bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alkylglycerol Prodrugs of Phosphonoformate Are Potent In Vitro Inhibitors of Nucleoside-Resistant Human Immunodeficiency Virus Type 1 and Select for Resistance Mutations That Suppress Zidovudine Resistance
Authors: Hammond Jennifer L. , Koontz Dianna L. , Bazmi Holly Z. , Beadle James R. , Hostetler Saskia E. , Kini Ganesh D. , Aldern Kathy A. , Richman Douglas D. , Hostetler Karl Y. , Mellors John W. 
Published: July 2002

ABSTRACT

Phosphonoformate (foscarnet; PFA) is a potent inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), but its use for the treatment of HIV-1 infection is limited by toxicity and the lack of an orally bioavailable formulation. Alkylglycerol-conjugated prodrugs of PFA (1-
O
-octadecyl-
sn
-glycero-3-PFA [B-PFA]) having
sn
-2 substituents of hydrogen (deoxybatyl-PFA [DB-PFA]), methyl (MB-PFA), or ethyl (EB-PFA) are more-potent inhibitors of wild-type HIV-1 in vitro than unmodified PFA and are orally bioavailable in mice. We have evaluated the activities of these compounds against a panel of nucleoside-resistant HIV-1 variants and have characterized the resistant variants that emerge following in vitro selection with the prodrugs. Except for an HIV-1 variant encoding the K65R mutation in RT that exhibited 3.3- to 8.2-fold resistance, the nucleoside-resistant viruses included in the panel were sensitive to the PFA prodrugs (<3-fold increase in 50% inhibitory concentration), including multinucleoside-resistant variants encoding the Q151M complex of mutations or the T69S[SA] insert. Viruses resistant to the PFA prodrugs (>10-fold) were selected in vitro after 15 or more serial passages of HIV-1 in MT-2 cells in escalating prodrug concentrations. Mutations detected in the resistant viruses were S117T, F160Y, and L214F (DB-PFA); M164I and L214F (MB-PFA); and W88G and L214F (EB-PFA). The S117T, F160Y, and M164I mutations have not been previously identified. Generation of recombinant viruses encoding the single and double mutations confirmed their roles in prodrug resistance, including 214F, which generally increased the level of resistance. When introduced into a zidovudine (AZT)-resistant background (67N 70R 215F 219Q), the W88G, S117T, F160Y, and M164I mutations reversed AZT resistance. This suppression of AZT resistance is consistent with the effects of other foscarnet resistance mutations that reduce ATP-dependent removal of AZT monophosphate from terminated template primers. The favorable activity and resistance profiles of these PFA prodrugs warrant their further evaluation as clinical candidates.
Intramacrophage Passage of
Mycobacterium tuberculosis
and
M. avium
Complex Alters the Drug Susceptibilities of the Organisms as Determined by Intracellular Susceptibility Testing Using Macrophages and Type II Alveolar Epithelial Cells
Authors: Tomioka Haruaki , Sato Katsumasa , Sano Chiaki , Sano Keisuke , Shimizu Toshiaki 
Published: July 2002

ABSTRACT

Mycobacterium tuberculosis
and
M. avium
complex strains given intramacrophage passage (I-type) were compared with those cultured in a liquid medium (E-type) for their drug susceptibilities when they were replicating in Mono-Mac-6 macrophages or A-549 cells. Their intracellular susceptibilities to rifalazil, clarithromycin, and levofloxacin were decreased more in I-type organisms than in E-type organisms, except that their rifalazil susceptibility inside A-549 cells was markedly increased in I-type organisms.
Chromosomal System for Studying AmpC-Mediated β-Lactam Resistance Mutation in
Escherichia coli
Authors: Petrosino Joseph F. , Pendleton Amanda R. , Weiner Joel H. , Rosenberg Susan M. 
Published: July 2002

