bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Structure and Population Dynamics of
Xanthomonas axonopodis
pv. manihotis in Colombia from 1995 to 1999
Authors: Restrepo Silvia , Velez Claudia M. , Duque Myriam C. , Verdier Valérie 
Published: January 2004

ABSTRACT

Restriction fragment length polymorphisms (RFLPs) were used to study the population genetics and temporal dynamics of the cassava bacterial pathogen
Xanthomonas axonopodis
pv. manihotis. The population dynamics were addressed by comparing samples collected from 1995 to 1999 from six locations, spanning four different edaphoclimatic zones (ECZs). Forty-five different
X. axonopodis
pv. manihotis RFLP types or haplotypes were identified between 1995 and 1999. High genetic diversity of the
X. axonopodis
pv. manihotis strains was evident within most of the fields sampled. In all but one site, diversity decreased over time within fields. Haplotype frequencies significantly differed over the years in all but one location. Studies of the rate of change of
X. axonopodis
pv. manihotis populations during the cropping cycle in two sites showed significant changes in the haplotype frequencies but not composition. However, variations in pathotype composition were observed from one year to the next at a single site in ECZs 1 and 2 and new pathotypes were described after 1997 in these ECZs, thus revealing the dramatic change in the pathogen population structure of
X. axonopodis
pv. manihotis. Disease incidence was used to show the progress of cassava bacterial blight in Colombia during the 5-year period in different ecosystems. Low disease incidence values were correlated with low rainfall in 1997 in ECZ 1.
Characterization of Lipopolysaccharides Present in Settled House Dust
Authors: Park Ju-Hyeong , Szponar Bogumila , Larsson Lennart , Gold Diane R. , Milton Donald K. 
Published: January 2004

ABSTRACT

The 3-hydroxy fatty acids (3-OHFAs) in lipopolysaccharides (LPS) play an important role in determining endotoxin activity, and childhood exposure to endotoxin has recently been associated with reduced risk of atopic diseases. To characterize the 3-OHFAs in house dust (HD), we used gas chromatography-mass spectrometry to assay 190 HD samples. Dust from beds, bedroom floors, family rooms, and kitchen floors was collected as part of a birth cohort study of childhood asthma (study 1) and a longitudinal study of home allergen and endotoxin (study 2). We also measured endotoxin activity with a
Limulus
assay and computed specific activity (endotoxin activity per nanomole of LPS). Longer-chain (C
16:0
and C
18:0
) 3-OHFAs were predominant in HD compared with short-chain (C
10:0
, C
12:0
, and C
14:0
) acids. Endotoxin activity was positively correlated with short-chain 3-OHFAs in both studies. In study 2, 3-OH C
16:0
was negatively correlated and 3-OH C
18:0
was not correlated with endotoxin activity, consistent with previous findings that the
Limulus
assay responds preferentially to LPS containing short-chain 3-OHFAs. Kitchen dust contained the highest concentrations of 3-OH C
10:0
, the highest endotoxin activities, and the highest specific activities (
P
< 0.03). Bed dust contained the largest amounts of long-chain 3-OHFAs, the highest concentrations of LPS, and the lowest specific activities. Apartments had significantly different types of LPS (
P
= 0.03) compared with single-family homes in study 2. These data suggest that the
Limulus
assay may underestimate exposure to certain types of LPS. Because nontoxic LPS may have immune modulating effects, analysis of 3-OHFAs may be useful in epidemiologic studies.
Cell Size and Water Permeability as Determining Factors for Cell Viability after Freezing at Different Cooling Rates
Authors: Dumont Frédéric , Marechal Pierre-André , Gervais Patrick 
Published: January 2004

