bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Primary Colonization and Early Succession on Surfaces in Marine Waters as Determined by Amplified rRNA Gene Restriction Analysis and Sequence Analysis of 16S rRNA Genes
Authors: Dang Hongyue , Lovell Charles R. 
Published: July 2002

ABSTRACT

The nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. However, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. Experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tidal creek for 24 or 72 h. The organisms colonizing these surfaces were examined by using a cultivation-independent approach, amplified ribosomal DNA restriction analysis. The goals of this study were to assess the diversity of bacterial colonists involved in early succession on a variety of surfaces and to determine the phylogenetic affiliations of the most common early colonists. Substantial differences in the representation of different cloned ribosomal DNA sequences were found when the 24- and 72-h incubations were compared, indicating that some new organisms were recruited and some other organisms were lost. Phylogenetic analyses of the most common sequences recovered showed that the colonists were related to organisms known to inhabit surfaces or particles in marine systems. A total of 22 of the 26 clones sequenced were affiliated with the
Roseobacter
subgroup of the α subdivision of the division
Proteobacteria
(α-
Proteobacteria
), and most of these clones were recovered at a high frequency from all surfaces after 24 or 72 h of incubation. Two clones were affiliated with the
Alteromonas
group of the γ-
Proteobacteria
and appeared to be involved only in the very early stages of colonization (within the first 24 h). A comparison of the colonization patterns on the test surfaces indicated that the early bacterial community succession rate and/or direction may be influenced by surface physicochemical properties. However, organisms belonging to the
Roseobacter
subgroup are ubiquitous and rapid colonizers of surfaces in coastal environments.
Controlling Instability in
gacS-gacA
Regulatory Genes during Inoculant Production of
Pseudomonas fluorescens
Biocontrol Strains
Authors: Duffy Brion K. , Défago Geneviève 
Published: July 2002

ABSTRACT

Secondary metabolism in fluorescent pseudomonads is globally regulated by
gacS
, which encodes a membrane-bound sensor kinase, and
gacA
, which encodes a transcriptional response regulator. Spontaneous mutation in either gene blocked biosynthesis of the antimicrobial compounds hydrogen cyanide, 2,4-diacetylphloroglucinol, pyoluteorin, and pyrrolnitrin by the model biocontrol strain
Pseudomonas fluorescens
CHA0. Spontaneous mutants also had altered abilities to utilize several carbon sources and to increase medium pH compared with the wild type, suggesting that
gacS
and
gacA
influence primary as well as secondary bacterial metabolism. Inoculant efficacy for biocontrol was significantly reduced by contamination with regulatory mutants which accumulated during inoculum production. Spontaneous mutants accumulated in all 192 separate liquid cultures examined, typically at a frequency of 1% or higher after 12 days. During scale-up in a simulated industrial fermentation process, mutants increased exponentially and accounted for 7, 23, and 61% of the total viable cells after transfer to 20-, 100-, and 500-ml preparations, respectively. GacS
−
and GacA
−
mutants had identical phenotypes and occurred at the same frequency, indicating that the selective pressures for the two mutants were similar. We developed a simple screening method for monitoring inoculant quality based on the distinctive appearance of mutant colonies (i.e., orange color, enlarged diameter, hyperfluorescence). Mutant competitiveness was favored in a nutrient-rich medium with a high electrolyte concentration (nutrient broth containing yeast extract). We were able to control mutant accumulation and to clean up contaminated cultures by using certain mineral amendments (i.e., zinc, copper, cobalt, manganese, and ammonium molybdate) or by diluting media 1/10. Spontaneous mutants and genetic constructs had the same response to culture conditions. Zinc and medium dilution were also effective for improving the genetic stability of other
P. fluorescens
biocontrol strains obtained from Ghana and Italy.
Rapid Characterization of Spores of
Bacillus cereus
Group Bacteria by Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry
Authors: Ryzhov Victor , Hathout Yetrib , Fenselau Catherine 
Published: July 2002

