bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Structure, Function, and Origin of the Microcin H47 ATP-Binding Cassette Exporter Indicate Its Relatedness to That of Colicin V
Authors: Azpiroz Marı́a F. , Rodrı́guez Eliana , Laviña Magela 
Published: July 2002

ABSTRACT

Microcin H47, a gene-encoded peptide antibiotic produced by a natural
Escherichia coli
strain, was shown to be secreted by a three-component ATP-binding cassette exporter which was revealed to be strongly related to that of colicin V. The results of sequence and gene fusion analyses, as well as heterologous complementation assays, are presented.
Accurate Prediction of Macrolide Resistance in
Helicobacter pylori
by a PCR Line Probe Assay for Detection of Mutations in the 23S rRNA Gene: Multicenter Validation Study
Authors: van Doorn Leen-Jan , Glupczynski Youri , Kusters Johannes G. , Mégraud Francis , Midolo Peter , Maggi-Solcà Nadia , Queiroz Dulciene M. M. , Nouhan Nathalie , Stet Els , Quint Wim G. V. 
Published: July 2002

ABSTRACT

Helicobacter pylori
strains from 299 patients were tested in six laboratories in different countries. Macrolide susceptibility of the strains was determined by agar dilution (17.4%) or the epsilometer test (82.6%). Mutations in the 23S ribosomal DNA (rDNA) that are associated with macrolide resistance were analyzed by PCR and reverse hybridization (PCR-line probe assay [LiPA]). This method identifies A2115G, G2141A, A2142G, A2142C, A2142T, A2143G, and A2143C mutations in the 23S rDNA.
vacA
s-region (s1a, s1b, s1c, and s2) and m-region (m1, m2a, and m2b) genotypes and
cagA
status were also determined using another PCR-LiPA system. Of the 299 strains investigated by MIC testing, 130 (43.5%) were resistant and 169 (56.5%) were susceptible to clarithromycin. Of the 130 resistant strains, 127 (97.7%) contained 23S rDNA mutations, whereas 167 (98.8%) of the 169 susceptible strains contained wild-type sequences. The predominant mutations were A2143G (45.2%) and A2142G (33.3%). Twenty-eight (19.8%) strains contained multiple 23S rDNA mutations. Only five resistant strains contained the A2142C mutation (three of these in combination with the A2142G mutation), and the A2115G, G2141A, A2142T, and A2143C mutations were not found. MICs of clarithromycin for the A2142G mutant strains were significantly higher than MICs for the A2143G strains. Although there was no significant association between 23S rDNA mutations and the
vacA
and
cagA
status, clarithromycin-susceptible strains more often contained mixed
vacA
genotypes, indicating the presence of multiple
H. pylori
strains. In conclusion, our data confirmed the very strong association between 23S rDNA mutations and macrolide resistance and showed that the PCR-LiPA permits accurate and reliable diagnosis of macrolide resistance in
H. pylori
.
Genomic Profiling of the Response of
Candida albicans
to Itraconazole Treatment Using a DNA Microarray
Authors: De Backer Marianne D. , Ilyina Tatiana , Ma Xiao-Jun , Vandoninck Sandy , Luyten Walter H. M. L. , Vanden Bossche Hugo 
Published: July 2002

ABSTRACT

The application of genome-wide expression profiling to determine how drugs achieve their therapeutic effect has provided the pharmaceutical industry with an exciting new tool for drug mode-of-action studies. We used DNA chip technology to study cellular responses to perturbations of ergosterol biosynthesis caused by the broad-spectrum antifungal agent itraconazole. Simultaneous examination of over 6,600
Candida albicans
gene transcript levels, representing the entire genome, upon treatment of cells with 10 μM itraconazole revealed that 296 genes were responsive. For 116 genes transcript levels were decreased at least 2.5-fold, while for 180 transcript levels were similarly increased. A global upregulation of
ERG
genes in response to azole treatment was observed.
ERG11
and
ERG5
were found to be upregulated approximately 12-fold. In addition, a significant upregulation was observed for
ERG6, ERG1, ERG3, ERG4, ERG10, ERG9, ERG26, ERG25, ERG2, IDII, HMGS, NCP1,
and
FEN2,
all of which are genes known to be involved in ergosterol biosynthesis. The effects of itraconazole on a wide variety of known metabolic processes are discussed. As over 140 proteins with unknown function were responsive to itraconazole, our analysis might provide—in combination with phenotypic data—first hints of their potential function. The present report is the first to describe the application of DNA chip technology to study the response of a major human fungal pathogen to drug treatment.
Antibiotic Susceptibility and Mechanisms of Erythromycin Resistance in Clinical Isolates of
Streptococcus agalactiae
: French Multicenter Study
Authors: De Mouy Dany , Cavallo Jean-Didier , Leclercq Roland , Fabre Roland ,   The Aforcopi-Bio Network
Published: July 2002

