bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro Chemosensitization ofPlasmodium falciparumto Antimalarials by Verapamil and Probenecid
Authors: Masseno Victor , Muriithi Steven , Nzila Alexis 
Published: April 2009

ABSTRACTWe tested the effect of probenecid and verapamil in chemosensitizingPlasmodium falciparumto 14 antimalarials using the multidrug-resistant strain V1S and the drug-sensitive 3D7. Verapamil chemosensitizes V1S to quinine and chloroquine. Interestingly, probenecid profoundly chemosensitizes V1S to piperaquine. Thus, probenecid could be used to increase piperaquine efficacy in vivo.
High Prevalence of
qnr
Genes in Commensal Enterobacteria from Healthy Children in Peru and Bolivia
Authors: Pallecchi Lucia , Riccobono Eleonora , Mantella Antonia , Bartalesi Filippo , Sennati Samanta , Gamboa Herlan , Gotuzzo Eduardo , Bartoloni Alessandro , Rossolini Gian Maria 
Published: April 2009

ABSTRACT

A remarkable prevalence of
qnrB
(54%) and, at a lower level, of
qnrS
(14%) was discovered in pools of commensal enterobacteria from 310 healthy children living in Peru and Bolivia, using a metagenomic approach. Analysis of randomly selected enterobacterial pools revealed that
qnrB
was mainly carried by
Escherichia coli
and
qnrS
by
Klebsiella pneumoniae
. Investigation of 11
qnrB
-positive isolates and 9
qnrS
-positive isolates revealed the presence of plasmid-borne
qnrB19
(
n
= 8),
qnrB2
(
n
= 2),
qnrB10
(
n
= 1), and
qnrS1
(
n
= 9) genes.
Inter- and Intraspecific Variations of Bacterial Communities Associated with Marine Sponges from San Juan Island, Washington
Authors: Lee On On , Wong Yue Him , Qian Pei-Yuan 
Published: April 2009

ABSTRACT

This study attempted to assess whether conspecific or congeneric sponges around San Juan Island, Washington, harbor specific bacterial communities. We used a combination of culture-independent DNA fingerprinting techniques (terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis [DGGE]) and culture-dependent approaches. The results indicated that the bacterial communities in the water column consisted of more diverse bacterial ribotypes than and were drastically different from those associated with the sponges. High levels of similarity in sponge-associated bacterial communities were found only in
Myxilla incrustans
and
Haliclona rufescens
, while the bacterial communities in
Halichondria panicea
varied substantially among sites. Certain terminal restriction fragments or DGGE bands were consistently obtained for different individuals of
M. incrustans
and
H. rufescens
collected from different sites, suggesting that there are stable or even specific associations of certain bacteria in these two sponges. However, no specific bacterial associations were found for
H. panicea
or for any one sponge genus. Sequencing of nine DGGE bands resulted in recovery of seven sequences that best matched the sequences of uncultured
Proteobacteria
. Three of these sequences fell into the sponge-specific sequence clusters previously suggested. An uncultured alphaproteobacterium and a culturable
Bacillus
sp. were found exclusively in all
M. incrustans
sponges, while an uncultured gammaproteobacterium was unique to
H. rufescens
. In contrast, the cultivation approach indicated that sponges contained a large proportion of
Firmicutes
, especially
Bacillus
, and revealed large variations in the culturable bacterial communities associated with congeneric and conspecific sponges. This study revealed sponge species-specific but not genus- or site-specific associations between sponges and bacterial communities and emphasized the importance of using a combination of techniques for studying microbial communities.
Plutonium(V/VI) Reduction by the Metal-Reducing Bacteria
Geobacter metallireducens
GS-15 and
Shewanella oneidensis
MR-1
Authors: Icopini Gary A. , Lack Joe G. , Hersman Larry E. , Neu Mary P. , Boukhalfa Hakim 
Published: April 2009

