.
Published: February 2010

A fragment specific to Nogo-A is internalized to trigger growth cone collapse.
Cellular Plasticity
Authors: Foley John F.
Published: February 2010

T helper 2 (T
H
2) cells can be induced to adopt both T
H
1 and T
H
2 phenotypes in the context of viral infection.
Effecting Entry
Authors: Adler Elizabeth M.
Published: February 2010

Anthrax toxin stimulates intracellular signaling events to facilitate its entry into the target cell.
Transcriptional Regulation of Chitin Synthases by Calcineurin Controls Paradoxical Growth of
Aspergillus fumigatus
in Response to Caspofungin
Authors: Fortwendel Jarrod R. , Juvvadi Praveen R. , Perfect B. Zachary , Rogg Luise E. , Perfect John R. , Steinbach William J.
Published: February 2010

Attenuated activity of echinocandin antifungals at high concentrations, known as the “paradoxical effect,” is a well-established phenomenon in
Candida albicans
and
Aspergillus fumigatus
. In the yeast
C. albicans
, upregulation of chitin biosynthesis via the protein kinase C (PKC), high-osmolarity glycerol response (HOG), and Ca
2+
/calcineurin signaling pathways is an important cell wall stress response that permits growth in the presence of high concentrations of echinocandins. However, nothing is known of the molecular mechanisms regulating the mold
A. fumigatus
and its paradoxical response to echinocandins. Here, we show that the laboratory strain of
A. fumigatus
and five of seven clinical
A. fumigatus
isolates tested display various magnitudes of paradoxical growth in response to caspofungin. Interestingly, none of the eight strains showed paradoxical growth in the presence of micafungin or anidulafungin. Treatment of the Δ
cnaA
and Δ
crzA
strains, harboring gene deletions of the calcineurin A subunit and the calcineurin-dependent transcription factor, respectively, with high concentrations of caspofungin revealed that the
A. fumigatus
paradoxical effect is calcineurin pathway dependent. Exploring a molecular role for CnaA in the compensatory chitin biosynthetic response, we found that caspofungin treatment resulted in increased chitin synthase gene expression, leading to a calcineurin-dependent increase in chitin synthase activity. Taken together, our data suggest a mechanistic role for
A. fumigatus
calcineurin signaling in the chitin biosynthetic response observed during paradoxical growth in the presence of high-dose caspofungin treatment.
Evaluation by Data Mining Techniques of Fluconazole Breakpoints Established by the Clinical and Laboratory Standards Institute (CLSI) and Comparison with Those of the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
Authors: Cuesta Isabel , Bielza Concha , Cuenca-Estrella Manuel , Larrañaga Pedro , Rodríguez-Tudela Juan L.
Published: February 2010

The EUCAST and the CLSI have established different breakpoints for fluconazole and
Candida
spp. However, the reference methodologies employed to obtain the MICs provide similar results. The aim of this work was to apply supervised classification algorithms to analyze the clinical data used by the CLSI to establish fluconazole breakpoints for
Candida
infections and to compare these data with the results obtained with the data set used to set up EUCAST fluconazole breakpoints, where the MIC for detecting failures was >4 mg/liter, with a sensitivity of 87%, a false-positive rate of 8%, and an area under the receiver operating characteristic (ROC) curve of 0.89. Five supervised classifiers (J48 and CART decision trees, the OneR decision rule, the naïve Bayes classifier, and simple logistic regression) were used to analyze the original cohort of patients (Rex's data set), which was used to establish CLSI breakpoints, and a later cohort of candidemia (Clancy's data set), with which CLSI breakpoints were validated. The target variable was the outcome of the infections, and the predictor variable was the MIC or dose/MIC ratio. For Rex's data set, the MIC detecting failures was >8 mg/liter, and for Clancy's data set, the MIC detecting failures was >4 mg/liter, in close agreement with the EUCAST breakpoint (MIC > 4 mg/liter). The sensitivities, false-positive rates, and areas under the ROC curve obtained by means of CART, the algorithm with the best statistical results, were 52%, 18%, and 0.7, respectively, for Rex's data set and 65%, 6%, and 0.72, respectively, for Clancy's data set. In addition, the correlation between outcome and dose/MIC ratio was analyzed for Clancy's data set, where a dose/MIC ratio of >75 was associated with successes, with a sensitivity of 93%, a false-positive rate of 29%, and an area under the ROC curve of 0.83. This dose/MIC ratio of >75 was identical to that found for the cohorts used by EUCAST to establish their breakpoints (a dose/MIC ratio of >75, with a sensitivity of 91%, a false-positive rate of 10%, and an area under the ROC curve of 0.90).
Testing the Efficacy and Toxicity of Adenylyl Cyclase Inhibitors against Enteric Pathogens Using
In Vitro
and
In Vivo
Models of Infection
Authors: Moen Scott T. , Blumentritt Carla A. , Slater Terry M. , Patel Shilpa D. , Tutt Christopher B. , Estrella-Jimenez Maria E. , Pawlik Jennifer , Sower Laurie , Popov Vsevolod L. , Schein Catherine H. , Gilbertson Scott R. , Peterson Johnny W. , Torres Alfredo G.
Published: February 2010

