bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of tinea capitis in primary schools in Turkey
Authors: Altindis M. , Bilgili E. , Kiraz N. , Ceri A. 
Published: July 2003

SummaryThe aim of our study was to determine the prevalence of tinea capitis in Middle Anatolia. Between February 2000 and April 2000, a school survey of 4760 primary school children was carried out and 34 cases of tinea capitis were clinically diagnosed. Sixteen (0.3%) of them were diagnosed both clinically and using culture. Eighteen cases (52.9%) were diagnosed microscopically whereas the remaining 16 cases (47.0%) had a clinical diagnose. We also isolated and identified the following species of fungi causing the infection: Trichophyton verrucosum (five cases), T. rubrum (three), T. mentagrophytes var. mentagrophytes (three), Microsporum canis (three) and T. tonsurans (two). We detected a higher rate of infection than that of the country's average.
Heterotrophic Bacterial Growth Efficiency and Community Structure at Different Natural Organic Carbon Concentrations
Authors: Eiler Alexander , Langenheder Silke , Bertilsson Stefan , Tranvik Lars J. 
Published: July 2003

ABSTRACT

Batch cultures of aquatic bacteria and dissolved organic matter were used to examine the impact of carbon source concentration on bacterial growth, biomass, growth efficiency, and community composition. An aged concentrate of dissolved organic matter from a humic lake was diluted with organic compound-free artificial lake water to obtain concentrations of dissolved organic carbon (DOC) ranging from 0.04 to 2.53 mM. The bacterial biomass produced in the cultures increased linearly with the DOC concentration, indicating that bacterial biomass production was limited by the supply of carbon. The bacterial growth rate in the exponential growth phase exhibited a hyperbolic response to the DOC concentration, suggesting that the maximum growth rate was constrained by the substrate concentration at low DOC concentrations. Likewise, the bacterial growth efficiency calculated from the production of biomass and CO
2
increased asymptotically from 0.4 to 10.4% with increasing DOC concentration. The compositions of the microbial communities that emerged in the cultures were assessed by separation of PCR-amplified 16S rRNA fragments by denaturing gradient gel electrophoresis. Nonmetric multidimensional scaling of the gel profiles showed that there was a gradual change in the community composition along the DOC gradient; members of the β subclass of the class
Proteobacteria
and members of the
Cytophaga-Flavobacterium
group were well represented at all concentrations, whereas members of the α subclass of the
Proteobacteria
were found exclusively at the lowest carbon concentration. The shift in community composition along the DOC gradient was similar to the patterns of growth efficiency and growth rate. The results suggest that the bacterial growth efficiencies, the rates of bacterial growth, and the compositions of bacterial communities are not constrained by substrate concentrations in most natural waters, with the possible exception of the most oligotrophic environments.
Differential Transfer and Dissemination of Hypovirus and Nuclear and Mitochondrial Genomes of a Hypovirus-Infected
Cryphonectria parasitica
Strain after Introduction into a Natural Population
Authors: Hoegger Patrik J. , Heiniger Ursula , Holdenrieder Ottmar , Rigling Daniel 
Published: July 2003

ABSTRACT

Biological control of plant diseases generally requires release of living organisms into the environment. Cryphonectria hypoviruses function as biological control agents for the chestnut blight fungus,
Cryphonectria parasitica
, and hypovirus-infected
C. parasitica
strains can be used to treat infected trees. We used naturally occurring molecular marker polymorphisms to examine the persistence and dissemination of the three genomes of a hypovirus-infected
C. parasitica
strain, namely, the double-stranded RNA genome of
Cryphonectria
hypovirus 1 (CHV1) and the nuclear and mitochondrial genomes of its fungal host. The hypovirus-infected strain was experimentally introduced into a blight-infested chestnut coppice forest by treating 73 of 246 chestnut blight cankers. Two years after introduction, the hypovirus had disseminated to 36% of the untreated cankers and to 35% of the newly established cankers. Spread of the hypovirus was more frequent within treated sprout clusters than between sprout clusters. Mitochondrial DNA of the introduced fungus also was transferred into the resident
C. parasitica
population. Concomitant transfer of both the introduced hypovirus and mitochondrial DNA was detected in almost one-half of the treated cankers analyzed. The introduced mitochondrial DNA haplotype also was found in three resident isolates from newly established cankers. The nuclear genome of the introduced strain persisted in the treated cankers but did not spread beyond them.
Construction of Deoxyriboaldolase-Overexpressing
Escherichia coli
and Its Application to 2-Deoxyribose 5-Phosphate Synthesis from Glucose and Acetaldehyde for 2′-Deoxyribonucleoside Production
Authors: Horinouchi Nobuyuki , Ogawa Jun , Sakai Takafumi , Kawano Takako , Matsumoto Seiichiro , Sasaki Mie , Mikami Yoichi , Shimizu Sakayu 
Published: July 2003

