bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology ofCryptosporidium molnariin Spanish Gilthead Sea Bream (Sparus aurataL.) and European Sea Bass (Dicentrarchus labraxL.) Cultures: from Hatchery to Market Size
Authors: Sitjà-Bobadilla A. , Padrós F. , Aguilera C. , Alvarez-Pellitero P. 
Published: January 2005

ABSTRACTA long-term epidemiological study ofCryptosporidium molnariin aquacultured European sea bass (ESB) and gilthead sea bream (GSB) was performed in different types of facilities on the Atlantic, Cantabric, and Mediterranean coasts. Four types of studies were carried out. In study A, fish raised from juveniles to marketable size (ongrowing stage) were periodically sampled in three different types of cultures. Studies B and C focused on hatchery and nursery facilities. In study D, occasional samplings were performed during mortality or morbidity outbreaks. As a general trend,C. molnariwas more prevalent in GSB than in ESB. Data on the distribution pattern ofC. molnariin total sampled GSB (studies A, B, and D) had a variance higher than the mean (overdispersion). In GSB (study A), the type of ongrowing system (sea cages, earth ponds, or indoor tanks) was found to have no significant effect. There was a significant relationship between the presence of the parasite and both fish weight and season. The highest infection values were recorded in spring. Prevalence and intensity had convex weight profiles, with a peak in 30- to 100-g fish. In study D, the prevalence of infection was higher in fish recently introduced in sea cages and in preongrowing systems. In studies B and C, fish were almost never infected before entering the postlarval and nursery facilities. The parasite seems to enter the host mainly through the water in production steps with less stringent water treatment. Recirculation systems and fish cannibalism could contribute to oocyst concentration and dispersion in aquaculture facilities.
Seasonal Variation of
Ralstonia solanacearum
Biovar 2 Populations in a Spanish River: Recovery of Stressed Cells at Low Temperatures
Authors: Caruso Paola , Palomo Jose Luis , Bertolini Edson , Álvarez Belén , López María M. , Biosca Elena G. 
Published: January 2005

ABSTRACT

The presence of
Ralstonia solanacearum
biovar 2 in the watercourses of European countries is increasing, but little is known about its ecology in aquatic habitats. The detection of this pathogen in 2000 in one Spanish river led us to study its population density at different locations on the river over a period of 3 years. During 2000 and 2001, the pathogen was recovered at low densities (10 to 80 CFU/ml) by direct plating on modified SMSA agar from water samples at 14°C or higher, but its isolation was usually unsuccessful at temperatures below 9°C. To monitor the pathogen's abundance in winter, we used two liquid selective media for enrichment (at 29 and 35°C) and compared them by using spiked river water samples: modified Wilbrink broth (MWB) was more efficient than modified SMSA broth for double-antibody-sandwich indirect enzyme-linked immunosorbent assay (DASI-ELISA) detection of
R. solanacearum
. Enrichment in MWB at both temperatures allowed us to recover
R. solanacearum
cells that were nonculturable on solid media up to 25 days after their entry into the viable but nonculturable state. When we applied this technique to water samples during the cold months of 2001 and 2002, we obtained the best detection results by the most-probable-number method after enrichment at 35°C with MWB. The enrichment protocol was combined with DASI-ELISA and validated by Co-PCR to detect both naturally and artificially starved and cold-stressed cells in water, which were still infective. Overall, the data from this study demonstrate the effects of temperature variation on the population and culturability of
R. solanacearum
cells on solid media and their survival at low temperatures.
Prevalence and Antimicrobial Resistance of Thermophilic
Campylobacter
spp. from Cattle Farms in Washington State
Authors: Bae Wonki , Kaya Katherine N. , Hancock Dale D. , Call Douglas R. , Park Yong Ho , Besser Thomas E. 
Published: January 2005