ABSTRACT

This work studied the viabilities of five types of cells (two yeast cells,
Saccharomyces cerevisiae
CBS 1171 and
Candida utilis
; two bacterial strains,
Escherichia coli
and
Lactobacillus plantarum
; and one human leukemia K562 cell) as a function of cooling rate during freezing. The range of investigated cooling rates extended from 5 to 30,000°C/min. Cell viability was classified into three ranges: (i) high viability for low cooling rates (5 to 180°C/min), which allow cell water outflow to occur completely and do not allow any intracellular crystallization; (ii) low viability for rapid cooling rates (180 to 5,000°C/min), which allow the heat flow to prevail over water outflow (in this case, cell water crystallization would occur as water was flowing out of the cell); (iii) high viability for very high cooling rates (>5,000°C/min), which allow the heat flow to be very rapid and induce intracellular crystallization and/or vitrification before any water outflow from the cell. Finally, an assumption relating cell death to the cell water crystallization as water is flowing out of the cell is made. In addition, this general cell behavior is different for each type of cell and seems to be moderated by the cell size, the water permeability properties, and the presence of a cell wall.
WolbachiaTransfer fromRhagoletis cerasitoDrosophila simulans: Investigating the Outcomes of Host-Symbiont Coevolution
Authors: Riegler Markus , Charlat Sylvain , Stauffer Christian , Merçot Hervé 
Published: January 2004

ABSTRACTWolbachiais an endosymbiont of diverse arthropod lineages that can induce various alterations of host reproduction for its own benefice. Cytoplasmic incompatibility (CI) is the most common phenomenon, which results in embryonic lethality when males that bearWolbachiaare mated with females that do not. In the cherry fruit fly,Rhagoletis cerasi,Wolbachiaseems to be responsible for previously reported patterns of incompatibility between populations. Here we report on the artificial transfer of twoWolbachiavariants (wCer1 andwCer2) fromR. cerasiintoDrosophila simulans, which was performed with two major goals in mind: first, to isolatewCer1 fromwCer2 in order to individually test their respective abilities to induce CI in the new host; and, second, to test the theoretical prediction that recentWolbachia-host associations should be characterized by high levels of CI, fitness costs to the new host, and inefficient transmission from mothers to offspring.wCer1 was unable to develop in the new host, resulting in its rapid loss after successful injection, whilewCer2 was established in the new host. Transmission rates ofwCer2 were low, and the infection showed negative fitness effects, consistent with our prediction, but CI levels were unexpectedly lower in the new host. Based on these parameter estimates, neitherwCer1 norwCer2 could be naturally maintained inD. simulans. The experiment thus suggests that naturalWolbachiatransfer between species might be restricted by many factors, should the ecological barriers be bypassed.
Characterization of a New
erm
-Related Macrolide Resistance Gene Present in Probiotic Strains of
Bacillus clausii
Authors: Bozdogan Bülent , Galopin Sébastien , Leclercq Roland 
Published: January 2004

ABSTRACT

The mechanism of resistance to macrolides, lincosamides, and streptogramins B was studied in four
Bacillus clausii
strains that are mixed in a probiotic administered to humans for prevention of gastrointestinal side effects due to oral antibiotic chemotherapy and in three reference strains of
B. clausii
, DSM8716, ATCC 21536, and ATCC 21537. An 846-bp gene called
erm
(34), which is related to the
erm
genes conferring resistance to these antibiotics by ribosomal methylation, was cloned from total DNA of
B. clausii
DSM8716 into
Escherichia coli
. The deduced amino acid sequence presented 61% identity with that of Erm(D) from
B. licheniformis
,
B. halodurans
, and
B. anthracis
. Pulsed-field gel electrophoresis of total DNA digested by I-
Ceu
I, followed by hybridization with an
erm
(34)-specific probe, indicated a chromosomal location of the gene in all
B. clausii
strains. Repeated attempts to transfer resistance to macrolides by conjugation from
B. clausii
strains to
Enterococcus faecalis
JH2-2,
E. faecium
HM1070, and
B. subtilis
UCN19 were unsuccessful.
Nitrobenzoates and Aminobenzoates Are Chemoattractants for
Pseudomonas
Strains
Authors: Parales Rebecca E. 
Published: January 2004