ABSTRACT

The gene encoding a deoxyriboaldolase (DERA) was cloned from the chromosomal DNA of
Klebsiella pneumoniae
B-4-4. This gene contains an open reading frame consisting of 780 nucleotides encoding 259 amino acid residues. The predicted amino acid sequence exhibited 94.6% homology with the sequence of DERA from
Escherichia coli
. The DERA of
K. pneumoniae
was expressed in recombinant
E. coli
cells, and the specific activity of the enzyme in the cell extract was as high as 2.5 U/mg, which was threefold higher than the specific activity in the
K. pneumoniae
cell extract. One of the
E. coli
transformants, 10B5/pTS8, which had a defect in alkaline phosphatase activity, was a good catalyst for 2-deoxyribose 5-phosphate (DR5P) synthesis from glyceraldehyde 3-phosphate and acetaldehyde. The
E. coli
cells produced DR5P from glucose and acetaldehyde in the presence of ATP. Under the optimal conditions, 100 mM DR5P was produced from 900 mM glucose, 200 mM acetaldehyde, and 100 mM ATP by the
E. coli
cells. The DR5P produced was further transformed to 2′-deoxyribonucleoside through coupling the enzymatic reactions of phosphopentomutase and nucleoside phosphorylase. These results indicated that production of 2′-deoxyribonucleoside from glucose, acetaldehyde, and a nucleobase is possible with the addition of a suitable energy source, such as ATP.
Two-Step Freezing Procedure for Cryopreservation of Rumen Ciliates, an Effective Tool for Creation of a Frozen Rumen Protozoa Bank
Authors: Nsabimana E. , Kišidayová S. , Macheboeuf D. , Newbold C. J. , Jouany J. P. 
Published: July 2003

ABSTRACT

The present study aimed at the long-term storage of rumen protozoa as living cells in liquid nitrogen. The two-step or interrupted slow freezing procedure was used to cryopreserve six of the dominant species of rumen ciliates isolated from monofaunated animals,
Dasytricha ruminantium
,
Entodinium caudatum
,
Epidinium ecaudatum caudatum
,
Eudiplodinium maggii
,
Isotricha prostoma
, and
Polyplastron multivesiculatum
. We optimized the first step in the interrupted slow freezing procedure, from the extracellular ice nucleation temperature to the holding temperature, and studied the effects of the cooling rates on survival. In addition to the nature of the cryoprotectant (dimethyl sulfoxide), the equilibration temperature and equilibration time (25°C and 5 min, respectively), and the holding time at subzero temperature (45 min) recommended previously (S. Kišidayová, J. Microbiol. Methods
22:
185-192, 1995), we found that a holding temperature of −30°C, a cooling rate from extracellular ice nucleation temperature to holding temperature of between 1.2°C/min and 2.5°C/min, depending on the ciliate, and rumen juice as the freezing and thawing medium markedly improved the survival rate. Survival rates determined after 2 weeks in liquid nitrogen were 100% for
Isotricha
, 98% for
Dasytricha
, 85% for
Epidinium
, 79% for
Polyplastron
, 63% for
Eudiplodinium
, and 60% for
Entodinium
. They were not significantly modified after a period of 1 year in liquid nitrogen. Four of the five ciliate species cryopreserved for 8 months in liquid nitrogen successfully colonized the rumen when inoculated into defaunated animals. These results have made it possible to set up a bank of cryopreserved rumen protozoa.
Characterization and Molecular Cloning of a Novel Enzyme, Inorganic Polyphosphate/ATP-Glucomannokinase, of
Arthrobacter
sp. Strain KM
Authors: Mukai Takako , Kawai Shigeyuki , Matsukawa Hirokazu , Matuo Yuhsi , Murata Kousaku 
Published: July 2003

ABSTRACT

A bacterium exhibiting activities of several inorganic polyphosphate [poly(P)]- and ATP-dependent kinases, including glucokinase, NAD kinase, mannokinase, and fructokinase, was isolated, determined to belong to the genus
Arthrobacter
, and designated
Arthrobacter
sp. strain KM. Among the kinases, a novel enzyme responsible for the poly(P)- and ATP-dependent mannokinase activities was purified 2,200-fold to homogeneity from a cell extract of the bacterium. The purified enzyme was a monomer with a molecular mass of 30 kDa. This enzyme phosphorylated glucose and mannose with a high affinity for glucose, utilizing poly(P) as well as ATP, and was designated poly(P)/ATP-glucomannokinase. The
K