Enterotoxigenic
Escherichia coli
(ETEC) produces the ADP-ribosyltransferase toxin known as heat-labile enterotoxin (LT). In addition to the toxic effect of LT resulting in increases of cyclic AMP (cAMP) and disturbance of cellular metabolic processes, this toxin promotes bacterial adherence to intestinal epithelial cells (A. M. Johnson, R. S. Kaushik, D. H. Francis, J. M. Fleckenstein, and P. R. Hardwidge, J. Bacteriol. 191:178-186, 2009). Therefore, we hypothesized that the identification of a compound that inhibits the activity of the toxin would have a suppressive effect on the ETEC colonization capabilities. Using
in vivo
and
in vitro
approaches, we present evidence demonstrating that a fluorenone-based compound, DC5, which inhibits the accumulation of cAMP in intoxicated cultured cells, significantly decreases the colonization abilities of adenylyl cyclase toxin-producing bacteria, such as ETEC. These findings established that DC5 is a potent inhibitor both of toxin-induced cAMP accumulation and of ETEC adherence to epithelial cells. Thus, DC5 may be a promising compound for treatment of diarrhea caused by ETEC and other adenylyl cyclase toxin-producing bacteria.
Bacterial Guanine Nucleotide Exchange Factors SopE-Like and WxxxE Effectors
Authors: Bulgin Richard , Raymond Benoit , Garnett James A. , Frankel Gad , Crepin Valerie F. , Berger Cedric N. , Arbeloa Ana
Published: February 2010

Subversion of Rho family small GTPases, which control actin dynamics, is a common infection strategy used by bacterial pathogens. In particular,Salmonella entericaserovar Typhimurium,Shigella flexneri, enteropathogenicEscherichia coli(EPEC), and enterohemorrhagicEscherichia coli(EHEC) translocate type III secretion system (T3SS) effector proteins to modulate the Rho GTPases RhoA, Cdc42, and Rac1, which trigger formation of stress fibers, filopodia, and lamellipodia/ruffles, respectively. TheSalmonellaeffector SopE is a guanine nucleotide exchange factor (GEF) that activates Rac1 and Cdc42, which induce “the trigger mechanism of cell entry.” Based on a conserved Trp-xxx-Glu motif, the T3SS effector proteins IpgB1 and IpgB2 ofShigella, SifA and SifB ofSalmonella, and Map of EPEC and EHEC were grouped together into a WxxxE family; recent studies identified the T3SS EPEC and EHEC effectors EspM and EspT as new family members. Recent structural and functional studies have shown that representatives of the WxxxE effectors share with SopE a 3-D fold and GEF activity. In this minireview, we summarize contemporary findings related to the SopE and WxxxE GEFs in the context of their role in subverting general host cell signaling pathways and infection.
Expression of the BabA Adhesin during Experimental Infection with
Helicobacter pylori
Authors: Styer Cathy M. , Hansen Lori M. , Cooke Cara L. , Gundersen Amy M. , Choi Sung Sook , Berg Douglas E. , Benghezal Mohammed , Marshall Barry J. , Peek Richard M. , Borén Thomas , Solnick Jay V.
Published: February 2010

The
Helicobacter pylori babA
gene encodes an outer membrane protein that mediates binding to fucosylated ABH antigens of the ABO blood group. We recently demonstrated that BabA expression is lost during experimental infection of rhesus macaques with
H. pylori
J166. We sought to test the generality of this observation by comparison of different
H. pylori
strains and different animal hosts. Challenge of macaques with
H. pylori
J99 yielded output strains that lost BabA expression, either by selection and then expansion of a subpopulation of J99 that had a single-base-pair mutation that encoded a stop codon or by gene conversion of
babA
with a duplicate copy of
babB
, a paralog of unknown function. Challenge of mice with
H. pylori
J166, which unlike J99, has 5′ CT repeats in
babA
, resulted in loss of BabA expression due to phase variation. In the gerbil, Leb binding was lost by replacement of the
babA
gene that encoded Leb binding with a nonbinding allele that differed at six amino acid residues. Complementation experiments confirmed that change in these six amino acids of BabA was sufficient to eliminate binding to Leb and to gastric tissue. These results demonstrate that BabA expression
in vivo
is highly dynamic, and the findings implicate specific amino acid residues as critical for binding to fucosylated ABH antigens. We hypothesize that modification of BabA expression during
H. pylori
infection is a mechanism to adapt to changing conditions of inflammation and glycan expression at the epithelial surface.
Vibrio choleraePhosphoenolpyruvate Phosphotransferase System Control of Carbohydrate Transport, Biofilm Formation, and Colonization of the Germfree Mouse Intestine
Authors: Houot Laetitia , Chang Sarah , Absalon Cedric , Watnick Paula I.
Published: February 2010

