bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activity of the Ketolide Telithromycin Is Refractory to Erm Monomethylation of Bacterial rRNA
Authors: Liu Mingfu , Douthwaite Stephen 
Published: July 2002

ABSTRACT

Methylation of specific nucleotides in rRNA is one of the means by which bacteria achieve resistance to macrolides-lincosamides-streptogramin B (MLS
B
) and ketolide antibiotics. The degree of resistance is determined by how effectively the rRNA is methylated. We have implemented a bacterial system in which the rRNA methylations are defined, and in this study we investigate what effect Erm mono- and dimethylation of the rRNA has on the activity of representative MLS
B
and ketolide antibiotics. In the test system, >80% of the rRNA molecules are monomethylated by ErmN (TlrD) or dimethylated by ErmE. ErmE dimethylation confers high resistance to all the MLS
B
and ketolide drugs. ErmN monomethylation predictably confers high resistance to the lincosamides clindamycin and lincomycin, intermediate resistance to the macrolides clarithromycin and erythromycin, and low resistance to the streptogramin B pristinamycin IA. In contrast to the macrolides, monomethylation only mildly affects the antimicrobial activities of the ketolides HMR 3647 (telithromycin) and HMR 3004, and these drugs remain 16 to 250 times as potent as clarithromycin and erythromycin. These differences in the macrolide and ketolide activities could explain the recent reports of variation in the MICs of telithromycin for streptococcal strains that have constitutive
erm
MLS
B
resistance and are highly resistant to erythromycin.
Pharmacology of β-
l
-Thymidine and β-
l
-2′-Deoxycytidine in HepG2 Cells and Primary Human Hepatocytes: Relevance to Chemotherapeutic Efficacy against Hepatitis B Virus
Authors: Hernandez-Santiago B. , Placidi L. , Cretton-Scott E. , Faraj A. , Bridges E. G. , Bryant M. L. , Rodriguez-Orengo J. , Imbach J. L. , Gosselin G. , Pierra C. , Dukhan D. , Sommadossi J. P. 
Published: July 2002

ABSTRACT

β-
l
-Thymidine (
l
-dT) and β-
l
-2′-deoxycytidine (
l
-dC) are potent and highly specific inhibitors of hepatitis B virus (HBV) replication both in vivo and in vitro (50% effective concentrations, 0.19 to 0.24 μM in 2.2.15 cells). The intracellular metabolisms of
l
-dT and
l
-dC were investigated in HepG2 cells and primary cultured human hepatocytes.
l
-dT and
l
-dC were extensively phosphorylated in both cell types, with the 5′-triphosphate derivative being the predominant metabolite. In HepG2 cells, the 5′-triphosphate levels were 27.7 ± 12.1 and 72.4 ± 1.8 pmol/10
6
cells for
l
-dT and
l
-dC, respectively. In primary human hepatocytes, the 5′-triphosphate levels were 16.5 ± 9.8 and 90.1 ± 36.4 pmol/10
6
cells for
l
-dT and
l
-dC, respectively. Furthermore, a choline derivative of
l
-dCDP was detected at concentrations of 15.8 ± 1.8 and 25.6 ± 0.1 pmol/10
6
cells in human hepatocytes and HepG2 cells, respectively. In HepG2 cells exposed to
l
-dC, the 5′-monophosphate and 5′-triphosphate derivatives of β-
l
-2′-deoxyuridine (
l
-dUMP and
l
-dUTP, respectively) were also observed, reaching intracellular concentrations of 6.7 ± 0.4 and 18.2 ± 1.0 pmol/10
6
cells, respectively. In human hepatocytes,
l
-dUMP and
l
-dUTP were detected at concentrations of 5.7 ± 2.4 and 43.5 ± 26.8 pmol/10
6
cells, respectively. It is likely that deamination of
l
-dCMP by deoxycytidylate deaminase leads to the formation of
l
-dUMP, as the parent compound,
l
-dC, was not a substrate for deoxycytidine deaminase. The intracellular half-lives of
l
-dTTP,
l
-dCTP, and
l
-dUTP were at least 15 h, with intracellular concentrations of each metabolite remaining above their respective 50% inhibitory concentrations for the woodchuck hepatitis virus DNA polymerase for as long as 24 h after removal of the drug from cell cultures. Exposure of HepG2 cells to
l
-dT in combination with
l
-dC led to concentrations of the activated metabolites similar to those achieved with either agent alone. These results suggest that the potent anti-HBV activities of
l
-dT and
l
-dC are associated with their extensive phosphorylation.
Antifungal Susceptibility ofCandidaBiofilms: Unique Efficacy of Amphotericin B Lipid Formulations and Echinocandins
Authors: Kuhn D. M. , George T. , Chandra J. , Mukherjee P. K. , Ghannoum M. A. 
Published: July 2002