ABSTRACT

In some enterobacterial pathogens, but not in
Escherichia coli
, loss-of-function mutations in the
ampD
gene are a common route to β-lactam antibiotic resistance. We constructed an assay system for studying mechanism(s) of enterobacterial
ampD
mutation using the well-developed genetics of
E. coli
. We integrated the
Enterobacter ampRC
genes into the
E. coli
chromosome. These cells acquire spontaneous recombination- and SOS response-independent β-lactam resistance mutations in
ampD
. This chromosomal system is useful for studying mutation mechanisms that promote antibiotic resistance.
TEM-71, a Novel Plasmid-Encoded, Extended-Spectrum β-Lactamase Produced by a Clinical Isolate of
Klebsiella pneumoniae
Authors: Rasheed J. Kamile , Anderson Gregory J. , Queenan Anne Marie , Biddle James W. , Oliver Antonio , Jacoby George A. , Bush Karen , Tenover Fred C. 
Published: July 2002

ABSTRACT

TEM-71, a novel extended-spectrum β-lactamase from a
Klebsiella pneumoniae
clinical isolate, had an isoelectric point of 6.0 and a substrate profile showing preferential hydrolysis of cefotaxime over ceftazidime. It differed from TEM-1 by two substitutions, Gly238Ser and Glu240Lys, and was under the control of the strong
P4
promoter.
Efficacy of β-Lactams for Treating Experimentally Induced Pneumonia Due to a Carbapenem-Hydrolyzing Metallo-β-Lactamase-Producing Strain of
Pseudomonas aeruginosa
Authors: Bellais Samuel , Mimoz Olivier , Léotard Sophie , Jacolot Anne , Petitjean Olivier , Nordmann Patrice 
Published: July 2002

ABSTRACT

A rat pneumonia model was established with a
Pseudomonas aeruginosa
strain that produced the plasmid-encoded metallocarbapenemase VIM-2. A significant decrease in lung bacterial titers was observed when imipenem, cefepime, ceftazidime, and piperacillin-tazobactam were given at the highest doses recommended for humans, despite their high MICs. Aztreonam at high doses produced a similar decrease in bacterial titers.
Osmotic Stress-Induced Genetic Rearrangements in
Escherichia coli
H10407 Detected by Randomly Amplified Polymorphic DNA Analysis
Authors: Jolivet-Gougeon Anne , David-Jobert Sandrine , Tamanai-Shacoori Zohreh , Ménard Christian , Cormier Michel 
Published: July 2002

ABSTRACT

Randomly amplified polymorphic DNA (RAPD) analysis is a DNA polymorphism assay commonly used for fingerprinting genomes. After optimizing the reaction conditions, samples of
Escherichia coli
H10407 DNA were assayed to determine the influence of osmotic and/or oligotrophic stress on variations in RAPD banding patterns. Genetic rearrangements or DNA topology variations could be detected as changes in agarose gel electrophoresis banding profiles. A new amplicon generated using DNA extracted from bacteria prestarved by an osmotic stress and resuscitated in rich medium was observed. Enrichment improved recovery of mutator cells and allowed them to be detected in samples, suggesting that DNA modifications, such as stress-induced alterations and supercoiling phenomena, should be taken into consideration before beginning RAPD analyses.
Utilization of Dimethyl Sulfide as a Sulfur Source with the Aid of Light by
Marinobacterium
sp. Strain DMS-S1
Authors: Fuse Hiroyuki , Takimura Osamu , Murakami Katsuji , Yamaoka Yukiho , Omori Toshio 
Published: July 2002