ABSTRACT

The prevalence of thermophilic
Campylobacter
spp. was investigated in cattle on Washington State farms. A total of 350 thermophilic
Campylobacter
isolates were isolated from 686 cattle sampled on 15 farms (eight dairies, two calf rearer farms, two feedlots, and three beef cow-calf ranches). Isolate species were identified with a combination of phenotypic tests,
hipO
colony blot hybridization, and multiplex
lpxA
PCR. Breakpoint resistance to four antimicrobials (ciprofloxacin, nalidixic acid, erythromycin, and doxycycline) was determined by agar dilution.
Campylobacter jejuni
was the most frequent species isolated (34.1%), followed by
Campylobacter coli
(7.7%) and other thermophilic campylobacters (1.5%). The most frequently detected resistance was to doxycycline (42.3% of 350 isolates). Isolates from calf rearer facilities were more frequently doxycycline resistant than isolates from other farm types.
C. jejuni
was most frequently susceptible to all four of the antimicrobial drugs studied (58.8% of 272 isolates).
C. coli
isolates were more frequently resistant than
C. jejuni
, including resistance to quinolone antimicrobials (89.3% of isolates obtained from calves on calf rearer farms) and to erythromycin (72.2% of isolates obtained from feedlot cattle). Multiple drug resistance was more frequent in
C. coli
(51.5%) than in
C. jejuni
(5.1%). The results of this study demonstrate that
C. jejuni
is widely distributed among Washington cattle farms, while
C. coli
is more narrowly distributed but significantly more resistant.
Diversity of Green-Like and Red-Like Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes (
cbbL
) in Differently Managed Agricultural Soils
Authors: Selesi Draženka , Schmid Michael , Hartmann Anton 
Published: January 2005

ABSTRACT

A PCR-based approach was developed to detect ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) form I large-subunit genes (
cbbL
) as a functional marker of autotrophic bacteria that fix carbon dioxide via the Calvin-Benson-Bassham cycle. We constructed two different primer sets, targeting the green-like and red-like phylogenetic groups of
cbbL
genes. The diversity of these
cbbL
genes was analyzed by the use of three differently managed agricultural soils from a long-term field experiment.
cbbL
gene fragments were amplified from extracted soil DNAs, and PCR products were cloned and screened by restriction fragment length polymorphism analysis. Selected unique
cbbL
clones were sequenced and analyzed phylogenetically. The green-like
cbbL
sequences revealed a very low level of diversity, being closely related to the
cbbL
genes of
Nitrobacter winogradskyi
and
Nitrobacter vulgaris
. In contrast, the red-like
cbbL
gene libraries revealed a high level of diversity in the two fertilized soils and less diversity in unfertilized soil. The majority of environmental red-like
cbbL
genes were only distantly related to already known
cbbL
sequences and even formed separate clusters. In order to extend the database of available red-like
cbbL
sequences, we amplified
cbbL
sequences from bacterial type culture strains and from bacterial isolates obtained from the investigated soils. Bacterial isolates harboring the
cbbL
gene were analyzed phylogenetically on the basis of their 16S rRNA gene sequences. These analyses revealed that bacterial genera such as
Bacillus
,
Streptomyces
, and
Arthrobacter
harbor red-like
cbbL
genes which fall into the
cbbL
gene clusters retrieved from the investigated soils.
Feedback-Resistant Acetohydroxy Acid Synthase Increases Valine Production in
Corynebacterium glutamicum
Authors: Elišáková Veronika , Pátek Miroslav , Holátko Jiří , Nešvera Jan , Leyval Damien , Goergen Jean-Louis , Delaunay Stéphane 
Published: January 2005

ABSTRACT

Acetohydroxy acid synthase (AHAS), which catalyzes the key reactions in the biosynthesis pathways of branched-chain amino acids (valine, isoleucine, and leucine), is regulated by the end products of these pathways. The whole
Corynebacterium glutamicum ilvBNC
operon, coding for acetohydroxy acid synthase (
ilvBN
) and aceto hydroxy acid isomeroreductase (
ilvC
), was cloned in the newly constructed
Escherichia coli
-
C. glutamicum
shuttle vector pECKA (5.4 kb, Km
r
). By using site-directed mutagenesis, one to three amino acid alterations (mutations M8, M11, and M13) were introduced into the small (regulatory) AHAS subunit encoded by
ilvN
. The activity of AHAS and its inhibition by valine, isoleucine, and leucine were measured in strains carrying the
ilvBNC
operon with mutations on the plasmid or the
ilvN
M13 mutation within the chromosome. The enzyme containing the M13 mutation was feedback resistant to all three amino acids. Different combinations of branched-chain amino acids did not inhibit wild-type AHAS to a greater extent than was measured in the presence of 5 mM valine alone (about 57%). We infer from these results that there is a single binding (allosteric) site for all three amino acids in the enzyme molecule. The strains carrying the
ilvN
M13 mutation in the chromosome produced more valine than their wild-type counterparts. The plasmid-free
C. glutamicum
Δ
ilvA
Δ
panB ilvN
M13 strain formed 90 mM valine within 48 h of cultivation in minimal medium. The same strain harboring the plasmid pECKAilvBNC produced as much as 130 mM valine under the same conditions.
Geographic and Environmental Sources of Variation in Lake Bacterial Community Composition
Authors: Yannarell Anthony C. , Triplett Eric W. 
Published: January 2005