ABSTRACT

Matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry was used to characterize the spores of 14 microorganisms of the
Bacillus cereus
group. This group includes the four
Bacillus
species
B. anthracis
,
B. cereus
,
B. mycoides
, and
B. thuringiensis
. MALDI mass spectra obtained from whole bacterial spores showed many similarities between the species, except for
B. mycoides
. At the same time, unique mass spectra could be obtained for the different
B. cereus
and
B. thuringiensis
strains, allowing for differentiation at the strain level. To increase the number of detectable biomarkers in the usually peak-poor MALDI spectra of spores, the spores were treated by corona plasma discharge (CPD) or sonicated prior to MALDI analysis. Spectra of sonicated or CPD-treated spores displayed an ensemble of biomarkers common for
B. cereus
group bacteria. Based on the spectra available, these biomarkers differentiate
B. cereus
group spores from those of
Bacillus subtilis
and
Bacillus globigii
. The effect of growth medium on MALDI spectra of spores was also explored.
Distinct Combinations of
Borrelia burgdorferi
Sensu Lato Genospecies Found in Individual Questing Ticks from Europe
Authors: Kurtenbach Klaus , De Michelis Simona , Sewell Henna-Sisko , Etti Susanne , Schäfer Stefanie M. , Hails Rosie , Collares-Pereira Margarida , Santos-Reis Margarida , Haninçová Klára , Labuda Milan , Bormane Antra , Donaghy Michael 
Published: July 2002

ABSTRACT

The genetic diversity of
Borrelia burgdorferi
sensu lato was assessed in individual adult
Ixodes ricinus
ticks from Europe by direct PCR amplification of spirochetal DNA followed by genospecies-specific hybridization. Analysis of mixed infections in the ticks showed that
B
.
garinii
and
B
.
valaisiana
segregate from
B
.
afzelii
. This and previous findings suggest that host complement interacts with spirochetes in the tick, thereby playing an important role in the ecology of Lyme borreliosis.
Rapid Extraction of DNA From
Escherichia coli
and
Cryptosporidium parvum
for Use in PCR
Authors: Higgins James A. , Jenkins Mark C. , Shelton Daniel R. , Fayer Ron , Karns Jeffrey S. 
Published: July 2002

ABSTRACT

The Xtra Amp tube, Isocode paper, Instagene matrix, and PrepMan matrix methods were evaluated for their ability to rapidly extract PCR-quality DNAs from
Escherichia coli
O157:H7 and
Cryptosporidium parvum
. All methods provided satisfactory DNA from
E. coli
, and the Xtra Amp and Instagene reagents provided satisfactory DNA from
C. parvum
.
Shewanella putrefaciens
Adhesion and Biofilm Formation on Food Processing Surfaces
Authors: Bagge Dorthe , Hjelm Mette , Johansen Charlotte , Huber Ingrid , Gram Lone 
Published: July 2002

ABSTRACT

Laboratory model systems were developed for studying
Shewanella putrefaciens
adhesion and biofilm formation under batch and flow conditions.
S. putrefaciens
plays a major role in food spoilage and may cause microbially induced corrosion on steel surfaces.
S. putrefaciens
bacteria suspended in buffer adhered readily to stainless steel surfaces. Maximum numbers of adherent bacteria per square centimeter were reached in 8 h at 25°C and reflected the cell density in suspension. Numbers of adhering bacteria from a suspension containing 10
8
CFU/ml were much lower in a laminar flow system (modified Robbins device) (reaching 10
2
CFU/cm
2
) than in a batch system (reaching 10
7
CFU/cm
2
), and maximum numbers were reached after 24 h. When nutrients were supplied,
S. putrefaciens
grew in biofilms with layers of bacteria. The rate of biofilm formation and the thickness of the film were not dependent on the availability of carbohydrate (lactate or glucose) or on iron starvation. The number of
S. putrefaciens
bacteria on the surface was partly influenced by the presence of other bacteria (
Pseudomonas fluorescens
) which reduced the numbers of
S. putrefaciens
bacteria in the biofilm. Numbers of bacteria on the surface must be quantified to evaluate the influence of environmental factors on adhesion and biofilm formation. We used a combination of fluorescence microscopy (4′,6′-diamidino-2-phenylindole staining and in situ hybridization, for mixed-culture studies), ultrasonic removal of bacteria from surfaces, and indirect conductometry and found this combination sufficient to quantify bacteria on surfaces.
Evidence that Certain Clones of
Campylobacter jejuni
Persist during Successive Broiler Flock Rotations
Authors: Petersen L. , Wedderkopp A. 
Published: July 2002