ABSTRACTBiofilms, likely the predominant mode of device-related microbial infection, exhibit resistance to antimicrobial agents. Evidence suggests thatCandidabiofilms have dramatically reduced susceptibility to antifungal drugs. We examined antifungal susceptibilities ofCandida albicansandCandida parapsilosisbiofilms grown on a bioprosthetic model. In addition to conventional agents, we determined if new antifungal agents (triazoles, amphotericin B lipid formulations, and echinocandins) have activities againstCandidabiofilms. We also explored effects of preincubation ofC. albicanscells with subinhibitory concentrations (sub-MICs) of drugs to see if they could modify subsequent biofilm formation. Finally, we used confocal scanning laser microscopy (CSLM) to image planktonic- and biofilm-exposed blastospores to examine drug effects on cell structure.Candidabiofilms were formed on silicone elastomer and quantified by tetrazolium and dry weight (DW) assays. Susceptibility testing of fluconazole, nystatin, chlorhexidine, terbenafine, amphotericin B (AMB), and the triazoles voriconazole (VRC) and ravuconazole revealed resistance in allCandidaisolates examined when grown as biofilms, compared to planktonic forms. In contrast, lipid formulations of AMB (liposomal AMB and AMB lipid complex [ABLC]) and echinocandins (caspofungin [Casp] and micafungin) showed activity againstCandidabiofilms. Preincubation ofC. albicanscells with sub-MIC levels of antifungals decreased the ability of cells to subsequently form biofilm (measured by DW;P< 0.0005). CSLM analysis of planktonic and biofilm-associated blastospores showed treatment with VRC, Casp, and ABLC resulted in morphological alterations, which differed with each agent. In conclusion, our data show thatCandidabiofilms show unique susceptibilities to echinocandins and AMB lipid formulations.
Longitudinal Use of a Line Probe Assay for Human Immunodeficiency Virus Type 1 Protease Predicts Phenotypic Resistance and Clinical Progression in Patients Failing Highly Active Antiretroviral Therapy
Authors: Servais Jean , Lambert Christine , Plesséria Jean-Marc , Fontaine Elodie , Robert Isabelle , Arendt Vic , Staub Thérèse , Hemmer Robert , Schneider François , Schmit Jean-Claude 
Published: July 2002

ABSTRACT

An observational study assessed the longitudinal use of a new line probe assay for the detection of protease mutations. Probe assays for detection of reverse transcriptase (Inno-LiPA HIV-1 RT; Innogenetics) and protease (prototype kit Inno-LiPA HIV Protease; Innogenetics) mutations gave results for 177 of 199 sequential samples collected over 2 years from 26 patients failing two nucleoside reverse transcriptase inhibitors and one protease inhibitor (first line: indinavir,
n
= 6; ritonavir,
n
= 10; and saquinavir,
n
= 10). Results were compared to recombinant virus protease inhibitor susceptibility data (
n
= 87) and to clinical and virological data. Combinations of protease mutations (M46I, G48V, I54V, V82A or -F, I84V, and L90M) predicted phenotypic resistance to the protease inhibitor and to nelfinavir. The sum of protease mutations was associated with virological and clinical outcomes from 6 and 3 months on, respectively. Moreover, a poorer clinical outcome was linked to the sum of reverse transcriptase mutations. In conclusion, despite the limited number of patients studied and the restricted number of codons investigated, probe assay-based genotyping correlates with phenotypic drug resistance and predicts new Centers for Disease Control and Prevention stage B and C clinical events and virological outcome. Line probe assays provide additional prognostic information and should be prospectively investigated for their potential for treatment monitoring.
Erythromycin Modulates Eosinophil Chemotactic Cytokine Production by Human Lung Fibroblasts in Vitro
Authors: Sato Etsuro , Nelson Dan K. , Koyama Sekiya , Hoyt Jeffrey C. , Robbins Richard A. 
Published: July 2002