ABSTRACT
This study used a genetic fingerprinting technique (automated ribosomal intergenic spacer analysis [ARISA]) to characterize microbial communities from a culture-independent perspective and to identify those environmental factors that influence the diversity of bacterial assemblages in Wisconsin lakes. The relationships between bacterial community composition and 11 environmental variables for a suite of 30 lakes from northern and southern Wisconsin were explored by canonical correspondence analysis (CCA). In addition, the study assessed the influences of ARISA fragment detection threshold (sensitivity) and the quantitative, semiquantitative, and binary (presence-absence) use of ARISA data. It was determined that the sensitivity of ARISA was influential only when presence-absence-transformed data were used. The outcomes of analyses depended somewhat on the data transformation applied to ARISA data, but there were some features common to all of the CCA models. These commonalities indicated that differences in bacterial communities were best explained by regional (i.e., northern versus southern Wisconsin lakes) and landscape level (i.e., seepage lakes versus drainage lakes) factors. ARISA profiles from May samples were consistently different from those collected in other months. In addition, communities varied along gradients of pH and water clarity (Secchi depth) both within and among regions. The results demonstrate that environmental, temporal, regional, and landscape level features interact to determine the makeup of bacterial assemblages in northern temperate lakes.
Quantification of Ammonia-Oxidizing Bacteria and Factors Controlling Nitrification in Salt Marsh Sediments
Authors: Dollhopf Sherry L. , Hyun Jung-Ho , Smith April C. , Adams Harold J. , O'Brien Sean , Kostka Joel E. 
Published: January 2005

ABSTRACT

To elucidate the geomicrobiological factors controlling nitrification in salt marsh sediments, a comprehensive approach involving sediment geochemistry, process rate measurements, and quantification of the genetic potential for nitrification was applied to three contrasting salt marsh habitats: areas colonized by the tall (TS) or short (SS) form of
Spartina alterniflora
and unvegetated creek banks (CBs). Nitrification and denitrification potential rates were strongly correlated with one another and with macrofaunal burrow abundance, indicating that coupled nitrification-denitrification was enhanced by macrofaunal burrowing activity. Ammonia monooxygenase (
amoA
) gene copy numbers were used to estimate the ammonia-oxidizing bacterial population size (5.6 × 10
4
to 1.3 × 10
6
g of wet sediment
−1
), which correlated with nitrification potentials and was 1 order of magnitude higher for TS and CB than for SS. TS and CB sediments also had higher Fe(III) content, higher Fe(III)-to-total reduced sulfur ratios, higher Fe(III) reduction rates, and lower dissolved sulfides than SS sediments. Iron(III) content and reduction rates were positively correlated with nitrification and denitrification potential and
amoA
gene copy number. Laboratory slurry incubations supported field data, confirming that increased amounts of Fe(III) relieved sulfide inhibition of nitrification. We propose that macrofaunal burrowing and high concentrations of Fe(III) stimulate nitrifying bacterial populations, and thus may increase nitrogen removal through coupled nitrification-denitrification in salt marsh sediments.
A
clp
Gene Homologue Belonging to the Crp Gene Family Globally Regulates Lytic Enzyme Production, Antimicrobial Activity, and Biological Control Activity Expressed by
Lysobacter enzymogenes
Strain C3
Authors: Kobayashi Donald Y. , Reedy Ralph M. , Palumbo Jeffrey D. , Zhou Jun-Ma , Yuen Gary Y. 
Published: January 2005