The bacterial phosphoenolpyruvate phosphotransferase system (PTS) is a highly conserved phosphotransfer cascade whose components modulate many cellular functions in response to carbohydrate availability. Here, we further elucidate PTS control ofVibrio choleraecarbohydrate transport and activation of biofilm formation on abiotic surfaces. We then define the role of the PTS inV. choleraecolonization of the adult germfree mouse intestine. We report thatV. choleraecolonizes both the small and large intestines of the mouse in a distribution that does not change over the course of a month-long experiment. BecauseV. choleraepossesses many PTS-independent carbohydrate transporters, the PTS is not essential for bacterial growthin vitro. However, we find that the PTS is essential for colonization of the germfree adult mouse intestine and that this requirement is independent of PTS regulation of biofilm formation. Therefore, competition for PTS substrates may be a dominant force in the success ofV. choleraeas an intestinal pathogen. Because the PTS plays a role in colonization of environmental surfaces and the mammalian intestine, we propose that it may be essential to successful transit ofV. choleraethrough its life cycle of pathogenesis and environmental persistence.
Cytotoxicity and insecticidal activity of endophytic fungi from black spruce (Picea mariana) needles
Authors: Johnson J. A. , Whitney N. J.
Published: February 2010

Hyphae and hyphal extracts from fungi isolated from inside healthy black spruce needles were assayed for their effect on spruce budworm (Choristoneura fumiferana Clem.) cell cultures and larvae. Isolates were from needles of four age-classes (current –3 years old) collected throughout a 4-month sampling period. Hyphal extracts from 21 of the 100 isolates tested were toxic to spruce budworm cell cultures and isolates from older needles (2 and 3 years old) negatively affected cells more frequently (p < 0.05) than isolates from younger needles (current and 1 year old). Hyphae from five isolates and hyphal extracts from seven increased mortality (p < 0.05) when fed to second instar larvae in a laboratory bioassay. Development was delayed and larval dry mass reduced when budworm were fed hyphae from Cryptocline abietina Petrak (isolate number 69). Larval dry mass was reduced when budworm were fed the extract from Aureobasidium pullulons (de Bary) Am. (isolate 87) but increased when fed Cryptocline abietina (isolates 40 and 80), a coelomycete (isolate 12), and Hormonema dematioides (isolates 28, 63, and 96).Key words: endophytic fungi, budworm, Choristoneura fumiferana, Picea mariana, toxicity.
Production and characterization of monoclonal antibodies to the sapstaining fungus Ophiostoma piceae
Authors: Banerjee Srabani , Little Judy , Chan Maria , Luck Brian T. , Breuil Colette , Brown David L.
Published: February 2010

A sensitive immunological tool has been developed to detect the sapstaining fungus Ophiostoma piceae 3871, which plagues the wood industry. Monoclonal antibodies (1F3(1), 4G3(14), 4G2(4), and 2B6(24)) produced against cell wall protein extracts of this fungus were specific. Specificity was estimated by enzyme linked immunosorbent assay, western blotting, and light and electron microscopy using the immunogold technique. Electron microscopy revealed gold particles localized on the outer surface of the cell wall. When screened against 24 biological control fungi the antibodies showed pratically no cross-reactivity (< 4%). When tested against 19 other staining fungi, the antibodies recognized three strains of Ophiostoma piceae, 1F3(1) recognized Phialophora botulispora, and the antibodies showed less than 5% reactivity with the other fungi. Chemical and enzymatic modification of the antigen revealed that the epitopes recognized by the monoclonal antibodies were glycospecific. Although the antibodies were produced against the cell wall protein extracts of the fungus grown in liquid culture, they also recognized the fungus growing in wood and therefore can be employed to investigate wood colonization by this fungus.Key words: Ophiostoma piceae, monoclonal antibodies, glycoprotein.
Biochemical and physiological characteristics of Yarrowia lipolytica strains in relation to isolation source
Authors: Sinigaglia Milena , Lanciotti Rosalba , Guerzonil Maria Elisabetta
Published: February 2010

The physiological characteristics and fatty acid composition of 40 strains of Yarrowia lipolytica isolated from irradiated poultry meat, commercial chilled foods, the superficial water of lagoons of an Italian river delta, and commercial light butter were compared. Discriminant analysis of the results permitted the 40 strains to be classified into four groups according to their isolation source. The lag phase length at 3, 5, and 7 °C, the proteolytic and lipolytic activities, and the growth on sorbitol, gluconate, and N-acetylglucosamine, as well as the relative percentages of C12:0, C15:0, C17:1, C18:1, C18:2, the unsaturation level, and the percentage of total odd chain fatty acids were the characteristics exhibiting the highest discriminatory power. These results indicate that the isolates are well adapted and significant biochemical characteristics may account for the success of individual strains in their original habitat.Key words: Yarrowia lipolytica, fatty acid composition, discriminant analysis.
Molecular analysis of archaeal flagellins: similarity to the type IV pilin – transport superfamily widespread in bacteria
Authors: Faguy David M. , Jarrell Ken F. , Kuzio John , Kalmokoff Martin L.
Published: February 2010

