bluuebunny/crossref_metadata_2025_split huggingface dataset:
4′-Ethynyl Nucleoside Analogs: Potent Inhibitors of Multidrug-Resistant Human Immunodeficiency Virus Variants In Vitro
Authors: Kodama Ei-Ichi , Kohgo Satoru , Kitano Kenji , Machida Haruhiko , Gatanaga Hiroyuki , Shigeta Shiro , Matsuoka Masao , Ohrui Hiroshi , Mitsuya Hiroaki 
Published: July 2002

ABSTRACT

A series of 4′-ethynyl (4′-
E
) nucleoside analogs were designed, synthesized, and identified as being active against a wide spectrum of human immunodeficiency viruses (HIV), including a variety of laboratory strains of HIV-1, HIV-2, and primary clinical HIV-1 isolates. Among such analogs examined, 4′-
E
-2′-deoxycytidine (4′-
E
-dC), 4′-
E
-2′-deoxyadenosine (4′-
E
-dA), 4′-
E
-2′-deoxyribofuranosyl-2,6-diaminopurine, and 4′-
E
-2′-deoxyguanosine were the most potent and blocked HIV-1 replication with 50% effective concentrations ranging from 0.0003 to 0.01 μM in vitro with favorable cellular toxicity profiles (selectivity indices ranging 458 to 2,600). These 4′-
E
analogs also suppressed replication of various drug-resistant HIV-1 clones, including HIV-1
M41L/T215Y
, HIV-1
K65R
, HIV-1
L74V
, HIV-1
M41L/T69S-S-G/T215Y
, and HIV-1
A62V/V75I/F77L/F116Y/Q151M
. Moreover, these analogs inhibited the replication of multidrug-resistant clinical HIV-1 strains carrying a variety of drug resistance-related amino acid substitutions isolated from HIV-1-infected individuals for whom 10 or 11 different anti-HIV-1 agents had failed. The 4′-
E
analogs also blocked the replication of a non-nucleoside reverse transcriptase inhibitor-resistant clone, HIV-1
Y181C
, and showed an HIV-1 inhibition profile similar to that of zidovudine in time-of-drug-addition assays. The antiviral activity of 4′-
E
-thymidine and 4′-
E
-dC was blocked by the addition of thymidine and 2′-deoxycytidine, respectively, while that of 4′-
E
-dA was not affected by 2′-deoxyadenosine, similar to the antiviral activity reversion feature of 2′,3′-dideoxynucleosides, strongly suggesting that 4′-
E
analogs belong to the family of nucleoside reverse transcriptase inhibitors. Further development of 4′-
E
analogs as potential therapeutics for infection with multidrug-resistant HIV-1 is warranted.
Genetic Organization of the Chromosome Region Surrounding
mecA
in Clinical Staphylococcal Strains: Role of IS
431
-Mediated
mecI
Deletion in Expression of Resistance in
mecA
-Carrying, Low-Level Methicillin- Resistant
Staphylococcus haemolyticus
Authors: Katayama Yuki , Ito Teruyo , Hiramatsu Keiichi 
Published: July 2002