ABSTRACT

Lysobacter enzymogenes
strain C3, a biological control agent for plant diseases, produces multiple extracellular hydrolytic enzymes and displays antimicrobial activity against various fungal and oomycetous species. However, little is known about the regulation of these enzymes or their roles in antimicrobial activity and biocontrol. A study was undertaken to identify mutants of strain C3 affected in extracellular enzyme production and to evaluate their biocontrol efficacy. A single mini-Tn
5-lacZ
1
-cat
transposon mutant of
L. enzymogenes
strain C3 that was globally affected in a variety of phenotypes was isolated. In this mutant, 5E4, the activities of several extracellular lytic enzymes, gliding motility, and in vitro antimicrobial activity were reduced. Characterization of 5E4 indicated that the transposon inserted in a
clp
gene homologue belonging to the Crp gene family of regulators. Immediately downstream was a second open reading frame similar to that encoding acetyltransferases belonging to the Gcn5-related
N
-acetyltransferase superfamily, which reverse transcription-PCR confirmed was cotranscribed with
clp
. Chromosomal deletion mutants with mutations in
clp
and between
clp
and the acetyltransferase gene verified the 5E4 mutant phenotype. The
clp
gene was chromosomally inserted in mutant 5E4, resulting in complemented strain P1. All mutant phenotypes were restored in P1, although the gliding motility was observed to be excessive compared with that of the wild-type strain.
clp
mutant strains were significantly affected in biological control of
pythium
damping-off of sugar beet and
bipolaris
leaf spot of tall fescue, which was partially or fully restored in the complemented strain P1. These results indicate that
clp
is a global regulatory gene that controls biocontrol traits expressed by
L. enzymogenes
C3.
Different Inactivation Behaviors of MS-2 Phage and
Escherichia coli
in TiO
2
Photocatalytic Disinfection
Authors: Cho Min , Chung Hyenmi , Choi Wonyong , Yoon Jeyong 
Published: January 2005

ABSTRACT

Despite a wealth of experimental evidence concerning the efficacy of the biocidal action associated with the TiO
2
photocatalytic reaction, our understanding of the photochemical mechanism of this particular biocidal action remains largely unclear. It is generally accepted that the hydroxyl radical (·OH), which is generated on the surface of UV-illuminated TiO
2
, plays the main role. However, our understanding of the exact mode of action of the hydroxyl radical in killing microorganisms is far from complete, and some studies report that other reactive oxygen species (ROS) (H
2
O
2
and O
2
·
−
, etc.) also play significant roles. In particular, whether hydroxyl radicals remain bound to the surface or diffuse into the solution bulk is under active debate. In order to examine the exact mode of action of ROS in inactivating the microorganism, we tested and compared the levels of photocatalytic inactivation of MS-2 phage and
Escherichia coli
as representative species of viruses and bacteria, respectively. To compare photocatalytic microbial inactivation with the photocatalytic chemical degradation reaction,
para
-chlorobenzoic acid, which rapidly reacts with a hydroxyl radical with a diffusion-limited rate, was used as a probe compound. Two different hydroxyl radical scavengers,
tert
-butanol and methanol, and an activator of the bulk phase hydroxyl radical generation, Fe
2+
, were used to investigate their effects on the photocatalytic mode of action of the hydroxyl radical in inactivating the microorganism. The results show that the biocidal modes of action of ROS are very different depending on the specific microorganism involved, although the reason for this is not clear. It seems that MS-2 phage is inactivated mainly by the free hydroxyl radical in the solution bulk but that
E. coli
is inactivated by both the free and the surface-bound hydroxyl radicals.
E. coli
might also be inactivated by other ROS, such as O
2
·
−
and H
2
O
2
, according to the present results.
Development and Validation of PCR Primers To Assess the Diversity of
Clostridium
spp. in Cheese by Temporal Temperature Gradient Gel Electrophoresis
Authors: Le Bourhis Anne-Gaëlle , Saunier Katiana , Doré Joël , Carlier Jean-Philippe , Chamba Jean-François , Popoff Michel-Robert , Tholozan Jean-Luc 
Published: January 2005