Ultrastructural, biochemical and genetic evidence has shown that the flagella and flagellin proteins from members of the archaea are distinct from their bacterial counterparts. The most important evidence is the sequence dissimilarity between archaeal and bacterial flagellins. We report here similarity between archaeal flagellins and members of the bacterial type IV pilin – transport superfamily. In addition to sequence similarity, the archaeal flagellins and the type IV pilin – transport superfamily share an unusual signal sequence cleavage site and may have functional parallels. This relationship has important implications for the assembly and biogenesis of archaeal flagella.Key words: flagellin, type IV pilin, homology, general secretion proteins, archaea.
The surface structure of Leptotrichia buccalis
Authors: Smith S. H. , Murray R. G. E. , Hall M.
Published: February 2010

Leptotrichia buccalis shows a mosaic of surface structure on its outer membrane consisting of curved ridges 35 nm high and 22 nm apart, and erect on that surface. Fimbriae (common pili) are not present and nor is an S layer. The flap-like ridges consist of strings of macromolecules radiating from the cell surface. This ridge structure is not soluble in any of the usual chaotropes and can only be released when the outer membrane has been damaged or dispersed by extracting envelope preparations with 0.5% SDS at room temperature. The ridge is then found to be attached firmly to the peptidoglycan sacculus, which may be the point of origin of the structure. When so prepared the macromolecules forming the ridge can be removed from the sacculus by treatment with 6 M guanidine HCl, and SDS-PAGE analysis of the extract reveals a 210-kDa polypeptide as a major component and a 15-kDa minor component. The latter is probably a peptidoglycan-associated protein and much of it remains with the sacculus. Each string forming the ridge is of a volume consistent with being made of three elongated 210-kDa molecules, which are united in series by strong hydrophobic association and laterally with neighboring strings by slightly weaker forces. We confirm that L. buccalis causes haemagglutination and the bacteria are known to attach to various tissue cells. Human group A red blood corpuscles remove both of the proteins from solution, which supports the hypothesis that the ridges are adhesin structures. It is likely but not proven that the 210-kDa molecule is the adhesin.Key words: Leptotrichia buccalis, cell wall, S layer, protein array, adhesin.
Some characteristics of extracellular proteases produced by members of the Chytridiales and the Spizellomycetales (Chytridiomycetes)
Authors: Krarup Thomas , Olson Lauritz W. , Heldt-Hansen Hans Peter
Published: February 2010

The extracellular proteolytic enzymes of eight saprophytic, eucarpic, and monocentric isolates from two genera of the order Spizellomycetales and from one genus of the order Chytridiales (Chytridiomycetes) have been partially characterized. The isolectric points of the proteases were estimated from zymograms and demonstrate the existence of three types of proteolytic activity in most isolates. The proteases were tested against synthetic chromogenic peptide substrates and a selection of cations and more complex compounds, and the results suggest that parts of the extracellular proteolytic activities are due to proteases from two groups: the Ca2+ stabilized proteases and the alkaline serine proteases.Key words: serine proteases, metalloproteases, Chytridiomycetes, isoelectric focusing, chromogenic peptide substrates.
Relationship between in vitro growth inhibition of pathogens and suppression of preemergence damping-off and postemergence root rot of white bean seedlings in the greenhouse by bacteria
Authors: Reddy M. S. , Hynes R. K. , Lazarovits G.
Published: February 2010

One hundred and twenty diverse bacterial strains were screened under greenhouse conditions for their ability to protect white bean seedlings from preemergence damping-off caused by Pythium ultimum and Rhizoctonia solani and postemergence root rot by Fusarium solani f.sp. phaseoli. Preemergence mortality or root rot increased with an increase in the inoculum concentration of fungal isolates. For further testing, 200 propagules/g soil of P. ultimum, 3 propagules/g soil of R. solani, and log 3 conidia/g vermiculite of F. solani f.sp. phaseoli were used, as these rates provided an optimal level (approximately 50%) of disease severity. Bacterial strains suspended in sterile distilled water were added to pathogen-amended soil or vermiculite at log 7 colony-forming units/g soil or vermiculite prior to seeding. Final healthy stand and root rot were recorded 4 weeks after planting. Nine bacterial strains on P. ultimum, five on R. solani, and nine on F. solani f.sp. phaseoli provided significant (P = 0.05) suppression of disease severity compared with the nonbacterized control. Bacterial strains were also tested in vitro against the mycelial growth of the fungi on solid and liquid media. There was no relationship between the ability of bacterial strains to inhibit fungal vegetative growth on solid culture media and their ability to suppress pathogen activity in the greenhouse, but, for a few strains, the reduction in disease was linked to reduced growth of the pathogens in liquid media.Key words: White bean, damping-off, root rot, Pythium ultimum, Rhizoctonia solani, Fusarium solani f.sp. phaseoli.
Survival and recovery of Aeromonas hydrophila in water: development of methodology for testing bottled water in Canada
Authors: Warburton Donald W. , McCormick John K. , Bowen Bruce
Published: February 2010