ABSTRACT

We report on the structural diversity of
mecA
gene complexes carried by 38 methicillin-resistant
Staphylococcus aureus
and 91 methicillin-resistant coagulase-negative
Staphylococcus
strains of seven different species with a special reference to its correlation with phenotypic expression of methicillin resistance. The most prevalent and widely disseminated
mec
complex had the structure
mecI-mecR1-mecA
-IS
431R
(or IS
431mec
), designated the class A
mecA
gene complex. In contrast, in
S. haemolyticus, mecA
was bracketed by two copies of IS
431
, forming the structure IS
431L-mecA
-IS
431R
. Of the 38
S. haemolyticus
strains, 5 had low-level methicillin resistance (MIC, 1 to 4 mg/liter) and characteristic heterogeneous methicillin resistance as judged by population analysis. In these five strains, IS
431L
was located to the left of an intact
mecI
gene, forming the structure IS
431L
-class A
mecA
-gene complex. In other
S. haemolyticus
strains, IS
431L
was associated with the deletion of
mecI
and
mecR1
, forming the structure IS
431L
-Δ
mecR1-mecA
-IS
431mec
, designated the class C
mecA
gene complex. Mutants with the class C
mecA
gene complex were obtained in vitro by selecting strain SH621, containing the IS
431L
-class A
mecA
gene complex with low concentrations of methicillin (1 and 3 mg/liter). The mutants had intermediate level of methicillin resistance (MIC, 16 to 64 mg/liter). The
mecA
gene transcription was shown to be derepressed in a representative mutant strain, SH621-37. Our study indicated that the
mecI
-encoded repressor function is responsible for the low-level methicillin resistance of some
S. haemolyticus
clinical strains and that the IS
431
-mediated
mecI
gene deletion causes the expression of methicillin resistance through the derepression of
mecA
gene transcription.
Convulsant and Subconvulsant Doses of Norfloxacin in the Presence and Absence of Biphenylacetic Acid Alter Extracellular Hippocampal Glutamate but Not Gamma-Aminobutyric Acid Levels in Conscious Rats
Authors: Smolders I. , Gousseau C. , Marchand S. , Couet W. , Ebinger G. , Michotte Y. 
Published: July 2002

ABSTRACT

Fluoroquinolones are antibiotics with central excitatory side effects. These adverse effects presumably result from inhibition of γ-aminobutyric acid (GABA) binding to GABA
A
receptors. This GABA antagonistic effect is greatly potentiated by the active metabolite of fenbufen, biphenylacetic acid (BPAA). Nevertheless, it remains questionable whether GABA receptor antagonism alone can explain the convulsant activity potentials of these antimicrobial agents. The present study was undertaken to investigate the possible effects of norfloxacin, both in the absence and in the presence of BPAA, on the extracellular hippocampal levels of GABA and glutamate, the main central inhibitory and excitatory amino acid neurotransmitters, respectively. This in vivo microdialysis approach with conscious rats allows monitoring of behavioral alterations and concomitant transmitter modulation in the hippocampus. Peroral administration of 100 mg of BPAA per kg of body weight had no effect on behavior and did not significantly alter extracellular GABA or glutamate concentrations. Intravenous perfusion of 300 mg of norfloxacin per kg did not change the rat's behavior or the concomitant neurotransmitter levels in about half of the experiments, while the remaining animals exhibited severe seizures. These norfloxacin-induced convulsions did not affect extracellular hippocampal GABA levels but were accompanied by enhanced glutamate concentrations. Half of the rats receiving both 100 mg of BPAA per kg and 50 mg of norfloxacin per kg displayed lethal seizures, while the remaining animals showed no seizure-related behavior. In the latter subgroup, again no significant alterations in extracellular GABA levels were observed, but glutamate overflow remained significantly elevated for at least 3 h. In conclusion, norfloxacin exerts convulsant activity in rats, accompanied by elevations of extracellular hippocampal glutamate levels but not GABA levels, even in the presence of BPAA.
Presence of a Group II Intron in a Multiresistant
Serratia marcescens
Strain That Harbors Three Integrons and a Novel Gene Fusion
Authors: Centrón Daniela , Roy Paul H. 
Published: July 2002