ABSTRACT

Through the national surveillance program for
Campylobacter
spp., nine broiler chicken farms that were infected with
Campylobacter jejuni
in at least five rotations in 1998 were identified. One additional farm, located at the island of Bornholm where divided slaughter is used extensively, was also selected. Twelve broiler houses located on 10 farms were included in the study. The
C. jejuni
isolates collected from the selected houses during the surveillance were typed using
fla
typing and macrorestriction profiling (MRP), and a subset of the isolates, representing each of the identified clones, was serotyped according to the Penner scheme. Pulsed-field gel electrophoresis typing using
Sma
I and
Kpn
I revealed that the majority of houses (11 of 12) carried identical isolates in two or more broiler flocks. Such persistent clones were found in 63% of all flocks (47 of 75). The majority of persistent clones (7 of 13) had
fla
type 1/1, but MRPs distinguished between isolates from different houses, and
fla
type 1/1 clones belonged to different serotypes. Seven houses carried persistent clones that covered an interval of at least four broiler flock rotations, or at least one half year. The dominant
fla
type (1/1) was represented by 44% of isolates, or by at least one isolate from 31 of 62 broiler flocks. This significantly exceeded the prevalence of
fla
type 1/1
C. jejuni
isolates that we have estimated from other studies and suggests that isolates carrying this
fla
type are overrepresented in flocks with recurrent
Campylobacter
problems. The MRPs of clones belonging to
fla
type 1/1 serotype O:2 isolated from persistently infected flocks shared a high percentage of bands compared to the remaining isolates, indicating that some clones that have the ability to cause persistent infections in broiler farms are highly related to each other.
Salmonella enterica
Serovar Typhimurium DT104 Displays a Rugose Phenotype
Authors: Anriany Yuda A. , Weiner Ronald M. , Johnson Judith A. , De Rezende Christian E. , Joseph Sam W. 
Published: July 2002

ABSTRACT

Rugose phenotypes, such as those observed in
Vibrio cholerae
, have increased resistance to chlorine, oxidative stress, and complement-mediated killing. In this study we identified and defined a rugose phenotype in
Salmonella enterica
serovar Typhimurium DT104 and showed induction only on certain media at 25°C after 3 days of incubation. Incubation at 37°C resulted in the appearance of the smooth phenotype. Observation of the ultrastructure of the rugose form and a stable smooth variant (Stv), which was isolated following a series of passages of the rugose cells, revealed extracellular substances only in cells from the rugose colony. Observation of the extracellular substance by scanning electron microscopy (SEM) was correlated with the appearance of corrugation during development of rugose colony morphology over a 4-day incubation period at 25°C. In addition, the cells also formed a pellicle in liquid broth, which was associated with the appearance of interlacing slime and fibrillar structures, as observed by SEM. The pellicle-forming cells were completely surrounded by capsular material, which bound cationic ferritin, thus indicating the presence of an extracellular anionic component. The rugose cells, in contrast to Stv, showed resistance to low pH and hydrogen peroxide and an ability to form biofilms. Based on these results and analogy to the rugose phenotype in
V. cholerae
, we propose a possible role for the rugose phenotype in the survival of
S. enterica
serovar Typhimurium DT104.
Production of Penicillin by Fungi Growing on Food Products: Identification of a Complete Penicillin Gene Cluster in
Penicillium griseofulvum
and a Truncated Cluster in
Penicillium verrucosum
Authors: Laich Federico , Fierro Francisco , Martín Juan F. 
Published: July 2002

ABSTRACT

Mycobiota growing on food is often beneficial for the ripening and development of the specific flavor characteristics of the product, but it can also be harmful due to the production of undesirable compounds such as mycotoxins or antibiotics. Some of the fungi most frequently isolated from fermented and cured meat products such as
Penicillium chrysogenum
and
Penicillium nalgiovense
are known penicillin producers; the latter has been shown to be able to produce penicillin when growing on the surface of meat products and secrete it to the medium. The presence of penicillin in food must be avoided, since it can lead to allergic reactions and the arising of penicillin resistance in human-pathogenic bacteria. In this article we describe a study of the penicillin production ability among fungi of the genus
Penicillium
that are used as starters for cheese and meat products or that are frequently isolated from food products.
Penicillium griseofulvum
was found to be a new penicillin producer and to have a penicillin gene cluster similar to that of
Penicillium chrysogenum
. No other species among the studied fungi were found to produce penicillin or to possess the penicillin biosynthetic genes, except
P. verrucosum
, which contains the
pcbAB
gene (as shown by hybridization and PCR cloning of fragments of the gene) but lacks
pcbC
and
penDE
. Antibacterial activities due to the production of secondary metabolites other than penicillin were observed in some fungi.
Reduced Oxidative Pentose Phosphate Pathway Flux in Recombinant Xylose-Utilizing
Saccharomyces cerevisiae
Strains Improves the Ethanol Yield from Xylose
Authors: Jeppsson Marie , Johansson Björn , Hahn-Hägerdal Bärbel , Gorwa-Grauslund Marie F. 
Published: July 2002