ABSTRACT

Among 126
Streptococcus agalactiae
isolates collected in 10 French laboratories in 1999, 27 (21.4%) had macrolide resistance related to the presence of
erm
(B) (11 strains),
erm
(A) subclass
erm
(TR) (10 strains), and
mef
(A) genes (2 strains) and the presence of combinations of
erm
(B) and
erm
(A) genes or
mef
(A) genes (3 strains).
Detection of Intracellular Bacteria in the Buds of Scotch Pine (
Pinus sylvestris
L.) by In Situ Hybridization
Authors: Pirttilä Anna Maria , Laukkanen Hanna , Pospiech Helmut , Myllylä Raili , Hohtola Anja 
Published: July 2002

ABSTRACT

Bacterial isolates were obtained from pine (
Pinus sylvestris
L.) tissue cultures and identified as
Methylobacterium extorquens
and
Pseudomonas synxantha
. The existence of bacteria in pine buds was investigated by 16S rRNA in situ hybridization. Bacteria inhabited the buds of every tree examined, primarily colonizing the cells of scale primordia and resin ducts.
Microbial Biofilm Formation and Contamination of Dental-Unit Water Systems in General Dental Practice
Authors: Walker James T. , Bradshaw David J. , Bennett Allan M. , Fulford Martin R. , Martin Michael V. , Marsh Philip D. 
Published: July 2002

ABSTRACT

Dental-unit water systems (DUWS) harbor bacterial biofilms, which may serve as a haven for pathogens. The aim of this study was to investigate the microbial load of water from DUWS in general dental practices and the biofouling of DUWS tubing. Water and tube samples were taken from 55 dental surgeries in southwestern England. Contamination was determined by viable counts on environmentally selective, clinically selective, and pathogen-selective media, and biofouling was determined by using microscopic and image analysis techniques. Microbial loading ranged from 500 to 10
5
CFU · ml
−1
; in 95% of DUWS water samples, it exceeded European Union drinking water guidelines and in 83% it exceeded American Dental Association DUWS standards. Among visible bacteria, 68% were viable by
Bac
Light staining, but only 5% of this “viable by
Bac
Light” fraction produced colonies on agar plates.
Legionella pneumophila
,
Mycobacterium
spp.,
Candida
spp., and
Pseudomonas
spp. were detected in one, five, two, and nine different surgeries, respectively. Presumptive oral streptococci and
Fusobacterium
spp. were detected in four and one surgeries, respectively, suggesting back siphonage and failure of antiretraction devices. Hepatitis B virus was never detected. Decontamination strategies (5 of 55 surgeries) significantly reduced biofilm coverage but significantly increased microbial numbers in the water phase (in both cases,
P
< 0.05). Microbial loads were not significantly different in DUWS fed with soft, hard, deionized, or distilled water or in different DUWS (main, tank, or bottle fed). Microbiologically, no DUWS can be considered “cleaner” than others. DUWS deliver water to patients with microbial levels exceeding those considered safe for drinking water.
Accumulation of Poly[(
R
)-3-Hydroxyalkanoates] in
Pseudomonas oleovorans
during Growth with Octanoate in Continuous Culture at Different Dilution Rates
Authors: Durner Roland , Witholt Bernard , Egli Thomas 
Published: July 2002