ABSTRACT

We examined the ability of the metal-reducing bacteria
Geobacter metallireducens
GS-15 and
Shewanella oneidensis
MR-1 to reduce Pu(VI) and Pu(V). Cell suspensions of both bacteria reduced oxidized Pu [a mixture of Pu(VI) and Pu(V)] to Pu(IV). The rate of plutonium reduction was similar to the rate of U(VI) reduction obtained under similar conditions for each bacteria. The rates of Pu(VI) and U(VI) reduction by cell suspensions of
S. oneidensis
were slightly higher than the rates observed with
G. metallireducens
. The reduced form of Pu was characterized as aggregates of nanoparticulates of Pu(IV). Transmission electron microscopy images of the solids obtained from the cultures after the reduction of Pu(VI) and Pu(V) by
S. oneidensis
show that the Pu precipitates have a crystalline structure. The nanoparticulates of Pu(IV) were precipitated on the surface of or within the cell walls of the bacteria. The production of Pu(III) was not observed, which indicates that Pu(IV) was the stable form of reduced Pu under these experimental conditions. Experiments examining the ability of these bacteria to use Pu(VI) as a terminal electron acceptor for growth were inconclusive. A slight increase in cell density was observed for both
G. metallireducens
and
S. oneidensis
when Pu(VI) was provided as the sole electron acceptor; however, Pu(VI) concentrations decreased similarly in both the experimental and control cultures.
Proteomic and Transcriptomic Analyses Reveal Genes Upregulated bycis-Dichloroethene inPolaromonassp. Strain JS666
Authors: Jennings Laura K. , Chartrand Michelle M. G. , Lacrampe-Couloume Georges , Lollar Barbara Sherwood , Spain Jim C. , Gossett James M. 
Published: April 2009

ABSTRACTPolaromonassp. strain JS666 is the only bacterial isolate capable of usingcis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathioneS-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from −17.4 to −22.4‰. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (C═C cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.
Role of GerKB in Germination and Outgrowth of
Clostridium perfringens
Spores
Authors: Paredes-Sabja Daniel , Setlow Peter , Sarker Mahfuzur R. 
Published: April 2009

ABSTRACT

Previous work indicated that
Clostridium perfringens gerKA gerKC
spores germinate significantly, suggesting that
gerKB
also has a role in
C. perfringens
spore germination. We now find that (i)
gerKB
was expressed only during sporulation, likely in the forespore; (ii)
gerKB
spores germinated like wild-type spores with nonnutrient germinants and with high concentrations of nutrients but more slowly with low nutrient concentrations; and (iii)
gerKB
spores had lower colony-forming efficiency and slower outgrowth than wild-type spores. These results suggest that GerKB plays an auxiliary role in spore germination under some conditions and is required for normal spore viability and outgrowth.
Biofilm Bacterial Community Structure in Streams Affected by Acid Mine Drainage
Authors: Lear Gavin , Niyogi Dev , Harding Jon , Dong Yimin , Lewis Gillian 
Published: April 2009

ABSTRACTWe examined the bacterial communities of epilithic biofilms in 17 streams which represented a gradient ranging from relatively pristine streams to streams highly impacted by acid mine drainage (AMD). A combination of automated ribosomal intergenic spacer analysis with multivariate analysis and ordination provided a sensitive, high-throughput method to monitor the impact of AMD on stream bacterial communities. Significant differences in community structure were detected among neutral to alkaline (pH 6.7 to 8.3), acidic (pH 3.9 to 5.7), and very acidic (pH 2.8 to 3.5) streams. DNA sequence analysis revealed that the acidic streams were generally dominated by bacteria related to the iron-oxidizing genusGallionella, while the organisms in very acidic streams were less diverse and included a high proportion of acidophilic eukaryotes, including taxa related to the algal generaNaviculaandKlebsormidium. Despite the presence of high concentrations of dissolved metals (e.g., Al and Zn) and deposits of iron hydroxide in some of the streams studied, pH was the most important determinant of the observed differences in bacterial community variability. These findings confirm that any restoration activities in such systems must focus on dealing with pH as the first priority.
Detection ofToxoplasma gondiiOocysts in Water Sample Concentrates by Real-Time PCR
Authors: Yang Wenli , Lindquist H. D. Alan , Cama Vitaliano , Schaefer Frank W. , Villegas Eric , Fayer Ronald , Lewis Earl J. , Feng Yaoyu , Xiao Lihua 
Published: April 2009