ABSTRACT

Three
Pseudomonas
strains were tested for the ability to sense and respond to nitrobenzoate and aminobenzoate isomers in chemotaxis assays.
Pseudomonas putida
PRS2000, a strain that grows on benzoate and 4-hydroxybenzoate by using the β-ketoadipate pathway, has a well-characterized β-ketoadipate-inducible chemotactic response to aromatic acids. PRS2000 was chemotactic to 3- and 4-nitrobenzoate and all three isomers of aminobenzoate when grown under conditions that induce the benzoate chemotactic response.
P. putida
TW3 and
Pseudomonas
sp. strain 4NT grow on 4-nitrotoluene and 4-nitrobenzoate by using the
ortho
(β-ketoadipate) and
meta
pathways, respectively, to complete the degradation of protocatechuate derived from 4-nitrotoluene and 4-nitrobenzoate. However, based on results of catechol 1,2-dioxygenase and catechol 2,3-dioxygenase assays, both strains were found to use the β-ketoadipate pathway for the degradation of benzoate. Both strains were chemotactic to benzoate, 3- and 4-nitrobenzoate, and all three aminobenzoate isomers after growth with benzoate but not succinate. Strain TW3 was chemotactic to the same set of aromatic compounds after growth with 4-nitrotoluene or 4-nitrobenzoate. In contrast, strain 4NT did not respond to any aromatic acids when grown with 4-nitrotoluene or 4-nitrobenzoate, apparently because these substrates are not metabolized to the inducer (β-ketoadipate) of the chemotaxis system. The results suggest that strains TW3 and 4NT have a β-ketoadipate-inducible chemotaxis system that responds to a wide range of aromatic acids and is quite similar to that present in PRS2000. The broad specificity of this chemotaxis system works as an advantage in strains TW3 and 4NT because it functions to detect diverse carbon sources, including 4-nitrobenzoate.
Census of the Bacterial Community of the Gypsy Moth Larval Midgut by Using Culturing and Culture-Independent Methods
Authors: Broderick Nichole A. , Raffa Kenneth F. , Goodman Robert M. , Handelsman Jo 
Published: January 2004

ABSTRACTLittle is known about bacteria associated with Lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. We inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (Lymantria disparL.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. We also examined the effects of diet on microbial composition. Analysis of individual third-instar larvae revealed a high degree of similarity of microbial composition among insects fed on the same diet. DNA sequence analysis indicated that most of the PCR-amplified 16S rRNA genes belong to the γ-Proteobacteriaand low G+C gram-positive divisions and that the cultured members represented more than half of the phylotypes identified. Less frequently detected taxa included members of the α-Proteobacterium,Actinobacterium, andCytophaga/Flexibacter/Bacteroidesdivisions. The 16S rRNA gene sequences from 7 of the 15 cultured organisms and 8 of the 9 sequences identified by PCR amplification diverged from previously reported bacterial sequences. The microbial composition of midguts differed substantially among larvae feeding on a sterilized artificial diet, aspen, larch, white oak, or willow. 16S rRNA analysis of cultured isolates indicated that anEnterococcusspecies and culture-independent analysis indicated that anEntbactersp. were both present in all larvae, regardless of the feeding substrate; the sequences of these two phylotypes varied less than 1% among individual insects. These results provide the first comprehensive description of the microbial diversity of a lepidopteran midgut and demonstrate that the plant species in the diet influences the composition of the gut bacterial community.
Nitrous Oxide Reductase (
nosZ
) Gene Fragments Differ between Native and Cultivated Michigan Soils
Authors: Stres Blaž , Mahne Ivan , Avguštin Gorazd , Tiedje James M. 
Published: January 2004