ABSTRACT

Strain DMS-S1 isolated from seawater was able to utilize dimethyl sulfide (DMS) as a sulfur source only in the presence of light in a sulfur-lacking medium. Phylogenetic analysis based on 16S ribosomal DNA genes indicated that the strain was closely related to
Marinobacterium georgiense
. The strain produced dimethyl sulfoxide (DMSO), which was a main metabolite, and small amounts of formate and formaldehyde when grown on DMS as the sole sulfur source. The cells of the strain grown with succinate as a carbon source were able to use methyl mercaptan or methanesulfonate besides DMS but not DMSO or dimethyl sulfone as a sole sulfur source. DMS was transformed to DMSO primarily at wavelengths between 380 and 480 nm by heat-stable photosensitizers released by the strain. DMS was also degraded to formaldehyde in the presence of light by unidentified heat-stable factors released by the strain, and it appeared that strain DMS-S1 used the degradation products, which should be sulfite, sulfate, or methanesulfonate, as sulfur sources.
Effect of Copper Speciation on Whole-Cell Soluble Methane Monooxygenase Activity inMethylosinus trichosporiumOB3b
Authors: Morton John D. , Hayes Kim F. , Semrau Jeremy D. 
Published: July 2002

ABSTRACTSoluble methane monooxygenase (sMMO) activity inMethylosinus trichosporiumOB3b was found to be more strongly affected as copper-to-biomass ratios changed in a newly developed medium, M2M, which uses pyrophosphate for metal chelation, than in nitrate mineral salts (NMS), which uses EDTA. When M2M medium was amended with EDTA, sMMO activity was similar to that in NMS medium, indicating that EDTA-bound copper had lower bioavailability than pyrophosphate-bound copper. EDTA did not limit the association of copper with the cells; rather, copper was sequestered in a form which did not affect sMMO activity.
Application of Rapid Dot Blot Immunoassay for Detection of
Salmonella enterica
Serovar Enteritidis in Eggs, Poultry, and Other Foods
Authors: Yoshimasu Mark Akira , Zawistowski Jerzy 
Published: July 2002

ABSTRACT

Salmonella enterica
serovar Enteritidis was detected in artificially inoculated eggs within 24 h through a rapid monoclonal antibody-based dot blot immunoassay. Detection in poultry and other products required 28 h. Samples were directly enriched in homogenized egg without the need for pre- or postenrichment steps. Serovar Enteritidis was detected in the presence of other bacteria when outcompeted 1:400.
Organization and Transcriptional Analysis of a Six-Gene Cluster around the
rplK-rplA
Operon of
Corynebacterium glutamicum
Encoding the Ribosomal Proteins L11 and L1
Authors: Barreiro Carlos , González-Lavado Eva , Martı́n Juan F. 
Published: July 2002

ABSTRACT

A cluster of six genes, tRNA
Trp
-
secE-nusG-rplK-rplA-pkwR,
was cloned and sequenced from a
Corynebacterium glutamicum
cosmid library and shown to be contiguous in the
C. glutamicum
genome. These genes encode a tryptophanyl tRNA, the protein translocase component SecE, the antiterminator protein NusG, and the ribosomal proteins L11 and L1 in addition to PkwR, a putative regulatory protein of the LacI-GalR family. S1 nuclease mapping analysis revealed that
nusG
and
rplK
are expressed as separate transcriptional units and
rplK
and
rplA
are cotranscribed as a single mRNA. A 19-nucleotide inverted repeat that appears to correspond to a transcriptional terminator was located in the 3′ region downstream from
nusG
. Northern analysis with different probes confirmed the S1 mapping results and showed that the
secE-rplA
four-gene region gives rise to four transcripts.
secE
was transcribed as a 0.5-kb monocistronic mRNA,
nusG
formed two transcripts of 1.4 and 1.0 kb from different initiation sites, and the two ribosomal protein genes
rplK
and
rplA
were cotranscribed as a single mRNA of 1.6 kb. A consensus L1 protein binding sequence was identified in the leader region of the
rplK-rplA
transcript, suggesting that expression of the
rplK-rplA
cluster was regulated by autogenous regulation exerted by the L1 protein at the translation level. The promoters of the
nusG
and
rplK-rplA
genes were subcloned in a novel corynebacterial promoter-probe vector and shown to confer strong expression of the reporter gene.
Molecular Characterization of an Endopolygalacturonase from
Fusarium oxysporum
Expressed during Early Stages of Infection
Authors: Garcı́a-Maceira Fé I. , Di Pietro A. , Huertas-González M. Dolores , Ruiz-Roldán M. Carmen , Roncero M. Isabel G. 
Published: July 2002