ABSTRACTPCR techniques in combination with conventional parasite concentration procedures have potential for the sensitive and specific detection ofToxoplasma gondiioocysts in water. Three real-time PCR assays based on the B1 gene and a 529-bp repetitive element were analyzed for the detection ofT. gondiitachyzoites and oocysts. Lower sensitivity and specificity were obtained with the B1 gene-based PCR than with the 529-bp repeat-based PCR. New procedures for the real-time PCR detection ofT. gondiioocysts in concentrates of surface water were developed and tested in conjunction with a method for the direct extraction of inhibitor-free DNA from water. This technique detected as few as one oocyst seeded to 0.5 ml of packed pellets from water samples concentrated by Envirocheck filters. Thus, this real-time PCR may provide a detection method alternative to the traditional mouse assay and microscopy.
Characterization of a Unique Class C Acid Phosphatase from
Clostridium perfringens
Authors: Reilly Thomas J. , Chance Deborah L. , Calcutt Michael J. , Tanner John J. , Felts Richard L. , Waller Stephen C. , Henzl Michael T. , Mawhinney Thomas P. , Ganjam Irene K. , Fales William H. 
Published: April 2009

ABSTRACT

Clostridium perfringens
is a gram-positive anaerobe and a pathogen of medical importance. The detection of acid phosphatase activity is a powerful diagnostic indicator of the presence of
C. perfringens
among anaerobic isolates; however, characterization of the enzyme has not previously been reported. Provided here are details of the characterization of a soluble recombinant form of this cell-associated enzyme. The denatured enzyme was ∼31 kDa and a homodimer in solution. It catalyzed the hydrolysis of several substrates, including
para
-nitrophenyl phosphate, 4-methylumbelliferyl phosphate, and 3′ and 5′ nucleoside monophosphates at pH 6. Calculated

K
m

s ranged from 0.2 to 0.6 mM with maximum velocity ranging from 0.8 to 1.6 μmol of P
i
/s/mg. Activity was enhanced in the presence of some divalent cations but diminished in the presence of others. Wild-type enzyme was detected in all clinical
C. perfringens
isolates tested and found to be cell associated. The described enzyme belongs to nonspecific acid phosphatase class C but is devoid of lipid modification commonly attributed to this class.
Mitogen-Activated Protein Kinase hog1 in the Entomopathogenic FungusBeauveria bassianaRegulates Environmental Stress Responses and Virulence to Insects
Authors: Zhang Yongjun , Zhao Jianhua , Fang Weiguo , Zhang Jianqing , Luo Zhibing , Zhang Mi , Fan Yanhua , Pei Yan 
Published: April 2009

ABSTRACTBeauveria bassianais an economically important insect-pathogenic fungus which is widely used as a biocontrol agent to control a variety of insect pests. However, its insecticide efficacy in the field is often influenced by adverse environmental factors. Thus, understanding the genetic regulatory processes involved in the response to environmental stress would facilitate engineering and production of a more efficient biocontrol agent. Here, a mitogen-activated protein kinase (MAPK)-encoding gene, Bbhog1, was isolated fromB. bassianaand shown to encode a functional homolog of yeastHIGH-OSMOLARITY GLYCEROL 1(HOG1). A Bbhog1null mutation was generated inB. bassianaby targeted gene replacement, and the resulting mutants were more sensitive to hyperosmotic stress, high temperature, and oxidative stress than the wild-type controls. These results demonstrate the conserved function of HOG1 MAPKs in the regulation of abiotic stress responses. Interestingly, ΔBbhog1mutants exhibited greatly reduced pathogenicity, most likely due to a decrease in spore viability, a reduced ability to attach to insect cuticle, and a reduction in appressorium formation. The transcript levels of two hydrophobin-encoding genes,hyd1andhyd2, were dramatically decreased in a ΔBbhog1mutant, suggesting that Bbhog1 may regulate the expression of the gene associated with hydrophobicity or adherence.
Phylogenetic Analysis Indicates Evolutionary Diversity and Environmental Segregation of Marine Podovirus DNA Polymerase Gene Sequences
Authors: Labonté Jessica M. , Reid Karen E. , Suttle Curtis A. 
Published: April 2009