ABSTRACT

We analyzed the role of integrons in the dissemination of antibiotic resistance in a recent multiresistant clinical isolate,
Serratia marcescens
SCH88050909 (SCH909). This isolate harbors three integrons, all on a 60-kb conjugative plasmid. By PCR, hybridization, and sequencing analyses, we found that integron 1 has the
dfrA1
and
ant
(
3
")
-Ia
cassettes. The first cassette in integron 2 contains the
ant
(
2
")
-Ia
gene, separated from its
attC
site (59-base element) by a 1,971-bp insert containing a group II intron; this intron codes for a putative maturase-reverse transcriptase on the complementary strand and is the first such intron to be found associated with an integron. The
attC
site is followed by a novel aminoglycoside resistance gene,
ant
(
3
")
-Ii-aac
(
6
′)
-IId
, which has been characterized for its bifunctional ANT(3")-I and AAC(6′)-II activities. DNA sequence analysis of this fused cassette suggests that insertion and excision due to the integrase activity could have an important role in the evolution of aminoglycoside resistance genes. This gene is followed by an unknown open reading frame with a typical
attC
site and a partial cassette composed of the beginning of the
bla
OXA-10
cassette interrupted by IS
1
. The sequence downstream of IS
1
revealed that the
bla
OXA-10
cassette is incomplete and that the 3′ conserved segment of this integron is absent. Integron 3 is in a Tn
1696
-like transposon with the
aac
(
3
)
-Ia
cassette followed by three unknown cassettes and
ant
(
3
")
-Ia
. The presence of the group II intron and the relationship of group II introns in eubacteria with mobile elements suggest a possible role of this element in events such as cassette formation and/or plasmid evolution.
Imaging the Enzymatic Digestion of Bacterial Cellulose Ribbons Reveals the Endo Character of the Cellobiohydrolase Cel6A fromHumicola insolensand Its Mode of Synergy with Cellobiohydrolase Cel7A
Authors: Boisset Claire , Fraschini Carole , Schülein Martin , Henrissat Bernard , Chanzy Henri 
Published: July 2002

ABSTRACTDispersed cellulose ribbons from bacterial cellulose were subjected to digestion with cloned Cel7A (cellobiohydrolase [CBH] I) and Cel6A (CBH II) fromHumicola insolenseither alone or in a mixture and in the presence of an excess of β-glucosidase. Both Cel7A and Cel6A were effective in partially converting the ribbons into soluble sugars, Cel7A being more active than Cel6A. In combination, these enzymes showed substantial synergy culminating with a molar ratio of approximately two-thirds Cel6A and one-third Cel7A. Ultrastructural transmission electron microscopy (TEM) observations indicated that Cel7A induced a thinning of the cellulose ribbons, whereas Cel6A cut the ribbons into shorter elements, indicating an endo type of action. These observations, together with the examination of the digestion kinetics, indicate that Cel6A can be classified as an endo-processive enzyme, whereas Cel7A is essentially a processive enzyme. Thus, the synergy resulting from the mixing of Cel6A and Cel7A can be explained by the partial endo character of Cel6A. A preparation of bacterial cellulose ribbons appears to be an appropriate substrate, superior toValoniaor bacterial cellulose microcrystals, to visualize directly by TEM the endo-processivity of an enzyme such as Cel6A.
Sediment Microbial Community Structure and Mercury Methylation in Mercury-Polluted Clear Lake, California
Authors: Macalady J. L. , Mack E. E. , Nelson D. C. , Scow K. M. 
Published: July 2002

ABSTRACT

Spatial and temporal variations in sediment microbial community structure in a eutrophic lake polluted with inorganic mercury were identified using polar lipid fatty acid (PLFA) analysis. Microbial community structure was strongly related to mercury methylation potential, sediment organic carbon content, and lake location. Pore water sulfate, total mercury concentrations, and organic matter C/N ratios showed no relationships with microbial community structure. Seasonal changes and changes potentially attributable to temperature regulation of bacterial membranes were detectable but were less important influences on sediment PLFA composition than were differences due to lake sampling location. Analysis of biomarker PLFAs characteristic of
Desulfobacter
and
Desulfovibrio
groups of sulfate-reducing bacteria suggests that
Desulfobacter
-like organisms are important mercury methylators in the sediments, especially in the Lower Arm of Clear Lake.
Biofilm Community Structure in Polluted Rivers: Abundance of Dominant Phylogenetic Groups over a Complete Annual Cycle
Authors: Brümmer I. H. M. , Fehr W. , Wagner-Döbler I. 
Published: July 2002