ABSTRACT

The tomato vascular wilt pathogen
Fusarium oxysporum
f. sp
. lycopersici
produces an array of pectinolytic enzymes that may contribute to penetration and colonization of the host plant. Here we report the isolation of
pg5
, encoding a novel extracellular endopolygalacturonase (endoPG) that is highly conserved among different formae speciales of
F. oxysporum
. The putative mature
pg5
product has a calculated molecular mass of 35 kDa and a pI of 8.3 and is more closely related to endoPGs from other fungal plant pathogens than to PG1, the major endoPG of
F. oxysporum
. Overexpression of
pg5
in a bacterial heterologous system produced a 35-kDa protein with endoPG activity. Accumulation of
pg5
transcript is induced by citrus pectin and
d
-galacturonic acid and repressed by glucose. As shown by reverse transcription-PCR,
pg5
is expressed by
F. oxysporum
in tomato roots during the initial stages of infection. Targeted inactivation of
pg5
has no detectable effect on virulence toward tomato plants.
Survival of
Campylobacter jejuni
during Stationary Phase: Evidence for the Absence of a Phenotypic Stationary-Phase Response
Authors: Kelly Alison F. , Park Simon F. , Bovill Richard , Mackey Bernard M. 
Published: July 2002

ABSTRACT

When
Campylobacter jejuni
NCTC 11351 was grown microaerobically in rich medium at 39°C, entry into stationary phase was followed by a rapid decline in viable numbers to leave a residual population of 1% of the maximum number or less. Loss of viability was preceded by sublethal injury, which was seen as a loss of the ability to grow on media containing 0.1% sodium deoxycholate or 1% sodium chloride. Resistance of cells to mild heat stress (50°C) or aeration was greatest in exponential phase and declined during early stationary phase. These results show that
C. jejuni
does not mount the normal phenotypic stationary-phase response which results in enhanced stress resistance. This conclusion is consistent with the absence of
rpoS
homologues in the recently reported genome sequence of this species and their probable absence from strain NCTC 11351. During prolonged incubation of
C. jejuni
NCTC 11351 in stationary phase, an unusual pattern of decreasing and increasing heat resistance was observed that coincided with fluctuations in the viable count. During stationary phase of
Campylobacter coli
UA585, nonmotile variants and those with impaired ability to form coccoid cells were isolated at high frequency. Taken together, these observations suggest that stationary-phase cultures of campylobacters are dynamic populations and that this may be a strategy to promote survival in at least some strains. Investigation of two spontaneously arising variants (NM3 and SC4) of
C. coli
UA585 showed that a reduced ability to form coccoid cells did not affect survival under nongrowth conditions.
16S Ribosomal DNA Characterization of Nitrogen-Fixing Bacteria Isolated from Banana (
Musa
spp.) and Pineapple (
Ananas comosus
(L.) Merril)
Authors: Magalhães Cruz Leonardo , Maltempi de Souza Emanuel , Weber Olmar Baler , Baldani José Ivo , Döbereiner Johanna , de Oliveira Pedrosa Fábio 
Published: July 2002

ABSTRACT

Nitrogen-fixing bacteria isolated from banana (
Musa
spp.) and pineapple (
Ananas comosus
(L.) Merril) were characterized by amplified 16S ribosomal DNA restriction analysis and 16S rRNA sequence analysis.
Herbaspirillum seropedicae
,
Herbaspirillum rubrisubalbicans
,
Burkholderia brasilensis,
and
Burkholderia tropicalis
were identified. Eight other types were placed in close proximity to these genera and other alpha and beta
Proteobacteria
.
Comparison of Genotypes and Serotypes of
Campylobacter jejuni
Isolated from Danish Wild Mammals and Birds and from Broiler Flocks and Humans
Authors: Petersen L. , Nielsen E. M. , Engberg J. , On S. L. W. , Dietz H. H. 
Published: July 2002