ABSTRACT

The distribution of viral genotypes in the ocean and their evolutionary relatedness remain poorly constrained. This paper presents data on the genetic diversity and evolutionary relationships of 1.2-kb DNA polymerase (
pol
) gene fragments from podoviruses. A newly designed set of PCR primers was used to amplify DNA directly from coastal sediment and water samples collected from inlets adjacent to the Strait of Georgia, British Columbia, Canada, and from the northeastern Gulf of Mexico. Restriction fragment length polymorphism analysis of 160 cloned PCR products revealed 29 distinct operational taxonomic units (OTUs), with OTUs within a site typically being more similar than those among sites. Phylogenetic analysis of the DNA
pol
gene fragments demonstrated high similarity between some environmental sequences and sequences from the marine podoviruses roseophage SIO1 and cyanophage P60, while others were not closely related to sequences from cultured phages. Interrogation of the CAMERA database for sequences from metagenomics data demonstrated that the amplified sequences were representative of the diversity of podovirus
pol
sequences found in marine samples. Our results indicate high genetic diversity within marine podovirus communities within a small geographic region and demonstrate that the diversity of environmental polymerase gene sequences for podoviruses is far more extensive than previously recognized.
First Gene Cassettes of Integrons as Targets in Finding Adaptive Genes in Metagenomes
Authors: Huang Lionel , Cagnon Christine , Caumette Pierre , Duran Robert 
Published: April 2009

ABSTRACT
The first gene cassettes of integrons are involved in the last adaptation response to changing conditions and are also the most expressed. We propose a rapid method for the selection of clones carrying an integron first gene cassette that is useful for finding adaptive genes in environmental metagenomic libraries.
Identifying the Source of Unknown Microcystin Genes and Predicting Microcystin Variants by Comparing Genes within Uncultured Cyanobacterial Cells
Authors: Allender Christopher J. , LeCleir Gary R. , Rinta-Kanto Johanna M. , Small Randall L. , Satchwell Michael F. , Boyer Gregory L. , Wilhelm Steven W. 
Published: April 2009

ABSTRACT

While multiple phylogenetic markers have been used in the culture-independent study of microcystin-producing cyanobacteria, in only a few instances have multiple markers been studied within individual cells, and in all cases these studies have been conducted with cultured isolates. Here, we isolate and evaluate large DNA fragments (>6 kb) encompassing two genes involved in microcystin biosynthesis (
mcyA2
and
mcyB1
) and use them to identify the source of gene fragments found in water samples. Further investigation of these gene loci from individual cyanobacterial cells allowed for improved analysis of the genetic diversity within microcystin producers as well as a method to predict microcystin variants for individuals. These efforts have also identified the source of the novel
mcyA
genotype previously termed
Microcystis
-like that is pervasive in the Laurentian Great Lakes and they predict the microcystin variant(s) that it produces.
Cultivation of Anaerobic and Facultatively Anaerobic Bacteria from Spacecraft-Associated Clean Rooms
Authors: Stieglmeier Michaela , Wirth Reinhard , Kminek Gerhard , Moissl-Eichinger Christine 
Published: April 2009

ABSTRACT

In the course of this biodiversity study, the cultivable microbial community of European spacecraft-associated clean rooms and the Herschel Space Observatory located therein were analyzed during routine assembly operations. Here, we focused on microorganisms capable of growing without oxygen. Anaerobes play a significant role in planetary protection considerations since extraterrestrial environments like Mars probably do not provide enough oxygen for fully aerobic microbial growth. A broad assortment of anaerobic media was used in our cultivation strategies, which focused on microorganisms with special metabolic skills. The majority of the isolated strains grew on anaerobic, complex, nutrient-rich media. Autotrophic microorganisms or microbes capable of fixing nitrogen were also cultivated. A broad range of facultatively anaerobic bacteria was detected during this study and also, for the first time, some strictly anaerobic bacteria (
Clostridium
and
Propionibacterium
) were isolated from spacecraft-associated clean rooms. The multiassay cultivation approach was the basis for the detection of several bacteria that had not been cultivated from these special environments before and also led to the discovery of two novel microbial species of
Pseudomonas
and
Paenibacillus
.
Comparative Proteomic Analysis of Tolerance and Adaptation of EthanologenicSaccharomyces cerevisiaeto Furfural, a Lignocellulosic Inhibitory Compound
Authors: Lin Feng-Ming , Qiao Bin , Yuan Ying-Jin 
Published: April 2009