Proposed changes to the Regulations for bottled water in the Food and Drugs Act of Canada include criteria for Aeromonas hydrophila (0 colony-forming units/100 mL water). The development of the methodology used to support these proposed Regulations and the survival of A. hydrophila in inoculated water are described. The methodology used in the isolation of A. hydrophila includes the use of hydrophobic grid membrane filters (HGMF), a resuscitation step on tryptic soy agar, and selective plating on membrane–Aeromonas–trehalose agar and Aeromonas medium. Aeromonas hydrophila proliferated and survived in inoculated water for up to 60 days or longer depending on the other contaminating bacteria. The presence of Pseudomonas aeruginosa enhanced the survival of A. hydrophila and enabled this bacteria to survive for more than 60 days.Key words: Aeromonas hydrophila, bottled water, methodology, survival, recovery.
Interaction of mutants of Xenorhabdus nematophilus (Enterobacteriaceae) with antibacterial systems of Galleria mellonella larvae (Insecta: Pyralidae)
Authors: Dunphy Gary B.
Published: February 2010

Xenorhabdus nematophilus mutants that took longer to kill insects than did the wild type were used to determine the relationship of the physicochemical properties and outer membrane composition to bacterial interaction with the antibacterial systems of Galleria mellonella larvae and to bacterial virulence. Insect serum slowed the growth of the wild-type and mutant bacteria. This was attributed to increased spheroplast formation for the mutants. Spheroplast formation was associated with an increased sensitivity to insect lysozyme and a reduction in overall bacterial cationic charge. Increasing bacterial hydrophobicity was correlated with both increased bacterial attachment to the insect's haemocytes and the accelerated removal of the bacteria from the haemolymph. Attachment of the mutants to the insect haemocytes also increased as the bacterial lipopolysaccharide content increased, the level of prophenoloxidase activation increased, and cationic charge declined. Bacterial emergence into the haemolymph occurred in parallel with haemocyte damage but neither the total lipopolysaccharide levels in the bacteria nor the rate of bacterial emergence were associated with virulence. The rate of lipopolysaccharide release into the haemolymph influenced the rate of haemocyte damage. The contribution of outer membrane proteins to lipopolysaccharide release, bacterial adhesion to haemocytes, and virulence is discussed. Virulence reflects bacterial tolerance to the host's antibacterial defences, favouring an increase in bacteria and toxic lipopolysaccharides.Key words: Xenorhabdus, antibacterial systems, insects.
Degradability of chlorine-free bleachery effluent lignins by two fungi: effects on lignin subunit type and on polymer molecular weight
Authors: Bergbauer Matthias , Eggert Claudia
Published: February 2010

A bleachery effluent from a sulfite process pulp mill, which was extracted with alkali and treated with oxygen and hydrogen peroxide (EOP), was treated with two fungi, Trametes versicolor and Stagonospora gigaspora. Trametes versicolor did not cause any depolymerization or degradation of effluent lignins but increased the amount of chromophores, whereas S. gigaspora depolymerized the EOP lignins and caused a substantial reduction in aromatic compounds. For both fungal treatments, CuO oxidation caused a decrease in the yield of the aldehydes within the vanillyl and p-hydroxy phenol families, which was faster than the rates of decrease in the yields of the corresponding acids and ketones. However, only S. gigaspora caused changes in the pattern of the 11 characteristic lignin phenols produced by CuO oxidation, reflecting a preferential metabolism of some phenolic precursors. This fungus decreased the yield of total vanillyl phenols (V), which contributed the bulk of the 11 lignin oxidation products, from 93% initially to 59%. As a consequence, coumaryl (C), syringyl (S), and p-hydroxy phenols (P) became relatively enriched to 1.2, 6.5, and 33%, respectively. The stability of EOP-lignin constituent subunits is S > P > C > V. The two fungi differed significantly in their level of enzyme activities. In effluent-free medium, the ratio of laccase to peroxidase was higher for T. versicolor than for S. gigaspora. The presence of EOP-lignins significantly increased this ratio. No lignin peroxidase was detected but manganese peroxidase and laccase were detected during degradation activities.Key words: lignin phenols, CuO oxidation, laccase, manganese peroxidase, Trametes versicolor, Stagonospora gigaspora
Physicochemical characteristics of the mineral-forming S-layer from the cyanobacterium Synechococcus strain GL24
Authors: Schultze-Lam Susanne , Beveridge Terry J.
Published: February 2010