ABSTRACT

In recombinant, xylose-fermenting
Saccharomyces cerevisiae
, about 30% of the consumed xylose is converted to xylitol. Xylitol production results from a cofactor imbalance, since xylose reductase uses both NADPH and NADH, while xylitol dehydrogenase uses only NAD
+
. In this study we increased the ethanol yield and decreased the xylitol yield by lowering the flux through the NADPH-producing pentose phosphate pathway. The pentose phosphate pathway was blocked either by disruption of the
GND1
gene, one of the isogenes of 6-phosphogluconate dehydrogenase, or by disruption of the
ZWF1
gene, which encodes glucose 6-phosphate dehydrogenase. Decreasing the phosphoglucose isomerase activity by 90% also lowered the pentose phosphate pathway flux. These modifications all resulted in lower xylitol yield and higher ethanol yield than in the control strains. TMB3255, carrying a disruption of
ZWF1,
gave the highest ethanol yield (0.41 g g
−1
) and the lowest xylitol yield (0.05 g g
−1
) reported for a xylose-fermenting recombinant
S. cerevisiae
strain, but also an 84% lower xylose consumption rate. The low xylose fermentation rate is probably due to limited NADPH-mediated xylose reduction. Metabolic flux modeling of TMB3255 confirmed that the NADPH-producing pentose phosphate pathway was blocked and that xylose reduction was mediated only by NADH, leading to a lower rate of xylose consumption. These results indicate that xylitol production is strongly connected to the flux through the oxidative part of the pentose phosphate pathway.
Inducible Gene Expression by Nonculturable Bacteria in Milk after Pasteurization
Authors: Gunasekera Thusitha S. , Sørensen Anders , Attfield Paul V. , Sørensen Søren J. , Veal Duncan A. 
Published: July 2002

ABSTRACT

The viability of bacteria in milk after heat treatments was assessed by using three different viability indicators: (i) CFU on plate count agar, (ii) de novo expression of a
gfp
reporter gene, and (iii) membrane integrity based on propidium iodide exclusion. In commercially available pasteurized milk, direct viable counts, based on dye exclusion, were significantly (
P
< 0.05) higher than viable cell counts determined from CFU, suggesting that a significant subpopulation of cells in pasteurized milk are viable but nonculturable. Heating milk at 63.5°C for 30 min resulted in a >4-log-unit reduction in the number of CFU of
Escherichia coli
and
Pseudomonas putida
that were marked with
lac
-inducible
gfp
. However, the reduction in the number of
gfp
-expressing cells of both organisms under the same conditions was <2.5 log units. These results demonstrate that a substantial portion of cells rendered incapable of forming colonies by heat treatment are metabolically active and are able to transcribe and translate genes de novo.
High-Density Microarray of Small-Subunit Ribosomal DNA Probes
Authors: Wilson Kenneth H. , Wilson Wendy J. , Radosevich Jennifer L. , DeSantis Todd Z. , Viswanathan Vijay S. , Kuczmarski Thomas A. , Andersen Gary L. 
Published: July 2002

ABSTRACT

Ribosomal DNA sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven useful in many areas of biological research. Some of the most promising applications of this approach are presently limited by the rate at which sequences can be analyzed. As a step toward overcoming this limitation, we have investigated the use of photolithography chip technology to perform sequence analyses on amplified small-subunit rRNA genes. The GeneChip (Affymetrix Corporation) contained 31,179 20-mer oligonucleotides that were complementary to a subalignment of sequences in the Ribosomal Database Project (RDP) (B. L. Maidak et al., Nucleic Acids Res.
29:
173-174, 2001). The chip and standard Affymetrix software were able to correctly match small-subunit ribosomal DNA amplicons with the corresponding sequences in the RDP database for 15 of 17 bacterial species grown in pure culture. When bacteria collected from an air sample were tested, the method compared favorably with cloning and sequencing amplicons in determining the presence of phylogenetic groups. However, the method could not resolve the individual sequences comprising a complex mixed sample. Given these results and the potential for future enhancement of this technology, it may become widely useful.
Controlled Production of Stable Heterologous Proteins in
Lactococcus lactis
Authors: Miyoshi A. , Poquet I. , Azevedo V. , Commissaire J. , Bermudez-Humaran L. , Domakova E. , Le Loir Y. , Oliveira S. C. , Gruss A. , Langella P. 
Published: July 2002