ABSTRACT

The effect of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (
nosZ
) fragments from denitrifying prokaryotes in native and cultivated soil was explored. Thirty-six soil cores were composited from each of the two soil management conditions.
nosZ
gene fragments were amplified from triplicate samples, and PCR products were cloned and screened by restriction fragment length polymorphism (RFLP). The total
nosZ
RFLP profiles increased in similarity with soil sample size until triplicate 3-g samples produced visually identical RFLP profiles for each treatment. Large differences in total
nosZ
profiles were observed between the native and cultivated soils. The fragments representing major groups of clones encountered at least twice and four randomly selected clones with unique RFLP patterns were sequenced to verify
nosZ
identity. The sequence diversity of
nosZ
clones from the cultivated field was higher, and only eight patterns were found in clone libraries from both soils among the 182 distinct
nosZ
RFLP patterns identified from the two soils. A group of clones that comprised 32% of all clones dominated the gene library of native soil, whereas many minor groups were observed in the gene library of cultivated soil. The 95% confidence intervals of the Chao1 nonparametric richness estimator for
nosZ
RFLP data did not overlap, indicating that the levels of species richness are significantly different in the two soils, the cultivated soil having higher diversity. Phylogenetic analysis of deduced amino acid sequences grouped the majority of
nosZ
clones into an interleaved Michigan soil cluster whose cultured members are α-
Proteobacteria
. Only four
nosZ
sequences from cultivated soil and one from the native soil were related to sequences found in γ-
Proteobacteria.
Sequences from the native field formed a distinct, closely related cluster (
D
mean
= 0.16) containing 91.6% of the native clones. Clones from the cultivated field were more distantly related to each other (
D
mean
= 0.26), and 65% were found outside of the cluster from the native soil, further indicating a difference in the two communities. Overall, there appears to be a relationship between use and richness, diversity, and the phylogenetic position of
nosZ
sequences, indicating that agricultural use of soil caused a shift to a more diverse denitrifying community.
Selection and Characterization of Conditionally Active Promoters in
Lactobacillus plantarum
, Using Alanine Racemase as a Promoter Probe
Authors: Bron Peter A. , Hoffer Sally M. , Van Swam Iris I. , De Vos Willem M. , Kleerebezem Michiel 
Published: January 2004

ABSTRACT

This paper describes the use of the
alr
gene, encoding alanine racemase, as a promoter-screening tool for the identification of conditional promoters in
Lactobacillus plantarum
. Random fragments of the
L. plantarum
WCFS1 genome were cloned upstream of the promoterless
alr
gene of
Lactococcus lactis
in a low-copy-number plasmid vector. The resulting plasmid library was introduced into an
L. plantarum
Δ
alr
strain (MD007), and 40,000 clones were selected. The genome coverage of the library was estimated to be 98%, based on nucleotide insert sequence and restriction analyses of the inserts of randomly selected clones. The library was screened for clones that were capable of complementing the
d
-alanine auxotroph phenotype of MD007 in media containing up to 10, 100, or 300 μg of the competitive Alr inhibitor
d
-cycloserine per ml. Western blot analysis with polyclonal antibodies raised against lactococcal Alr revealed that the Alr production level required for growth increased in the presence of increasing concentrations of
d
-cycloserine, adding a quantitative factor to the primarily qualitative nature of the
alr
complementation screen. Screening of the
alr
complementation library for clones that could grow only in the presence of 0.8 M NaCl resulted in the identification of eight clones that upon Western blot analysis showed significantly higher Alr production under high-salt conditions than under low-salt conditions. These results established the effectiveness of the alanine racemase complementation screening method for the identification of promoters on their conditional or constitutive activity.
Use of Antibiotic Susceptibility Patterns and Pulsed-Field Gel Electrophoresis To Compare Historic and Contemporary Isolates of Multi-Drug-Resistant
Salmonella enterica
subsp.
enterica
Serovar Newport
Authors: Berge Anna Catharina B. , Adaska John M. , Sischo William M. 
Published: January 2004

ABSTRACT

Recently, multi-drug-resistant (MDR)
Salmonella enterica
subspecies
enterica
serovar Newport reemerged as a public and animal health problem. The antibiotic resistance of 198 isolates and the pulsed-field gel electrophoresis patterns (PFGE) of 139 isolates were determined. Serovar Newport isolates collected between 1988 and 2001 were included in the study. One hundred seventy-eight isolates were collected from the San Joaquin valley in California and came from dairy cattle clinical samples, human clinical samples, bulk tank milk samples, fecal samples from preweaned calves, and waterways. Twenty clinical isolates from humans from various regions of the United States were also included in the study. Resistance to 18 antibiotics was determined using a disk diffusion assay. PFGE patterns were determined using a single enzyme (
Xba
I). The PFGE and antibiogram patterns were described using cluster analysis. Although the antibiotic resistance patterns of historic (1988 to 1995) and contemporary (1999 to 2001) isolates were similar, the contemporary isolates differed from the historic isolates by being resistant to cephalosporins and florfenicol and in their general sensitivity to kanamycin and neomycin. With few exceptions, the contemporary isolates clustered together and were clearly separated from the historic isolates. One PFGE-antibiogram cluster combination was predominant for the recent isolates, which were taken from human samples from all parts of the United States, as well as in the isolates from California, indicating a rapid dissemination of this phenotypic strain. The data are consistent with the hypothesis that the reemergence of MDR serovar Newport is not simply an acquisition of further antibiotic resistance genes by the historic isolates but reflects a different genetic lineage.
Differential Stress-Induced Regulation of Two Quinone Reductases in the Brown Rot BasidiomyceteGloeophyllum trabeum
Authors: Cohen Roni , Suzuki Melissa R. , Hammel Kenneth E. 
Published: January 2004