ABSTRACT

The seasonal dynamics of river biofilm communities in two German rivers, the Elbe and one of its tributaries, the Spittelwasser, were investigated for the first time by using fluorescence in situ hybridization and a standardized biofilm sampling procedure. We show the importance of members of the β subclass of the class
Proteobacteria
, which formed the largest single group in the massively polluted Spittelwasser at all times. Clear seasonal peaks of abundance were observed for the planctomycetes and the
Cytophaga-Flavobacterium
cluster.
Extensive Polymorphism in
Cryptosporidium parvum
Identified by Multilocus Microsatellite Analysis
Authors: Feng Xiaochuan , Rich Stephen M. , Akiyoshi Donna , Tumwine James K. , Kekitiinwa Addy , Nabukeera Nicolette , Tzipori Saul , Widmer Giovanni 
Published: July 2002

ABSTRACT

Restriction fragment length polymorphism and DNA sequence analysis discern two main types of
Cryptosporidium parvum
. We present a survey of length polymorphism at several microsatellite loci for type 1 and type 2 isolates. A total of 14 microsatellite loci were identified from
C. parvum
DNA sequences deposited in public databases. All repeats were mono-, di-, and trinucleotide repeats of A, AT, and AAT, reflecting the high AT content of the
C. parvum
genome. Several of these loci showed significant length polymorphism, with as many as seven alleles identified for a single locus. Differences between alleles ranged from 1 to 27 bp. Karyotype analysis using probes flanking three microsatellites localized each marker to an individual chromosomal band, suggesting that these markers are single copy. In a sample of 19 isolates for which at least three microsatellites were typed, a majority of isolates displayed a unique multilocus fingerprint. Microsatellite analysis of isolates passaged between different host species identified genotypic changes consistent with changes in parasite populations.
Determination of the Sensitivity of a Rapid
Escherichia coli
O157:H7 Assay for Testing 375-Gram Composite Samples
Authors: Tsai Wan-Ling , Miller Cynthia E. , Richter Edward R. 
Published: July 2002

ABSTRACT

Both 25-g single-size ground beef samples and 375-g composite ground beef samples were tested by a method combining an immunomagnetic separation (IMS) technique with a sandwich enzyme-linked immunosorbent assay (ELISA) system (IMS-ELISA). The results demonstrated that IMS-ELISA could detect the target,
Escherichia coli
O157:H7, at the level of 10
−1
CFU/g of sample in either the 25- or 375-g sample size.
Plant Genome Complexity May Be a Factor Limiting In Situ the Transfer of Transgenic Plant Genes to the Phytopathogen
Ralstonia solanacearum
Authors: Bertolla Franck , Pepin Regis , Passelegue-Robe Eugenie , Paget Eric , Simkin Andrew , Nesme Xavier , Simonet Pascal 
Published: July 2002

ABSTRACT

The development of natural competence by bacteria in situ is considered one of the main factors limiting transformation-mediated gene exchanges in the environment.
Ralstonia solanacearum
is a plant pathogen that is also a naturally transformable bacterium that can develop the competence state during infection of its host. We have attempted to determine whether this bacterium could become the recipient of plant genes. We initially demonstrated that plant DNA was released close to the infecting bacteria. We constructed and tested various combinations of transgenic plants and recipient bacteria to show that the effectiveness of such transfers was directly related to the ratio of the complexity of the plant genome to the number of copies of the transgene.
Multiple Antibiotic Resistance (
mar
) Locus in
Salmonella enterica
Serovar Typhimurium DT104
Authors: Randall Luke P. , Woodward Martin J. 
Published: July 2002