ABSTRACTRecent studies suggest that erythromycin can suppress the production of some cytokines and may be an effective treatment for asthma. Eosinophil chemotactic cytokines have been suggested to contribute to the pathogenesis of asthma by the recruitment of eosinophils. We hypothesized that erythromycin modulates eosinophil chemotactic cytokine production. To test the hypothesis, we evaluated the potential of erythromycin to modulate the release of eosinophil chemoattractants from the human lung fibroblast cell line HFL-1. HFL-1 released eotaxin, granulocyte-macrophage colony-stimulating factor, and regulated and normal T-cell expressed and presumably secreted (RANTES) in response to interleukin-1β or tumor necrosis factor alpha. Erythromycin attenuated the release of these cytokines and eosinophil chemotactic activity by the HFL-1. The suppressive effect on eotaxin was the most marked of these cytokines. Erythromycin therapy also suppressed eotaxin mRNA significantly. These results suggest a mechanism that may account for the apparent beneficial action of macrolide antibiotics in the treatment of allergic airway disorders.
Rapid and Simple Determination of the
Escherichia coli
Phylogenetic Group
Authors: Clermont Olivier , Bonacorsi Stéphane , Bingen Edouard 
Published: July 2002

ABSTRACT

Phylogenetic analysis has shown that
Escherichia coli
is composed of four main phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D. Actually, phylogenetic groups can be determined by multilocus enzyme electrophoresis or ribotyping, both of which are complex, time-consuming techniques. We describe a simple and rapid phylogenetic grouping technique based on triplex PCR. The method, which uses a combination of two genes (
chuA
and
yjaA
) and an anonymous DNA fragment, was tested with 230 strains and showed excellent correlation with reference methods.
Fate of Selenate and Selenite Metabolized by
Rhodobacter sphaeroides
Authors: Van Fleet-Stalder Verena , Chasteen Thomas G. , Pickering Ingrid J. , George Graham N. , Prince Roger C. 
Published: July 2002

ABSTRACT

Cultures of a purple nonsulfur bacterium,
Rhodobacter sphaeroides
, amended with ∼1 or ∼100 ppm selenate or selenite, were grown phototrophically to stationary phase. Analyses of culture headspace, separated cells, and filtered culture supernatant were carried out using gas chromatography, X-ray absorption spectroscopy, and inductively coupled plasma spectroscopy-mass spectrometry, respectively. While selenium-amended cultures showed much higher amounts of SeO
3
2−
bioconversion than did analogous selenate experiments (94% uptake for SeO
3
2−
as compared to 9.6% for SeO
4
2−
-amended cultures from 100-ppm solutions), the chemical forms of selenium in the microbial cells were not very different except at exposure to high concentrations of selenite. Volatilization accounted for only a very small portion of the accumulated selenium; most was present in organic forms and the red elemental form.
Complete Nucleotide Sequence of Ubiquitous Plasmid pEA29 from
Erwinia amylovora
Strain Ea88: Gene Organization and Intraspecies Variation
Authors: McGhee Gayle C. , Jones Alan L. 
Published: July 2002