ABSTRACTQuinone reductases (QRDs) have two important functions in the basidiomyceteGloeophyllum trabeum, which causes brown rot of wood. First, a QRD is required to generate biodegradative hydroxyl radicals via redox cycling between twoG. trabeumextracellular metabolites, 2,5-dimethoxyhydroquinone (2,5-DMHQ) and 2,5-dimethoxy-1,4-benzoquinone (2,5-DMBQ). Second, because 2,5-DMBQ is cytotoxic and 2,5-DMHQ is not, a QRD is needed to maintain the intracellular pool of these metabolites in the reduced form. Given their importance inG. trabeummetabolism, QRDs could prove useful targets for new wood preservatives. We have identified twoG. trabeumgenes, each existing in two closely related, perhaps allelic variants, that encode QRDs in the flavodoxin family. Past work with QRD1 and heterologous expression of QRD2 in this study confirmed that both genes encode NADH-dependent, flavin-containing QRDs. Real-time reverse transcription PCR analyses of liquid- and wood-grown cultures showed thatqrd1expression was maximal during secondary metabolism, coincided with the production of 2,5-DMBQ, and was moderately up-regulated by chemical stressors such as quinones. By contrast,qrd2expression was maximal during fungal growth when 2,5-DMBQ levels were low, yet was markedly up-regulated by chemical stress or heat shock. The total QRD activity in lysates ofG. trabeummycelium was significantly enhanced by induction beforehand with a cytotoxic quinone. The promoter ofqrd2contains likely antioxidant, xenobiotic, and heat shock elements, absent inqrd1, that probably explain the greater response ofqrd2transcription to stress. We conclude from these results that QRD1 is the enzymeG. trabeumroutinely uses to detoxify quinones during incipient wood decay and that it could also drive the biodegradative quinone redox cycle. However, QRD2 assumes a more important role when the mycelium is stressed.
Successful Predation of Filamentous Bacteria by a Nanoflagellate Challenges Current Models of Flagellate Bacterivory
Authors: Wu Qinglong L. , Boenigk Jens , Hahn Martin W. 
Published: January 2004

ABSTRACT

Current models suggest that (i) filamentous bacteria are protected against predation by nanoflagellates, (ii) prey size is positively correlated with prey-predator contact probability, and (iii) contact probability is mainly responsible for size-selective predation by interception-feeding flagellates. We used five strains of filamentous bacteria and one bacterivorous nanoflagellate,
Ochromonas
sp. strain DS, to test these assumptions. The five strains, including one spirochete and four
Betaproteobacteria
strains, were isolated by the filtration-acclimatization method. All five strains possess flexible cells, but they differ in average cell length, which ranged from 4.5 to 13.7 μm. High-resolution video microscopy was used to measure contact, capture, and ingestion rates, as well as selectivity of the flagellate feeding. Growth and feeding experiments with satiating and nonsatiating food conditions, as well as experiments including alternative well-edible prey, were performed. In contrast to predictions by current models, the flagellate successfully consumed all the tested filamentous strains. The ingestion rate was negatively correlated with bacterial length. On the other hand, the lengths of the filamentous bacteria were not positively correlated to the contact rate and capture rate but were negatively correlated to ingestion efficiency. In experiments including alternative nonfilamentous prey, the flagellates showed negative selection for filamentous bacteria, which was independent of food concentration and is interpreted as a passive selection. Our observations indicate that (i) size alone is not sufficient to define a refuge for filamentous bacteria from nanoflagellate predation and (ii) for the investigated filamentous bacteria, prey-predator contact probability could be more influenced by factors other than the prey size.