ABSTRACT

Pseudomonas oleovorans
ATCC 29347 was grown in chemostat culture at different dilution rates with mineral media varying in their ratios of octanoate to ammonia (C
0
/N
0
ratio). At all dilution rates tested, three distinct growth regimes were observed: (i) carbon limitation with NH
4
+
in excess at low C
0
/N
0
ratios, (ii) purely nitrogen-limited growth conditions at high C
0
/N
0
ratios with residual octanoate in the culture supernatant, and (iii) an intermediate zone of dual-nutrient-limited growth conditions where both the concentration of octanoate and that of ammonia were very low. The dual-nutrient-limited growth zone shifted to higher C
0
/N
0
ratios with decreasing dilution rates, and the extension of the dual-nutrient-limited growth zone was inversely proportional to the growth rate. The cells accumulated the storage compound medium-chain-length poly[(
R
)-3-hydroxyalkanoate] (mcl-PHA) during dual (C and N)-nutrient-limited and N-limited growth conditions. Within the dual-nutrient-limited growth zone, the cellular mcl-PHA contents increased when the C
0
/N
0
ratio in the feed was increased, whereas the cellular mcl-PHA level was independent from the feed C
0
/N
0
ratio during N-limited growth. The monomeric composition of the accumulated mcl-PHA was independent of both the dilution rate and the feed C
0
/N
0
ratio and consisted of 12 mol% 3-hydroxyhexanoic acid and 88 mol% 3-hydroxyoctanoic acid. Accumulation of mcl-PHA led to an increase in the cellular C/N ratio and to changes in elemental growth yields for nitrogen and carbon.
Antigenic Characterization of the Fish Pathogen
Flavobacterium psychrophilum
Authors: Crump Elizabeth M. , Perry Malcolm B. , Clouthier Sharon C. , Kay William W. 
Published: July 2002

ABSTRACT

Flavobacteria are a poorly understood and speciated group of commensal bacteria and opportunistic pathogens. The psychrotroph
Flavobacterium psychrophilum
is the etiological agent of rainbow trout fry syndrome and bacterial cold water disease, septicemic diseases that heavily impact salmonids. Consequently, two verified but geographically diverse isolates were characterized phenotypically and biochemically. A facile typing system was devised which readily discriminated between closely related species and was verified against a pool of recent prospective isolates.
F. psychrophilum
was found to be enveloped in a loosely attached, strongly antigenic outer layer comprised of a predominant, highly immunogenic, low-molecular-mass carbohydrate antigen as well as several protein antigens. Surface-exposed antigens were visualized by a combination of immunoflourescence microscopy, immunogold transmission, and thin-section electron microscopy and were discriminated by Western blotting using rabbit antisera, by selective extraction with EDTA-polymyxin B agarose beads, and by extrinsic labeling of amines with sulfo–
N
-hydoxysuccinimide–biotin and glycosyl groups with biotin hydrazide. The predominant ∼16 kDa antigen was identified as low-molecular-mass lipopolysaccharide (LPS), whereas high-molecular-mass LPS containing O antigen was not as prevalent on whole cells but was abundant in culture supernatants. Rainbow trout convalescent antisera recognized both molecular mass classes of LPS as well as a predominant ∼20-kDa protein. This study represents the first description at the molecular level of the surface characteristics and potential vaccine targets of confirmed
F. psychrophilum
strains.
Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil
Authors: Weber Sabine , Stubner Stephan , Conrad Ralf 
Published: July 2002

ABSTRACT

Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera
Bacillus
(3 clones),
Nitrosospira
(1 clone),
Fluoribacter
(1 clones), and
Acidobacterium
(2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes)
Bacteria
detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus
Clostridium
, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to the
Cytophaga-Flavobacterium
cluster of the
Cytophaga-Flavobacterium-Bacteroides
phylum, 4% belonged to the α, β, and γ
Proteobacteria
, and 1.3% belonged to the
Bacillus
subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.
Diversity and Specificity of
Frankia
Strains in Nodules of Sympatric
Myrica gale, Alnus incana
, and
Shepherdia canadensis
Determined by
rrs
Gene Polymorphism
Authors: Huguet Valerie , Batzli Janet Mccray , Zimpfer Jeff F. , Normand Philippe , Dawson Jeffrey O. , Fernandez Maria P. 
Published: July 2002