ABSTRACTThe molecular mechanism involved in tolerance and adaptation of ethanologenicSaccharomyces cerevisiaeto inhibitors (such as furfural, acetic acid, and phenol) represented in lignocellulosic hydrolysate is still unclear. Here,18O-labeling-aided shotgun comparative proteome analysis was applied to study the global protein expression profiles ofS. cerevisiaeunder conditions of treatment of furfural compared with furfural-free fermentation profiles. Proteins involved in glucose fermentation and/or the tricarboxylic acid cycle were upregulated in cells treated with furfural compared with the control cells, while proteins involved in glycerol biosynthesis were downregulated. Differential levels of expression of alcohol dehydrogenases were observed. On the other hand, the levels of NADH, NAD+, and NADH/NAD+were reduced whereas the levels of ATP and ADP were increased. These observations indicate that central carbon metabolism, levels of alcohol dehydrogenases, and the redox balance may be related to tolerance of ethanologenic yeast for and adaptation to furfural. Furthermore, proteins involved in stress response, including the unfolded protein response, oxidative stress, osmotic and salt stress, DNA damage and nutrient starvation, were differentially expressed, a finding that was validated by quantitative real-time reverse transcription-PCR to further confirm that the general stress responses are essential for cellular defense against furfural. These insights into the response of yeast to the presence of furfural will benefit the design and development of inhibitor-tolerant ethanologenic yeast by metabolic engineering or synthetic biology.
Distribution and Rate of Microbial Processes in an Ammonia-Loaded Air Filter Biofilm
Authors: Juhler Susanne , Revsbech Niels Peter , Schramm Andreas , Herrmann Martina , Ottosen Lars D. M. , Nielsen Lars Peter 
Published: April 2009

ABSTRACT

The in situ activity and distribution of heterotrophic and nitrifying bacteria and their potential interactions were investigated in a full-scale, two-section, trickling filter designed for biological degradation of volatile organics and NH
3
in ventilation air from pig farms. The filter biofilm was investigated by microsensor analysis, fluorescence in situ hybridization, quantitative PCR, and batch incubation activity measurements. In situ aerobic activity showed a significant decrease through the filter, while the distribution of ammonia-oxidizing bacteria (AOB) was highly skewed toward the filter outlet. Nitrite oxidation was not detected during most of the experimental period, and the AOB activity therefore resulted in NO
2
−
, accumulation, with concentrations often exceeding 100 mM at the filter inlet. The restriction of AOB to the outlet section of the filter was explained by both competition with heterotrophic bacteria for O
2
and inhibition by the protonated form of NO
2
−
, HNO
2
. Product inhibition of AOB growth could explain why this type of filter tends to emit air with a rather constant NH
3
concentration irrespective of variations in inlet concentration and airflow.
Enumeration of
Escherichia coli
Cells on Chicken Carcasses as a Potential Measure of Microbial Process Control in a Random Selection of Slaughter Establishments in the United States
Authors: Altekruse Sean F. , Berrang Mark E. , Marks Harry , Patel Bharat , Shaw William K. , Saini Parmesh , Bennett Patricia A. , Bailey J. Stan 
Published: April 2009

ABSTRACT

To evaluate whether the number of
Escherichia coli
bacteria in carcass rinses from chicken slaughter establishments could be monitored for the purpose of microbial process control, we drew a random sample from 20 of 127 large USDA-inspected operations. In 2005, every 3 months, two sets of 10 carcass rinses, 100 ml each, were collected from establishments, netting 80 sample sets from the rehang and postchill stages.
E. coli
and
Campylobacter
numbers and
Salmonella
prevalence were measured. Mixed-effect models were used to estimate variance of mean log
10
E. coli
cell numbers of 10-carcass rinse sample sets. Relationships between
E. coli
and
Campylobacter
and
Salmonella
were examined. For 10-carcass rinse sets, at both the rehang and postchill stages the mean log
10
E. coli
CFU/ml fit the logistic distribution better than the normal distribution. The rehang overall mean log
10
E. coli
was 3.3 CFU/ml, with a within-sample set standard deviation of 0.6 CFU/ml. The overall postchill mean log
10
E. coli
was 0.8 CFU/ml, with 13 establishments having mean log
10
E. coli
CFU/ml values of less than 1.0 and 7 having mean values of 1.2 or more. At the midpoint separating these establishments, a mean log
10
E. coli
CFU/ml of 1.1, the within-sample set standard deviation was 0.5 CFU/ml, with smaller standard deviations as means increased. Postchill sample sets with mean log
10
E. coli
counts less than or equal to 1.1 CFU/ml had lower overall prevalence of
Salmonella
and mean log
10
Campylobacter
CFU/ml than sample sets with higher means. These findings regarding reductions in
E. coli
numbers provide insight relevant to microbial process control.