ABSTRACT

The complete sequence of plasmid pEA29 from
Erwinia amylovora
strain Ea88 consists of 28,185 bp with a 50.2% G+C content. As deletions and insertions were detected in other derivatives of pEA29, its size actually varied from 27.6 to 34.9 kb. Thirteen open reading frames that encoded predicted proteins with similarities to known proteins from other bacteria were identified along with two open reading frames related to hypothetical proteins found in GenBank and six open reading frames with no similarities to existing GenBank entries. Predicted products of open reading frames with similarity to the thiamine biosynthetic genes
thiO
,
thiG
, and
thiF
; a
betT
gene coding for choline transport; an
msrA
gene for the enzyme methionine sulfoxide reductase; a putative methyl-accepting chemotaxis gene; an aldehyde dehydrogenase gene; an
hns
DNA binding gene; a LysR-type transcriptional regulator; and
parA
and
parB
partitioning genes were identified. A putative iteron-containing theta-type origin of replication with an AT-rich region and a gene for a RepA protein was identified.
Pst
I and
Kpn
I restriction patterns for pEA29 isolated from tree fruit strains of
E. amylovora
were homogenous and different from those for pEA29 isolated from
Rubus
(raspberry) strains. All
Rubus
derivatives of pEA29 contained a point mutation that eliminated a
Pst
I site and a 1,264-bp region that replaced 1,890 bp of sequence found in pEA29 from strain Ea88. This change eliminated a second
Pst
I site and increased the length of a
Kpn
I fragment. An insertion sequence, IS
Eam1
, was detected in one
Rubus
strain, and transposon Tn
5393
was detected in three apple strains in two separate locations on the plasmid. Plasmid-cured strains exhibited reduced virulence and modified colony morphology on minimal medium without thiamine, indicating that some of the genes in pEA29 play a role in the physiology or metabolism of
E. amylovora.
Bradyrhizobium
sp. Strains That Nodulate the Leguminous Tree
Acacia albida
Produce Fucosylated and Partially Sulfated Nod Factors
Authors: Ferro Myriam , Lorquin Jean , Ba Salif , Sanon Kadidia , Promé Jean-Claude , Boivin Catherine 
Published: July 2002

ABSTRACT

We determined the structures of Nod factors produced by six different
Bradyrhizobium
sp. strains nodulating the legume tree
Acacia albida
(syn.
Faidherbia albida
). Compounds from all strains were found to be similar, i.e., O-carbamoylated and substituted by an often sulfated methyl fucose and different from compounds produced by
Rhizobium-Mesorhizobium-Sinorhizobium
strains nodulating other species of the Acaciae tribe.
Determination of
Escherichia coli
Contamination with Chromocult Coliform Agar Showed a High Level of Discrimination Efficiency for Differing Fecal Pollution Levels in Tropical Waters of Kampala, Uganda
Authors: Byamukama Dennis , Kansiime Frank , Mach Robert L. , Farnleitner Andreas H. 
Published: July 2002

ABSTRACT

Escherichia coli
, total coliforms, fecal coliforms, and sulfite-reducing anaerobic spore formers from different polluted sites in a tropical environment were determined in order to test for their indication ability for fecal contamination. Quantification of
E. coli
contamination with Chromocult coliform agar proved to be efficient and feasible for determining fecal pollutions in the investigated area within 24 h. The other microbial parameters showed a lower ability to differentiate sites and cannot be recommended for monitoring fecal pollution in the studied tropical surface waters.
Identification of Motile
Aeromonas
Strains with the MicroScan WalkAway System in Conjunction with the Combo Negative Type 1S Panels
Authors: Vivas J. , Sáa A. I. , Tinajas A. , Barbeyto L. , Rodríguez L. A. 
Published: July 2002

ABSTRACT

This study was performed to compare the MicroScan WalkAway automated identification system in conjunction with the new MicroScan Combo Negative type 1S panels with conventional biochemical methods for identifying 85 environmental, clinical, and reference strains of eight
Aeromonas
species.
Isolation of Adherent Polycyclic Aromatic Hydrocarbon (PAH)-Degrading Bacteria Using PAH-Sorbing Carriers
Authors: Bastiaens Leen , Springael Dirk , Wattiau Pierre , Harms Hauke , deWachter Rupert , Verachtert Hubert , Diels Ludo 
Published: July 2002