ABSTRACT

The incidence of human infection with
Campylobacter jejuni
is increasing in most developed countries and the reason for this is largely unknown. Although poultry meat is considered to be a major source, it is evident that other reservoirs exist, possibly common to humans and poultry. Environmental sources are believed to be important reservoirs of
Campylobacter
infection in broiler chicken flocks. We investigated the potential importance of wildlife as a source of infection in commercial poultry flocks and in humans by comparing the serotype distributions,
fla
types, and macrorestriction profiles (MRPs) of
C. jejuni
isolates from different sources. The serotype distribution in wildlife was significantly different from the known distributions in broilers and humans. Considerable sero- and genotype diversity was found within the wildlife collection, although two major groups of isolates within serotype O:12 and the O:4 complex were found. Common clonal lines among wildlife, chicken, and/or human isolates were identified within serotype O:2 and the O:4 complex. However, MRPs of O:12 and O:38 strains isolated from wildlife and other sources indicated that some clonal lines propagated in a wide selection of animal species but were not detected in humans or broilers in this study. The applied typing methods successfully identified different clonal groups within a strain collection showing large genomic diversity. However, the relatively low number of wildlife strains with an inferred clonal relationship to human and chicken strains suggests that the importance of wildlife as a reservoir of infection is limited.
Bioremediation (Natural Attenuation and Biostimulation) of Diesel-Oil-Contaminated Soil in an Alpine Glacier Skiing Area
Authors: Margesin R. , Schinner F. 
Published: July 2002

ABSTRACT

We investigated the feasibility of bioremediation as a treatment option for a chronically diesel-oil-polluted soil in an alpine glacier area at an altitude of 2,875 m above sea level. To examine the efficiencies of natural attenuation and biostimulation, we used field-incubated lysimeters (mesocosms) with unfertilized and fertilized (N-P-K) soil. For three summer seasons (July 1997 to September 1999), we monitored changes in hydrocarbon concentrations in soil and soil leachate and the accompanying changes in soil microbial counts and activity. A significant reduction in the diesel oil level could be achieved. At the end of the third summer season (after 780 days), the initial level of contamination (2,612 ± 70 μg of hydrocarbons g [dry weight] of soil
−1
) was reduced by (50 ± 4)% and (70 ± 2)% in the unfertilized and fertilized soil, respectively. Nonetheless, the residual levels of contamination (1,296 ± 110 and 774 ± 52 μg of hydrocarbons g [dry weight] of soil
−1
in the unfertilized and fertilized soil, respectively) were still high. Most of the hydrocarbon loss occurred during the first summer season ([42 ± 6]% loss) in the fertilized soil and during the second summer season ([41 ± 4]% loss) in the unfertilized soil. In the fertilized soil, all biological parameters (microbial numbers, soil respiration, catalase and lipase activities) were significantly enhanced and correlated significantly with each other, as well as with the residual hydrocarbon concentration, pointing to the importance of biodegradation. The effect of biostimulation of the indigenous soil microorganisms declined with time. The microbial activities in the unfertilized soil fluctuated around background levels during the whole study.
Development of a Quantitative Competitive PCR Assay for Detection and Quantification of
Escherichia coli
O157:H7 Cells
Authors: Li Wenli , Drake Mary Anne 
Published: July 2002

ABSTRACT

A quantitative competitive PCR (QC-PCR) assay was developed to detect and quantify
Escherichia coli
O157:H7 cells. From 10
3
to 10
8
CFU of
E. coli
O157:H7 cells/ml was quantified in broth or skim milk, and cell densities predicted by QC-PCR were highly related to viable cell counts (
r
2
= 0.99 and 0.93, respectively). QC-PCR has potential for quantitative detection of pathogenic bacteria in foods.
Antibiotic Resistance in
Salmonella enterica
Serovar Typhimurium Exposed to Microcin-Producing
Escherichia coli
Authors: Carlson Steve A. , Frana Timothy S. , Griffith Ronald W. 
Published: July 2002