ABSTRACT

A nested-PCR temporal temperature gradient gel electrophoresis (TTGE) approach was developed for the detection of bacteria belonging to phylogenetic cluster I of the genus
Clostridium
(the largest clostridial group, which represents 25% of the currently cultured clostridial species) in cheese suspected of late blowing. Primers were designed based on the 16S rRNA gene sequence, and the specificity was confirmed in PCRs performed with DNAs from cluster I and non-cluster I species as the templates. TTGE profiles of the PCR products, comprising the V5-V6 region of the 16S rRNA gene, allowed us to distinguish the majority of cluster I species. PCR-TTGE was applied to analyze commercial cheeses with defects. All cheeses gave a signal after nested PCR, and on the basis of band comigration with TTGE profiles of reference strains, all the bands could be assigned to a clostridial species. The direct identification of
Clostridium
spp. was confirmed by sequencing of excised bands.
C. tyrobutyricum
and
C. beijerinckii
contaminated 15 and 14 of the 20 cheese samples tested, respectively, and
C. butyricum
and
C. sporogenes
were detected in one cheese sample. Most-probable-number counts and volatile fatty acid were determined for comparison purposes. Results obtained were in agreement, but only two species,
C. tyrobutyricum
and
C. sporogenes
, could be isolated by the plating method. In all cheeses with a high amount of butyric acid (>100 mg/100 g), the presence of
C. tyrobutyricum
DNA was confirmed by PCR-TTGE, suggesting the involvement of this species in butyric acid fermentation. These results demonstrated the efficacy of the PCR-TTGE method to identify
Clostridium
in cheeses. The sensitivity of the method was estimated to be 100 CFU/g.
Identification, Cloning, and Characterization of a
Lactococcus lactis
Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation
Authors: Smit Bart A. , van Hylckama Vlieg Johan E. T. , Engels Wim J. M. , Meijer Laura , Wouters Jan T. M. , Smit Gerrit 
Published: January 2005

ABSTRACT

The biochemical pathway for formation of branched-chain aldehydes, which are important flavor compounds derived from proteins in fermented dairy products, consists of a protease, peptidases, a transaminase, and a branched-chain α-keto acid decarboxylase (KdcA). The activity of the latter enzyme has been found only in a limited number of
Lactococcus lactis
strains. By using a random mutagenesis approach, the gene encoding KdcA in
L. lactis
B1157 was identified. The gene for this enzyme is highly homologous to the gene annotated
ipd
, which encodes a putative indole pyruvate decarboxylase, in
L. lactis
IL1403. Strain IL1403 does not produce KdcA, which could be explained by a 270-nucleotide deletion at the 3′ terminus of the
ipd
gene encoding a truncated nonfunctional decarboxylase. The
kdcA
gene was overexpressed in
L. lactis
for further characterization of the decarboxylase enzyme. Of all of the potential substrates tested, the highest activity was observed with branched-chain α-keto acids. Moreover, the enzyme activity was hardly affected by high salinity, and optimal activity was found at pH 6.3, indicating that the enzyme might be active under cheese ripening conditions.
Isolation of Auxotrophic Mutants of Diploid Industrial Yeast Strains after UV Mutagenesis
Authors: Hashimoto Shinji , Ogura Mayumi , Aritomi Kazuo , Hoshida Hisashi , Nishizawa Yoshinori , Akada Rinji 
Published: January 2005

ABSTRACT

Auxotrophic mutants of the yeast
Saccharomyces cerevisiae
are usually isolated in haploid strains because the isolation of recessive mutations in diploids is thought to be difficult due to the presence of two sets of genes. We show here that auxotrophic mutants of diploid industrial sake yeast strains were routinely obtained by a standard mutant selection procedure following UV mutagenesis. We isolated His
−
, Met
−
, Lys
−
, Trp
−
, Leu
−
, Arg
−
, and Ura
−
auxotrophic mutants of five sake strains, Kyokai no. 7, no. 9, no. 10, no. 701, and no. 901, by screening only 1,700 to 3,400 colonies from each treated strain. Wild-type alleles were cloned and used as markers for transformation. With
HIS3
as a selectable marker, the yeast
TDH3
overexpression promoter was inserted upstream of
ATF1
, encoding alcohol acetyltransferase, by one-step gene replacement in a
his3
mutant of Kyokai no. 7. The resulting strain contained exclusively yeast DNA, making it acceptable for commercial use, and produced a larger amount of isoamyl acetate, a banana-like flavor. We argue that the generally recognized difficulty of isolating auxotrophic mutants of diploid industrial yeast strains is misleading and that genetic techniques used for haploid laboratory strains are applicable for this purpose.