ABSTRACT

In order to understand the role of the
mar
locus in
Salmonella
with regard to multiple antibiotic resistance, cyclohexane resistance, and outer membrane protein F (OmpF) regulation, a
marA
::
gfp
reporter mutant was constructed in an antibiotic-sensitive
Salmonella enterica
serovar Typhimurium DT104 background. Salicylate induced
marA
, whereas a number of antibiotics, disinfectants, and various growth conditions did not. Increased antibiotic resistance was observed upon salicylate induction, although this was shown to be by both
mar
-dependent and
mar
-independent pathways. Cyclohexane resistance, however, was induced by salicylate by a
mar
-dependent pathway. Complementation studies with a plasmid that constitutively expressed
marA
confirmed the involvement of
mar
in
Salmonella
with low-level antibiotic resistance and cyclohexane resistance, although the involvement of
mar
in down regulation of OmpF was unclear. However,
marA
overexpression did increase the expression of a ca. 50-kDa protein, but its identity remains to be elucidated. Passage of the
marA
::
gfp
reporter mutant with increasing levels of tetracycline, a method reported to select for
mar
mutants in
Escherichia coli
, led to both multiple-antibiotic and cyclohexane resistance. Collectively, these data indicate that low-level antibiotic resistance, cyclohexane resistance, and modulation of OMPs in
Salmonella
, as in
E. coli
, can occur in both a
mar
-dependent and
mar
-independent manner.
Use of Pulsed-Field Gel Electrophoresis and Flagellin Gene Typing in Identifying Clonal Groups of
Campylobacter jejuni
and
Campylobacter coli
in Farm and Clinical Environments
Authors: Fitzgerald Collette , Stanley Karen , Andrew Sarah , Jones Keith 
Published: July 2002

ABSTRACT

Although campylobacters have been isolated from a wide range of animal hosts, the association between campylobacters isolated from humans and animals in the farm environment is unclear. We used flagellin gene typing and pulsed-field gel electrophoresis (PFGE) to investigate the genetic diversity among isolates from animals (cattle, sheep, and turkey) in farm environments and sporadic cases of campylobacteriosis in the same geographical area. Forty-eight combined
fla
types were seen among the 315
Campylobacter
isolates studied. Six were found in isolates from all four hosts and represented 50% of the total number of isolates. Seventy-one different
Sma
I PFGE macrorestriction profiles (mrps) were observed, with 86% of isolates assigned to one of 29 different mrps. Fifty-seven isolates from diverse hosts, times, and sources had an identical
Sma
I mrp and combined
fla
type. Conversely, a number of genotypes were unique to a particular host. We provide molecular evidence which suggests a link between campylobacters in the farm environment with those causing disease in the community.
Map of the IncP1β Plasmid pTSA Encoding the Widespread Genes (
tsa
) for
p-
Toluenesulfonate Degradation in
Comamonas testosteroni
T-2
Authors: Tralau Tewes , Cook Alasdair M. , Ruff Juergen 
Published: July 2002

ABSTRACT

The catabolic IncP1β plasmid pTSA from
Comamonas testosteroni
T-2 was mapped by subtractive analysis of restriction digests, by sequencing outwards from the
tsa
operon (toluenesulfonate degradation), and by generating overlapping, long-distance-PCR amplification products. The plasmid was estimated to comprise 72 ± 4 kb. The
tsa
region was found to be a composite transposon flanked by two IS
1071
elements. A cryptic
tsa
operon was also present in the
tsa
transposon. Those backbone genes and regions which we sequenced were in the same order as the corresponding genes in resistance plasmid R751, and identities of about 99% were observed. Enrichment cultures with samples from four continents were done to obtain organisms able to utilize
p
-toluenesulfonate as the sole source of carbon and energy for aerobic growth. Most (15) of the 16 cultures (13 of them isolates) were obtained from contaminated sites and were attributed to three metabolic groups, depending on their metabolism of
p
-toluenesulfonate. The largest group contained the
tsa
transposon, usually (six of seven isolates) with negligible differences in sequence from strain T-2.
Intra- and Extracellular β-Galactosidases from
Bifidobacterium bifidum
and
B. infantis
: Molecular Cloning, Heterologous Expression, and Comparative Characterization
Authors: Møller Peter L. , Jørgensen Flemming , Hansen Ole C. , Madsen Søren M. , Stougaard Peter 
Published: July 2002