ABSTRACT

Microcin 24 is an antimicrobial peptide secreted by uropathogenic
Escherichia coli
. Secretion of microcin 24 provides an antibacterial defense mechanism for
E. coli
. In a plasmid-based system using transformed
Salmonella enterica
, we found that resistance to microcin 24 could be seen in concert with a multiple-antibiotic resistance phenotype. This multidrug-resistant phenotype appeared when
Salmonella
was exposed to an
E. coli
strain expressing microcin 24. Therefore, it appears that multidrug-resistant
Salmonella
can arise as a result of an insult from other pathogenic bacteria.
Purification and Characterization of Thermostable Endo-1,5-α-
l
-Arabinase from a Strain of
Bacillus thermodenitrificans
Authors: Takao Makoto , Akiyama Kana , Sakai Takuo 
Published: July 2002

ABSTRACT

A strain of a thermophilic bacterium, tentatively designated
Bacillus thermodenitrificans
TS-3, with arabinan-degrading activity was isolated. It produced an endo-arabinase (ABN) (EC 3.2.1.99) and two arabinofuranosidases (EC 3.2.1.55) extracellularly when grown at 60°C on a medium containing sugar beet arabinan. The ABN (tentatively called an ABN-TS) was purified 7,417-fold by anion-exchange, hydrophobic, size exclusion, and hydroxyapatite chromatographies. The molecular mass of ABN-TS was 35 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the isoelectric point was pH 4.5. The enzyme was observed to be more thermostable than known ABNs; it had a half-life of 4 h at 75°C. The enzyme had optimal activity at 70°C and pH 6.0. The enzyme had apparent

K
m

values of 8.5 and 45 mg/ml and apparent
V
max
values of 1.6 and 1.1 mmol/min/mg of protein against debranched arabinan (α-1,5-arabinan) and arabinan, respectively. The enzyme had no pectin-releasing activity (protopectinase activity) from sugar beet protopectin, differing from an ABN (protopectinase-C) from mesophilic
Bacillus subtilis
IFO 3134. The pattern of degradation of debranched arabinan by ABN-TS indicated that the enzyme was an endo-acting enzyme and the main end products were arabinobiose and arabinose. The results of preliminary experiments indicated that the culture filtrate of strain TS-3 is suitable for
l
-arabinose production from sugar beet pulp at high temperature.
Gene Expression Analysis of Cold and Freeze Stress in Baker's Yeast
Authors: Rodriguez-Vargas Sonia , Estruch Francisco , Randez-Gil Francisca 
Published: July 2002

ABSTRACT

We used mRNA differential display to assess yeast gene expression under cold or freeze shock stress conditions. We found both up- and down-regulation of genes, although repression was more common. We identified and sequenced several cold-induced genes exhibiting the largest differences. We confirmed, by Northern blotting, the specificity of the response for
TPI1
, which encodes triose-phosphate isomerase;
ERG10
, the gene for acetoacetyl coenzyme A thiolase; and
IMH1
, which encodes a protein implicated in protein transport. These genes also were induced under other stress conditions, suggesting that this cold response is mediated by a general stress mechanism. We determined the physiological significance of the cold-induced expression change of these genes in two baker's yeast strains with different sensitivities to freeze stress. The mRNA level of
TPI1
and
ERG10
genes was higher in freeze-stressed than in control samples of the tolerant strain. In contrast, both genes were repressed in frozen cells of the sensitive strain. Next, we examined the effects of
ERG10
overexpression on cold and freeze-thaw tolerance. Growth of wild-type cells at 10°C was not affected by high
ERG10
expression. However, YEpERG10 transformant cells exhibited increased freezing tolerance. Consistent with this, cells of an
erg10
mutant strain showed a clear phenotype of cold and freeze sensitivity. These results give support to the idea that a cause-and-effect relationship between differentially expressed genes and cryoresistance exists in
Saccharomyces cerevisiae
and open up the possibility of design strategies to improve the freeze tolerance of baker's yeast.