The hexagonal S-layer from the unicellular cyanobacterium Synechococcus strain GL24 can act as a template for sulfate and carbonate mineral formation by providing regularly spaced, chemically identical nucleation sites. This novel ability is a reflection of the S-layer's chemistry in addition to its structure. Few, if any, other cyanobacterial S-layers have been subjected to detailed chemical analysis and no other reports of the involvement of an S-layer in mineral formation can be found. We have investigated the surface charge and chemical characteristics of the Synechococcus strain GL24 S-layer in an attempt to unravel the mechanism(s) of mineral formation on this proteinaceous surface layer. The constituent proteins of the S-layer show up as two bands (Mr = 109 000 and 104 000) on SDS-PAGE gels. When assembled, the S-layer confers a net neutral charge on the cell surface with negatively charged sites (which can bind cations) exposed in the large holes of the array. Treatment of whole cells with a wide range of chemical agents failed to disrupt intralayer bonding and binding of the S-layer to the underlying outer membrane, indicating that this is a remarkably resilient S-layer in comparison to those found on other bacteria.Key words: S-layer, cyanobacteria, chemistry, carbonate minerals.
Hydrophobic cell wall protein glycosylation by the pathogenic fungus Candida albicans
Authors: Hazen Kevin C. , Glee Pati M.
Published: February 2010

Cell surface hydrophobicity influences adhesion and virulence of the opportunistic fungal pathogen Candida albicans. Previous studies have shown that cell surface hydrophobicity is due to specific proteins that are exposed on hydrophobic cells but are masked by long fibrils on hydrophilic cells. This observation suggests that hydrophobic cell wall proteins may contain little or no mannosylation. In the present study, the glycosylation levels of three hydrophobic cell wall proteins (molecular mass range between 36 and 40 kDa) derived from yeast cells were examined. One hydrophilic protein (90 kDa) was also tested. Various endoglycosidases (endoglycosidase F – N-glycosidase F, O-glycosidase, β-mannosidase, N-glycosidase F), an exoglycosidase (α-mannosidase), and trifluoromethane sulfonic acid were used to deglycosylate the proteins. All four proteins were reactive to the lectin concanavalin A, demonstrating that they were mannoproteins. However, gel electrophoresis of the control and treated proteins revealed that mannosyl groups of hydrophobic proteins were less than 2 kDa in size, while the mannosyl group of the hydrophilic protein had a molecular mass of approximately 20 kDa. These results suggest that unlike many hydrophilic proteins, hydrophobic proteins may have low levels of glycosylation. Changes in glycosylation may determine exposure of hydrophobic protein regions at the cell surface.Key words: Candida albicans, cell wall, mannoproteins, hydrophobicity, fibrils.
Characterization of F390 synthetase activity in cell extracts of Methanobacterium thermoautotrophicum Marburg
Authors: Purwantini Endang , Mukhopadhyay Biswarup , Daniels Lacy
Published: February 2010

The F390 synthetase activity in cell extracts of Methanobacterium thermoautotrophicum Marburg increased by two times upon preincubation at 37 °C with its substrates, ATP (or GTP) and coenzyme F420, but not with either of these compounds alone. In the 0–37 °C range, preincubation at 37 °C gave maximal enhancement in activity. F390 synthetase activity in cell extracts of strain Marburg was maximal at 45 °C, whereas F390 synthetase from M. thermoautotrophicum ΔH had maximal activity at 55 °C; both strains grew optimally at 65 °C. Data derived from the Arrhenius plot supported our earlier conclusion that the F390 synthetase activity of strain Marburg could lead to a loss of 70% of the available F420 during extraction of this factor from cells via an aerobic cell extract procedure even if the temperature was maintained at 4 °C.Key words: Methanobacterium thermoautotrophicum, F390 synthetase, activation, coenzyme F420
Phylogenetic studies on uncultured Frankia populations in nodules of Datisca cannabina
Authors: Mirza M. Sajjad , Hahn Dittmar , Dobritsa Svetlana V. , Akkermans Antoon D. L.
Published: February 2010

Part of the 16S rRNA gene was amplified directly from uncultured endophyte populations within the root nodules of Datisca cannabina and three strains isolated from nodules of Alnus glutinosa (AgKG′84/4), Coriaria nepalensis (Cn3), and D. cannabina (Dc2). Sequence comparison based on 930 nucleotides indicated that the endophyte of D. cannabina nodules belongs to the genus Frankia and is highly related to the endophyte of C. nepalensis root nodules. The relatedness of the endophytes of C. nepalensis and D. cannabina nodules was also reflected by closely related nifH sequences amplified from the nodules. 16S rRNA sequence analysis of the noninfective strains obtained from both D. cannabina (Dc2) and C. nepalensis (Cn3) nodules also revealed the close relationship of these strains to the genus Frankia.Key words: nitrogen fixation, Frankia, 16S rRNA, nifH.
The role of interactions, sessile growth, and nutrient amendments on the degradative efficiency of a microbial consortium
Authors: Wolfaardt G. M. , Lawrence J. R. , Robarts R. D. , Caldwell D. E.
Published: February 2010