ABSTRACT

The identity of
Frankia
strains from nodules of
Myrica gale, Alnus incana
subsp.
rugosa
, and
Shepherdia canadensis
was determined for a natural stand on a lake shore sand dune in Wisconsin, where the three actinorhizal plant species were growing in close proximity, and from two additional stands with
M. gale
as the sole actinorhizal component. Unisolated strains were compared by their 16S ribosomal DNA (rDNA) restriction patterns using a direct PCR amplification protocol on nodules. Phylogenetic relationships among nodular
Frankia
strains were analyzed by comparing complete 16S rDNA sequences of study and reference strains. Where the three actinorhizal species occurred together, each host species was nodulated by a different phylogenetic group of
Frankia
strains.
M. gale
strains from all three sites belonged to an
Alnus-Casuarina
group, closely related to
Frankia alni
representative strains, and were low in diversity for a host genus considered promiscuous with respect to
Frankia
microsymbiont genotype.
Frankia
strains from
A. incana
nodules were also within the
Alnus-Casuarina
cluster, distinct from
Frankia
strains of
M. gale
nodules at the mixed actinorhizal site but not from
Frankia
strains from two
M. gale
nodules at a second site in Wisconsin.
Frankia
strains from nodules of
S. canadensis
belonged to a divergent subset of a cluster of
Elaeagnaceae
-infective strains and exhibited a high degree of diversity. The three closely related local
Frankia
populations in
Myrica
nodules could be distinguished from one another using our approach. In addition to geographic separation and host selectivity for
Frankia
microsymbionts, edaphic factors such as soil moisture and organic matter content, which varied among locales, may account for differences in
Frankia
populations found in
Myrica
nodules.
Biochemical Characterization of Ochratoxin A-Producing Strains of the Genus
Penicillium
Authors: Larsen Thomas Ostenfeld , Svendsen Anne , Smedsgaard Jørn 
Published: July 2002

ABSTRACT

In order to explore the biochemical scope of ochratoxin A-producing penicillia, we screened 48
Penicillium verrucosum
isolates for the production of secondary metabolites. Fungal metabolites were analyzed by high-pressure liquid or gas chromatography coupled to diode array detection or mass spectrometry. The following metabolites were identified: ochratoxins A and B, citrinin, verrucolones, verrucines, anacines, sclerotigenin, lumpidin, fumiquinazolines, alantrypinones, daldinin D, dipodazine, penigequinolines A and B, 2-pentanone, and 2-
methyl
-isoborneol. By use of average linking clustering based on binary (nonvolatile) metabolite data, the 48 isolates could be grouped into two large and clearly separated groups and a small outlying group of four non-ochratoxin-producing isolates. The largest group, containing 24 isolates, mainly originating from plant sources, included the type culture of
P. verrucosum
. These isolates produced ochratoxin A, verrucolones, citrinin, and verrucines and had a characteristic dark brown reverse color on yeast extract-sucrose agar medium. Almost all of a group of 20 isolates mainly originating from cheese and meat products had a pale cream reverse color on yeast extract-sucrose agar medium and produced ochratoxin A, verrucolones, anacines, and sclerotigenin. This group included the former type culture of
P. nordicum
. We also found that
P. verrucosum
isolates and three
P. nordicum
isolates incorporated phenylalanine into verrucine and lumpidin metabolites, a finding which could explain why those isolates produced relatively lower levels of ochratoxins than did most isolates of
P. nordicum
.
Transfer of the Pheromone-Inducible Plasmid pCF10 among
Enterococcus faecalis
Microorganisms Colonizing the Intestine of Mini-Pigs
Authors: Licht Tine Rask , Laugesen Dorthe , Jensen Lars Bogø , Jacobsen Bodil Lund 
Published: July 2002

ABSTRACT

A new animal model, the streptomycin-treated mini-pig, was developed in order to allow colonization of defined strains of
Enterococcus faecalis
in numbers sufficient to study plasmid transfer. Transfer of the pheromone-inducible pCF10 plasmid between streptomycin-resistant strains of
E. faecalis
OG1 was investigated in the model. The plasmid encodes resistance to tetracycline. Numbers of recipient, donor, and transconjugant bacteria were monitored by selective plating of fecal samples, and transconjugants were subsequently verified by PCR. After being ingested by the mini-pigs, the recipient strain persisted in the intestine at levels between 10
6
and 10
7
CFU per g of feces throughout the experiment. The donor strain, which carried different resistance markers but was otherwise chromosomally isogenic to the recipient strain, was given to the pigs 3 weeks after the recipient strain. The donor cells were initially present in high numbers (10
6
CFU per g) in feces, but they did not persist in the intestine at detectable levels. Immediately after introduction of the donor bacteria, transconjugant cells appeared and persisted in fecal samples at levels between 10
3
and 10
4
CFU per g until the end of the experiment. These observations showed that even in the absence of selective tetracycline pressure, plasmid pCF10 was transferred from ingested
E. faecalis
cells to other
E. faecalis
organisms already present in the intestinal environment and that the plasmid subsequently persisted in the intestine.
An Exported Rhodanese-Like Protein Is Induced during Growth of
Acidithiobacillus ferrooxidans
in Metal Sulfides and Different Sulfur Compounds
Authors: Ramírez Pablo , Toledo Héctor , Guiliani Nicolas , Jerez Carlos A. 
Published: July 2002