m

values of the enzyme for glucose, mannose, ATP, and hexametaphosphate were determined to be 0.50, 15, 0.20, and 0.02 mM, respectively. The catalytic sites for poly(P)-dependent phosphorylation and ATP-dependent phosphorylation of the enzyme were found to be shared, and the poly(P)-utilizing mechanism of the enzyme was shown to be nonprocessive. The gene encoding the poly(P)/ATP-glucomannokinase was cloned from
Arthrobacter
sp. strain KM, and its nucleotide sequence was determined. This gene contained an open reading frame consisting of 804 bp coding for a putative polypeptide with a calculated molecular mass of 29,480 Da. The deduced amino acid sequence of the polypeptide exhibited homology to the amino acid sequences of the poly(P)/ATP-glucokinase of
Mycobacterium tuberculosis
H37Rv (level of homology, 45%), ATP-dependent glucokinases of
Corynebacterium glutamicum
(45%),
Renibacterium salmoninarum
(45%), and
Bacillus subtilis
(35%), and proteins of bacteria belonging to the order
Actinomyces
whose functions are not known. Alignment of these homologous proteins revealed seven conserved regions. The mannose and poly(P) binding sites of poly(P)/ATP-glucomannokinase are discussed.
Microbial Diversity of Cryptoendolithic Communities from the McMurdo Dry Valleys, Antarctica
Authors: de la Torre José R. , Goebel Brett M. , Friedmann E. Imre , Pace Norman R. 
Published: July 2003

ABSTRACT

In the McMurdo Dry Valleys of Antarctica, microorganisms colonize the pore spaces of exposed rocks and are thereby protected from the desiccating environmental conditions on the surface. These cryptoendolithic communities have received attention in microscopy and culture-based studies but have not been examined by molecular approaches. We surveyed the microbial biodiversity of selected cryptoendolithic communities by analyzing clone libraries of rRNA genes amplified from environmental DNA. Over 1,100 individual clones from two types of cryptoendolithic communities, cyanobacterium dominated and lichen dominated, were analyzed. Clones fell into 51 relatedness groups (phylotypes) with ≥98% rRNA sequence identity (46 bacterial and 5 eucaryal). No representatives of
Archaea
were detected. No phylotypes were shared between the two classes of endolithic communities studied. Clone libraries based on both types of communities were dominated by a relatively small number of phylotypes that, because of their relative abundance, presumably represent the main primary producers in these communities. In the lichen-dominated community, three rRNA sequences, from a fungus, a green alga, and a chloroplast, of the types known to be associated with lichens, accounted for over 70% of the clones. This high abundance confirms the dominance of lichens in this community. In contrast, analysis of the supposedly cyanobacterium-dominated community indicated, in addition to cyanobacteria, at least two unsuspected organisms that, because of their abundance, may play important roles in the community. These included a member of the α subdivision of the
Proteobacteria
that potentially is capable of aerobic anoxygenic photosynthesis and a distant relative of
Deinococcus
that defines, along with other
Deinococcus
-related sequences from Antarctica, a new clade within the
Thermus-Deinococcus
bacterial phylogenetic division.
Identification and Characterization of a GDSL Esterase Gene Located Proximal to theswrQuorum-Sensing System ofSerratia liquefaciensMG1
Authors: Riedel Kathrin , Talker-Huiber Daniela , Givskov Michael , Schwab Helmut , Eberl Leo 
Published: July 2003

ABSTRACTSerratia liquefaciensMG1 employs theswrquorum-sensing system to control various functions, including production of extracellular enzymes and swarming motility. Here we report the sequencing of theswrflanking DNA regions. We identified a gene upstream ofswrRand transcribed in the same direction, designatedestA, which encodes an esterase that belongs to family II of lipolytic enzymes. EstA was heterologously expressed inEscherichia coli, and the substrate specificity of the enzyme was determined in crude extracts. With the aid of zymograms visualizing EstA on polyacrylamide gels and by the analysis of a transcriptional fusion of theestApromoter to the promoterlessluxABgenes, we showed that expression of the esterase is not regulated by theswrquorum-sensing system. AnestAmutant was generated and was found to exhibit growth defects on minimal medium containing Tween 20 or Tween 80 as the sole carbon source. Moreover, we show that the mutant produces greatly reduced amounts ofN-acyl-homoserine lactone (AHL) signal molecules on Tween-containing medium compared with the wild type, suggesting that under certain growth conditions EstA may be important for providing the cell with precursors required for AHL biosynthesis.
Dominance of
Vibrio fischeri
in Secreted Mucus outside the Light Organ of
Euprymna scolopes
: the First Site of Symbiont Specificity
Authors: Nyholm Spencer V. , McFall-Ngai Margaret J. 
Published: July 2003