A degradative microbial consortium consisting of at least nine bacterial and one algal species was isolated from soil with diclofop methyl as the sole carbon source. In continuous flow culture, the presence of the algae increased diclofop methyl degradation and removal by 36%. Batch culture experiments with 14C-labeled diclofop methyl confirmed algal involvement in the mineralization of diclofop methyl as there was no significant difference in the amount of 14CO2 evolved by the bacterial consortium with and without the algal activity when the consortium was cultivated in the dark to inhibit algal growth, while 11% more 14CO2 was produced in the light by the algal–bacterial consortium. Pure cultures isolated from the bacterial consortium could not individually mineralize diclofop methyl as the sole carbon source. However, when supplied with an additional carbon source, two strains could mineralize diclofop methyl. Addition of either the complex growth medium, or a cell-free filtrate from the algal–bacterial consortium to batch systems containing 14C-labeled diclofop methyl resulted in a significant increase in the production of 14CO2 by the bacterial consortium, suggesting co-metabolism of diclofop methyl in the presence of a labile carbon source. Removal of diclofop methyl by the bacterial consortium was increased by 36% when a larger surface to volume ratio was provided by glass beads that allowed extensive biofilm formation. The requirement for exogenous carbon sources and the inability of isolated pure cultures to degrade diclofop methyl indicated that interspecies interactions are necessary for degradation. The positive effect of sessile growth suggested that spatial organization of cells may also be important for degradation.Key words: consortium, degradation, herbicide, microbial interactions.
Sequence of a Rhodococcus gene cluster encoding the subunits of ethanolamine ammonia-lyase and an APC-like permease
Authors: Mot René De , Nagy Istvan , Schoofs Geert , Vanderleyden Jos
Published: February 2010

Sequence analysis of a 5173-bp genomic fragment from the nocardioform actinomycete Rhodococcus sp. strain NI86/21 revealed the presence of two genes, eutB and eutC, encoding the putative homologues of the large and small subunits of the ethanolamine ammonia-lyase, respectively, from Salmonella typhimurium. This is the first report of the characterization of these genes in a Gram-positive species. Immediately upstream of eutB, a gene encoding a putative permease of the APC (amino acids, polyamines, choline) transporter family was located. At present, no other Gram-positive members of this permease family are known. The translational coupling of these eut genes suggests an operon-like organization of the ethanolamine genes in Rhodococcus species. A truncated open reading frame downstream of eutC contained an N-terminal motif characteristic of membrane-anchored lipoproteins.Key words: nocardioform actinomycete, cobalamin, APC transporter, membrane-anchored lipoprotein, Gram-positive bacterium.
Responses of diverse heterotrophic bacteria to elevated copper concentrations
Authors: Gordon A. S. , Howell L. D. , Harwood V.
Published: February 2010

The influence of copper on the growth of Escherichia coli, Pseudomonas aeruginosa, Bacillus cereus, Bacillus subtilis, Vibrio parahaemolyticus, Vibrio alginolyticus (three strains), and an unidentified Vibrio sp. was examined in batch cultures. The effects of copper at micromolar concentrations varied from undetectable to complete growth inhibition. Each strain was able to recover from a growth lag observed after copper addition at a characteristic concentration. Copper concentrations that allowed recovery ranged from 25 to 150 μM. Extracellular proteins in the medium of cultures that had recovered from copper stress were compared with those from control cultures. Protein profiles were analyzed for the presence of proteins similar to extracellular copper-binding proteins (CuBP) previously reported in V. alginolyticus. CuBP-like proteins were found in each Vibrio sp. examined. A protein of similar molecular mass was also detected in copper-stressed cultures of P. aeruginosa and not in control cultures. Escherichia coli and Bacillus spp. did not produce CuBP-like proteins. The data show that CuBP-like proteins are not produced by all bacteria in response to copper stress and indicate that such proteins are common in marine Vibrio spp.Key words: copper toxicity, heterotrophic bacteria, extracellular protein.
Virulence of patient and water isolates of Legionella pneumophila in guinea pigs and mouse L929 cells varies with bacterial genotype
Authors: Bezanson Gregory , Fernandez Rachel , Haldane David , Burbridge Susan , Marrie Thomas
Published: February 2010