ABSTRACT

Three β-galactosidase genes from
Bifidobacterium bifidum
DSM20215 and one β-galactosidase gene from
Bifidobacterium infantis
DSM20088 were isolated and characterized. The three
B. bifidum
β-galactosidases exhibited a low degree of amino acid sequence similarity to each other and to previously published β-galactosidases classified as family 2 glycosyl hydrolases. Likewise, the
B. infantis
β-galactosidase was distantly related to enzymes classified as family 42 glycosyl hydrolases. One of the enzymes from
B. bifidum
, termed BIF3, is most probably an extracellular enzyme, since it contained a signal sequence which was cleaved off during heterologous expression of the enzyme in
Escherichia coli
. Other exceptional features of the BIF3 β-galactosidase were (i) the monomeric structure of the active enzyme, comprising 1,752 amino acid residues (188 kDa) and (ii) the molecular organization into an N-terminal β-galactosidase domain and a C-terminal galactose binding domain. The other two
B. bifidum
β-galactosidases and the enzyme from
B. infantis
were multimeric, intracellular enzymes with molecular masses similar to typical family 2 and family 42 glycosyl hydrolases, respectively. Despite the differences in size, molecular composition, and amino acid sequence, all four β-galactosidases were highly specific for hydrolysis of β-
d
-galactosidic linkages, and all four enzymes were able to transgalactosylate with lactose as a substrate.
Genotypic Analyses of
Escherichia coli
O157:H7 and O157 Nonmotile Isolates Recovered from Beef Cattle and Carcasses at Processing Plants in the Midwestern States of the United States
Authors: Barkocy-Gallagher Genevieve A. , Arthur Terrance M. , Siragusa Gregory R. , Keen James E. , Elder Robert O. , Laegreid William W. , Koohmaraie Mohammad 
Published: July 2002

ABSTRACT

Escherichia coli
O157:H7 and O157 nonmotile isolates (
E. coli
O157) previously were recovered from feces, hides, and carcasses at four large Midwestern beef processing plants (R. O. Elder, J. E. Keen, G. R. Siragusa, G. A. Barkocy-Gallagher, M. Koohmaraie, and W. W. Laegreid, Proc. Natl. Acad. Sci. USA 97:2999–3003, 2000). The study implied relationships between cattle infection and carcass contamination within single-source lots as well as between preevisceration and postprocessing carcass contamination, based on prevalence. These relationships now have been verified based on identification of isolates by genomic fingerprinting.
E. coli
O157 isolates from all positive samples were analyzed by pulsed-field gel electrophoresis of genomic DNA after digestion with
Xba
I. Seventy-seven individual subtypes (fingerprint patterns) grouping into 47 types were discerned among 343 isolates. Comparison of the fingerprint patterns revealed three clusters of isolates, two of which were closely related to each other. Remarkably, isolates carrying both Shiga toxin genes and nonmotile isolates largely fell into specific clusters. Within lots analyzed, 68.2% of the postharvest (carcass) isolates matched preharvest (animal) isolates. For individual carcasses, 65.3 and 66.7% of the isolates recovered postevisceration and in the cooler, respectively, matched those recovered preevisceration. Multiple isolates were analyzed from some carcass samples and were found to include strains with different genotypes. This study suggests that most
E. coli
O157 carcass contamination originates from animals within the same lot and not from cross-contamination between lots. In addition, the data demonstrate that most carcass contamination occurs very early during processing.