ABSTRACT

The use of
Lactococcus lactis
(the most extensively characterized lactic acid bacterium) as a delivery organism for heterologous proteins is, in some cases, limited by low production levels and poor-quality products due to surface proteolysis. In this study, we combined in one
L. lactis
strain use of the nisin-inducible promoter P

nisA

and inactivation of the extracellular housekeeping protease HtrA. The ability of the mutant strain, designated
htrA
-NZ9000, to produce high levels of stable proteins was confirmed by using the staphylococcal nuclease (Nuc) and the following four heterologous proteins fused or not fused to Nuc that were initially unstable in wild-type
L. lactis
strains: (i)
Staphylococcus hyicus
lipase, (ii) the bovine rotavirus antigen nonstructural protein 4, (iii) human papillomavirus antigen E7, and (iv)
Brucella abortus
antigen L7/L12. In all cases, protein degradation was significantly lower in strain
htrA
-NZ9000, demonstrating the usefulness of this strain for stable heterologous protein production.
Species-Specific Monoclonal Antibodies to
Escherichia coli
-Expressed p36 Cytosolic Protein of
Mycoplasma hyopneumoniae
Authors: Caron J. , Sawyer N. , Moumen B. Ben Abdel , Bouh K. Cheikh Saad , Dea S. 
Published: July 2002

ABSTRACT

The p36 protein of
Mycoplasma hyopneumoniae
is a cytosolic protein carrying species-specific antigenic determinants. Based on the genomic sequence of the reference strain ATCC 25934, primers were designed for PCR amplification of the p36-encoding gene (948 bp). These primers were shown to be specific to
M. hyopneumoniae
since no DNA amplicons could be obtained with other mycoplasma species and pathogenic bacteria that commonly colonize the porcine respiratory tract. The amplified p36 gene was subcloned into the pGEX-4T-1 vector to be expressed in
Escherichia coli
as a fusion protein with glutathione
S
-transferase (GST). The GST-p36 recombinant fusion protein was purified by affinity chromatography and cut by thrombin, and the enriched p36 protein was used to immunize female BALB/c mice for the production of anti-p36 monoclonal antibodies (MAbs). The polypeptide specificity of the nine MAbs obtained was confirmed by Western immunoblotting with cell lysates prepared from the homologous strain. Cross-reactivity studies of the anti-p36 MAbs towards two other
M. hyopneumoniae
reference strains (ATCC 25095 and J strains) and Quebec field strains that had been isolated in culture suggested that these anti-p36 MAbs were directed against a highly conserved epitope, or closely located epitopes, of the p36 protein. No reactivity was demonstrated against other mycoplasma species tested. Clinical signs and lesions suggestive of enzootic pneumonia were reproduced in specific-pathogen-free pigs infected experimentally with a virulent Quebec field strain (IAF-DM9827) of
M. hyopneumoniae
. The bacteria could be recovered from lung homogenates of pigs that were killed after the 3-week observation period by both PCR and cultivation procedures. Furthermore, the anti-p36 MAbs permitted effective detection by indirect immunofluorescence of
M. hyopneumoniae
in frozen lung sections from experimentally infected pigs. However, attempts to use the recombinant p36 protein as an antigen in an indirect enzyme-linked immunosorbent assay for the detection of antibodies in sera from convalescent pigs showed no correlation with clinical and pathological findings.
Gastrointestinal Colonization by
Candida albicans
Mutant Strains in Antibiotic-Treated Mice
Authors: Wiesner Stephen M. , Jechorek Robert P. , Garni Robb M. , Bendel Catherine M. , Wells Carol L. 
Published: July 2002

ABSTRACT

Antibiotic-treated mice orally inoculated with one of three
Candida albicans
strains (including two mutant strains) or indigenous
Candida pelliculosa
showed levels of candidal gastrointestinal colonization that were strain specific. However, regardless of strain, the numbers of viable candida were intermediate to high in the stomach, were consistently lowest in the upper small intestine, and increased progressively down the intestinal tract.
Elastase Deficiency Phenotype ofPseudomonas aeruginosaCanine Otitis Externa Isolates
Authors: Petermann Shana R. , Doetkott Curt , Rust Lynn 
Published: July 2002

ABSTRACTPseudomonas aeruginosaveterinary isolates were assayed for elastase and total matrix protease activity. The elastase activity of canine ear isolates was much less than that of strain PAO1 and that of all other veterinary isolates (P< 0.0001). The results indicate that canine ear isolates have a distinct elastase phenotype.