ABSTRACT

By proteomic analysis we found a 21-kDa protein (P21) from
Acidithiobacillus ferrooxidans
ATCC 19859 whose synthesis was greatly increased by growth of the bacteria in pyrite, thiosulfate, elemental sulfur, CuS, and ZnS and was almost completely repressed by growth in ferrous iron. After we determined the N-terminal amino acid sequence of P21, we used the available preliminary genomic sequence of
A. ferrooxidans
ATCC 23270 to isolate the DNA region containing the
p21
gene. The nucleotide sequence of this DNA fragment contained a putative open reading frame (ORF) coding for a 23-kDa protein. This difference in size was due to the presence of a putative signal peptide in the ORF coding for P21. When
p21
was cloned and overexpressed in
Escherichia coli
, the signal peptide was removed, resulting in a mature protein with a molecular mass of 21 kDa and a calculated isoelectric point of 9.18. P21 exhibited 27% identity and 42% similarity to the
Deinococcus radiodurans
thiosulfate-sulfur transferase (rhodanese; EC 2.8.1.1) and similar values in relation to other rhodaneses, conserving structural domains and an active site with a cysteine, both characteristic of this family of proteins. However, the purified recombinant P21 protein did not show rhodanese activity. Unlike cytoplasmic rhodaneses, P21 was located in the periphery of
A. ferrooxidans
cells, as determined by immunocytochemical analysis, and was regulated depending on the oxidizable substrate. The genomic context around gene
p21
contained other ORFs corresponding to proteins such as thioredoxins and sulfate-thiosulfate binding proteins, clearly suggesting the involvement of P21 in inorganic sulfur metabolism in
A. ferrooxidans
.
Role of Acetate in Production of an Autoinducible Class IIa Bacteriocin in
Carnobacterium piscicola
A9b
Authors: Nilsson Lilian , Nielsen Michael K. , Ng Yin , Gram Lone 
Published: July 2002

ABSTRACT

Carnobacterium piscicola
strain A9b isolated from cold smoked salmon inhibits growth of the food-borne pathogen
Listeria monocytogenes
partly due to the production of a proteinaceous compound (L. Nilsson, L. Gram, and H. H. Huss. J. Food Prot. 62:336-342, 1999). The purpose of the present study was to purify the compound and describe factors affecting its production, with particular emphasis on food-relevant factors. Amino acid sequencing showed that the compound is a class IIa bacteriocin with an N-terminal amino acid sequence identical to that of carnobacteriocin B2. The production of the bacteriocin was autoinducible, and the threshold level for induction was 9.6 × 10
−10
M. We also report, for the first time, that acetate acts as an induction factor, with a threshold concentration of 0.3 to 12 mM. Acetate could not act as an inducer during the late exponential phase of
C. piscicola
A9b. The induction of bacteriocin production showed a dose-dependent relationship at acetate concentrations of up to 10 to 20 mM (depending on the growth medium) and at a concentration of 1.9 × 10
−8
M for the bacteriocin itself; a saturation level of bacteriocin specific activity was reached at these concentrations of induction factors. The combined use of both inducers did not enhance the saturation level of bacteriocin production compared to that seen with the use of each inducer alone. Increasing NaCl and glucose concentrations negatively influenced the efficiency of acetate as an induction factor. Based on the results, carnobacteriocin B2 was used as an induction factor to manipulate the production of bacteriocin in cold smoked salmon juice and thus improve the ability to inhibit
L. monocytogenes
.