ABSTRACT

Two different procedures were compared to isolate polycyclic aromatic hydrocarbon (PAH)-utilizing bacteria from PAH-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which PAHs were supplied as crystals and (ii) a new method in which PAH degraders were enriched on and recovered from hydrophobic membranes containing sorbed PAHs. Both techniques were successful, but selected from the same source different bacterial strains able to grow on PAHs as the sole source of carbon and energy. The liquid enrichment mainly selected for
Sphingomonas
spp., whereas the membrane method exclusively led to the selection of
Mycobacterium
spp. Furthermore, in separate membrane enrichment set-ups with different membrane types, three repetitive extragenic palindromic PCR-related
Mycobacterium
strains were recovered. The new
Mycobacterium
isolates were strongly hydrophobic and displayed the capacity to adhere strongly to different surfaces. One strain,
Mycobacterium
sp. LB501T, displayed an unusual combination of high adhesion efficiency and an extremely high negative charge. This strain may represent a new bacterial species as suggested by 16S rRNA gene sequence analysis. These results indicate that the provision of hydrophobic sorbents containing sorbed PAHs in the enrichment procedure discriminated in favor of certain bacterial characteristics. The new isolation method is appropriate to select for adherent PAH-degrading bacteria, which might be useful to biodegrade sorbed PAHs in soils and sludge.
Thermostabilization of Proteins by Diglycerol Phosphate, a New Compatible Solute from the Hyperthermophile
Archaeoglobus fulgidus
Authors: Lamosa Pedro , Burke Anthony , Peist Ralf , Huber Robert , Liu Ming-Y. , Silva Gabriela , Rodrigues-Pousada Claudina , LeGall Jean , Maycock Christopher , Santos Helena 
Published: July 2002

ABSTRACT

Diglycerol phosphate accumulates under salt stress in the archaeon
Archaeoglobus fulgidus
(L. O. Martins, R. Huber, H. Huber, K. O. Stetter, M. S. da Costa, and H. Santos, Appl. Environ. Microbiol. 63:896–902, 1997). This solute was purified after extraction from the cell biomass. In addition, the optically active and the optically inactive (racemic) forms of the compound were synthesized, and the ability of the solute to act as a protecting agent against heating was tested on several proteins derived from mesophilic or hyperthermophilic sources. Diglycerol phosphate exerted a considerable stabilizing effect against heat inactivation of rabbit muscle lactate dehydrogenase, baker's yeast alcohol dehydrogenase, and
Thermococcus litoralis
glutamate dehydrogenase. Highly homologous and structurally well-characterized rubredoxins from
Desulfovibrio gigas
,
Desulfovibrio desulfuricans
(ATCC 27774), and
Clostridium pasteurianum
were also examined for their thermal stabilities in the presence or absence of diglycerol phosphate, glycerol, and inorganic phosphate. These proteins showed different intrinsic thermostabilities, with half-lives in the range of 30 to 100 min. Diglycerol phosphate exerted a strong protecting effect, with approximately a fourfold increase in the half-lives for the loss of the visible spectra of
D. gigas
and
C. pasteurianum
rubredoxins. In contrast, the stability of
D. desulfuricans
rubredoxin was not affected. These different behaviors are discussed in the light of the known structural features of rubredoxins. The data show that diglycerol phosphate is a potentially useful protein stabilizer in biotechnological applications.
Mitotic Recombination and Genetic Changes inSaccharomyces cerevisiaeduring Wine Fermentation
Authors: Puig Sergi , Querol Amparo , Barrio Eladio , Pérez-Ortín JoséE. 
Published: July 2002