Thirteen isolates of Legionella pneumophila serogroup 1 (five from patients, eight from water) were screened for their virulence in guinea pigs after intraperitoneal injection and for their infectivity in L929 mouse cells. Since these isolates included three monoclonal antibody subtypes and four genotypes, the relative influence of these parameters on the pathogenicity of naturally occurring L. pneumophila could be assessed. There was no correlation between infectivity in the L929 assay and virulence for guinea pigs. The source of the isolate, patient or environmental, as well as the isolate's monoclonal antibody subtype did not correlate with virulence. At the p < 0.05 level, isolates with genotype IIb (20-MDa plasmid and EcoRI fragmentation pattern b) were significantly more virulent (mean log LD50 6.84) than genotype VIb (100-MDa plasmid, pattern b), IIId (72- and 96-MDa plasmids, pattern d) or Oc (no detectable plasmid, pattern c) isolates. Genotype IIId isolates were the least virulent (mean log LD50 9.49). Plasmid-containing isolates were more infective than plasmidless ones in L929 cells (p = 0.0001). We conclude that our strain types of L. pneumophila exhibit a gradation in virulence for guinea pigs and that infectivity in L929 cells does not correlate with virulence for guinea pigs.Key words: Legionella, virulence, genotype, plasmids.
Numerical analysis and the application of random amplified polymorphic DNA polymerase chain reaction to the differentiation of Vibrio strains from a seasonally cold ocean
Authors: Martin-Kearley Jennifer , Gow John A. , Péloquin Marc , Greer Charles W.
Published: February 2010

Eighty regional strains of Vibrio isolated from the seasonally cold waters of coastal Newfoundland, and a number of Vibrio reference cultures, were studied. The regional strains had been isolated from the brown macroalga Alaria esculenta and the giant scallop Placopecten magellanicus and were known to grow at 4 °C. The strains were grouped according to their arginine-dihydrolase reactions and examined by numerical analysis. According to phenotypic properties the arginine-dihydrolase positive strains closely resembled Vibrio splendidus biovar I. Most clusters of the arginine-dihydrolase negative strains appeared to be unique but the closest phenotypic resemblance among some strains was with Vibrio ordalii. Some strains were examined using the random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) technique for fingerprinting and it was shown that the regional strains were significantly different from either V. splendidus biovar I or V. ordalii. Generally, the strains from seaweed clustered separately from those that were from scallops. Strains in some clusters, especially those from the seaweed, were able to utilize most of the compounds that were tested as sole sources of carbon and energy.Key words: numerical taxonomy, marine bacteria, Vibrio, psychrotrophs, RAPD-PCR.
Nodulation efficiency of Bradyrhizobium japonicum strains with genotypes of soybean varying in the ability to restrict nodulation
Authors: Ferrey M. L. , Graham P. H. , Russelle M. P.
Published: February 2010

Competition from existing soil rhizobia has limited the benefits from nitrogen fixation for soybean grown in the American Midwest. A strategy being considered to overcome this problem is the use of varieties that are restricted in nodulation with soil strains, but nodulate normally with inoculant bradyrhizobia. In this study we examine the efficiency in nodulation of strains of Bradyrhizobium japonicum that have been reported as restricted in nodulation with specific genotypes of soybean, using a root-tip marking procedure in growth pouches. When B. japonicum USDA110 was applied to the soybean cultivars Hardee and Fiskeby V at the rate of 3.50 × 104 cells/pouch, more than 75% of the plants were nodulated above the root-tip mark, and average uppermost nodule position was above the root-tip mark. By contrast, when this strain was applied in similar concentration to the soybean cultivar Peking, few plants developed nodules above the root-tip mark, and the average position of the uppermost taproot nodule was nearly 30 mm below this mark. Nodulation was improved at higher rates of inoculation, but even when 3.50 × 106 cells were applied to each pouch, less than 50% of the plants were nodulated above the root-tip mark. Bradyrhizobium japonicum strain CB1809 (=USDA136) was also efficient in nodulation with cv. Fiskeby V, but with cv. Hardee, less than 65% of plants were nodulated above the root-tip mark, irrespective of inoculation rate. Because restriction of nodulation with the strains initially tested was not absolute, we examined the patterns of nodulation obtained following the inoculation of two restriction hosts, Peking and PI371607. In pure culture, serogroup USDA110 strains failed to induce significant taproot nodulation of cv. Peking in Leonard jars, but did induce lateral root nodulation. However, in a glasshouse experiment contrasting soil- and seed-applied inoculant, lateral-root nodulation of the restriction host PI371607 by USDA123 was not significant.Key words: Glycine max, competition, restriction, nodulation.
Transformation of Gluconobacter oxydans subsp. suboxydans by electroporation
Authors: Creaven Martina , Fitzgerald Richard J. , O'Gara Fergal
Published: February 2010

An efficient electroporation system for Gluconobacter oxydans subsp. suboxydans was developed that gave transformation frequencies of up to 105 transformants/μg of DNA. The system was studied with respect to different operating parameters including (i) the effect of electrical conditions, i.e., field strength and resistance, (ii) DNA concentration, (iii) composition of the electroporation buffer, (iv) initial cell concentration, and (v) stage of growth of the cells. Optimal electroporation conditions were found under the following conditions: 12.5 kV/cm field strength, 400 ? parallel resistor setting, 0.4–0.5 μg DNA/100 μL cell suspension, and electroporation buffer containing Mg ions and > 1011 colony-forming units/mL of early to mid log phase cells.Key words: Gluconobacter suboxydans, electroporation, field strength.