ABSTRACTNatural strains ofSaccharomyces cerevisiaeare prototrophic homothallic yeasts that sporulate poorly, are often heterozygous, and may be aneuploid. This genomic constitution may confer selective advantages in some environments. Different mechanisms of recombination, such as meiosis or mitotic rearrangement of chromosomes, have been proposed for wine strains. We studied the stability of theURA3locus of aURA3/ura3wine yeast in consecutive grape must fermentations.ura3/ura3homozygotes were detected at a rate of 1 × 10−5to 3 × 10−5per generation, and mitotic rearrangements for chromosomes VIII and XII appeared after 30 mitotic divisions. We used the karyotype as a meiotic marker and determined that sporulation was not involved in this process. Thus, we propose a hypothesis for the genome changes in wine yeasts during vinification. This putative mechanism involves mitotic recombination between homologous sequences and does not necessarily imply meiosis.
Multiplex PCR for the Detection of
Lactobacillus pontis
and Two Related Species in a Sourdough Fermentation
Authors: Müller Martin R. A. , Ehrmann Matthias A. , Vogel Rudi F. 
Published: July 2002

ABSTRACT

A specific multiplex PCR assay based on the amplification of parts of the 16S rRNA molecule was designed. Primers derived from variable regions of the 16S rRNA provided a means of easily differentiating the species
Lactobacillus pontis
and
Lactobacillus panis
. They could be clearly discriminated from the phylogenetically related species
Lactobacillus vaginalis
,
Lactobacillus oris
, and
Lactobacillus reuteri
and from other lactobacilli commonly known to be present in sourdough. Other strains isolated together with
L. pontis
from an industrial sourdough fermentation could be clearly separated from these species by comparative sequence analysis and construction of a specific PCR primer. For a fast identification a DNA isolation protocol based on the ultrasonic lysis of cells from single colonies was developed. To demonstrate the potential of such techniques for tracking these organisms in a laboratory-scale fermentation, we combined the specific PCR assay with direct DNA extraction from the organisms in the sourdough without previous cultivation.
Characterization of a Salt-Tolerant Family 42 β-Galactosidase from a Psychrophilic Antarctic
Planococcus
Isolate
Authors: Sheridan Peter P. , Brenchley Jean E. 
Published: July 2002

ABSTRACT

We isolated a gram-positive, halotolerant psychrophile from a hypersaline pond located on the McMurdo Ice Shelf in Antarctica. A phylogenetic analysis of the 16S rRNA gene sequence of this organism showed that it is a member of the genus
Planococcus
. This assignment is consistent with the morphology and physiological characteristics of the organism. A gene encoding a β-galactosidase in this isolate was cloned in an
Escherichia coli
host. Sequence analysis of this gene placed it in glycosidase family 42 most closely related to an enzyme from
Bacillus circulans
. Even though an increasing number of family 42 glycosidase sequences are appearing in databases, little information about the biochemical features of these enzymes is available. Therefore, we purified and characterized this enzyme. The purified enzyme did not appear to have any metal requirement, had an optimum pH of 6.5 and an optimum temperature of activity at 42°C, and was irreversibly inactivated within 10 min when it was incubated at 55°C. The enzyme had an apparent

K
m

of 4.9 μmol of
o
-nitrophenyl-β-
d
-galactopyranoside, and the
V
max
was 467 μmol of
o
-nitrophenol produced/min/mg of protein at 39°C. Of special interest was the finding that the enzyme remained active at high salt concentrations, which makes it a possible reporter enzyme for halotolerant and halophilic organisms.
Thiosulfate Disproportionation by
Desulfotomaculum thermobenzoicum
Authors: Jackson Bradley E. , McInerney Michael J. 
Published: July 2002

ABSTRACT

Desulfotomaculum thermobenzoicum
, but not
Desulfotomaculum nigrificans
,
Desulfotomaculum ruminis
, or
Desulfosporosinus orientis
, grew by disproportionation of thiosulfate, forming stoichiometric amounts of sulfate and sulfide; sulfite was not disproportionated. The addition of acetate enhanced growth and thiosulfate disproportionation by
D. thermobenzoicum
compared to those observed with thiosulfate alone.