ABSTRACT

Previous studies of the
Euprymna scolopes-Vibrio fischeri
symbiosis have demonstrated that, during colonization, the hatchling host secretes mucus in which gram-negative environmental bacteria amass in dense aggregations outside the sites of infection. In this study, experiments with green fluorescent protein-labeled symbiotic and nonsymbiotic species of gram-negative bacteria were used to characterize the behavior of cells in the aggregates. When hatchling animals were exposed to 10
3
to 10
6
V. fischeri
cells/ml added to natural seawater, which contains a mix of approximately 10
6
nonspecific bacterial cells/ml,
V. fischeri
cells were the principal bacterial cells present in the aggregations. Furthermore, when animals were exposed to equal cell numbers of
V. fischeri
(either a motile or a nonmotile strain) and either
Vibrio parahaemolyticus
or
Photobacterium leiognathi
, phylogenetically related gram-negative bacteria that also occur in the host's habitat, the symbiont cells were dominant in the aggregations. The presence of
V. fischeri
did not compromise the viability of these other species in the aggregations, and no significant growth of
V. fischeri
cells was detected. These findings suggested that dominance results from the ability of
V. fischeri
either to accumulate or to be retained more effectively within the mucus. Viability of the
V. fischeri
cells was required for both the formation of tight aggregates and their dominance in the mucus. Neither of the
V. fischeri
quorum-sensing compounds accumulated in the aggregations, which suggested that the effects of these small signal molecules are not critical to
V. fischeri
dominance. Taken together, these data provide evidence that the specificity of the squid-vibrio symbiosis begins early in the interaction, in the mucus where the symbionts aggregate outside of the light organ.
Identification of a NovelCryptosporidiumGenotype in Pigs
Authors: Ryan U. M. , Samarasinghe B. , Read C. , Buddle J. R. , Robertson I. D. , Thompson R. C. A. 
Published: July 2003

ABSTRACTOver a 3-year period, a total of 646 fecal samples from pigs in 22 indoor and outdoor herds from Western Australia were screened forCryptosporidiumspp. by microscopy. Results revealed that 39 of 646 samples (6.03%) were positive forCryptosporidium. Cryptosporidiumwas much more common in outdoor herds (17.2%) than in indoor herds (0.5%) and was more common in animals between the ages of 5 and 8 weeks (69.2%) than in younger animals (P< 0.0001). Molecular characterization of the positive samples at the 18S ribosomal DNA locus identified two distinct genotypes ofCryptosporidium: the previously identified pig genotype I and a novel pig genotype (pig genotype II), both of which warrant species status.
Role of the
Bacillus methanolicus
Citrate Synthase II Gene,
citY
, in Regulating the Secretion of Glutamate in
l
-Lysine-Secreting Mutants
Authors: Brautaset Trygve , Williams Mark D. , Dillingham Richard D. , Kaufmann Christine , Bennaars Assumpta , Crabbe Edward , Flickinger Michael C. 
Published: July 2003

ABSTRACT

The thermotolerant, restrictive methylotroph
Bacillus methanolicus
MGA3 (ATCC 53907) can secrete 55 g of glutamate per liter (maximum yield, 0.36 g/g) at 50°C with methanol as a carbon source and a source of ammonia in fed-batch bioreactors. A homoserine dehydrogenase mutant, 13A52-8A66, secreting up to 35 g of
l
-lysine per liter in fed-batch fermentations had minimal 2-oxoglutarate dehydrogenase activity [7.3 nmol min
−1
(mg of protein)
−1
], threefold-increased pyruvate carboxylase activity [535 nmol min
−1
(mg of protein)
−1
], and elevated citrate synthase (CS) activity [292 nmol min
−1
(mg of protein)
−1
] and simultaneously secreted glutamate (20 to 30 g per liter) and
l
-lysine. The flow of carbon from oxaloacetate is split between transamination to aspartate and formation of citrate. To investigate the regulation of this branch point, the
B. methanolicus
gene
citY
encoding a CSII protein with activity at 50°C was cloned from 13A52-8A66 into a CS-deficient
Escherichia coli
K2-1-4 strain. A
citY
-deficient
B. methanolicus
mutant, NCS-L-7, was also isolated from the parent strain of 13A52-8A66 by
N
-methyl-
N
′-nitro-
N
-nitrosoguanidine mutagenesis, followed by selection with monofluoroacetate disks on glutamate plates. Characterization of these strains confirmed that
citY
in strain 13A52-8A66 was not altered and that
B. methanolicus
possessed several forms of CS. Analysis of
citY
cloned from NCS-L-7 showed that the reduced CS activity resulted from a frameshift mutation. The level of glutamate secreted by NCS-L-7 was reduced sevenfold and the ratio of
l
-lysine to glutamate secreted was increased 4.5-fold compared to the wild type in fed-batch cultures with glutamate feeding. This indicates that glutamate secretion in
l
-lysine-overproducing mutants can be altered in favor of increased
l
-lysine secretion by regulating in vivo CS activity.
Thermal Inactivation of Nonproteolytic
Clostridium botulinum
Type E Spores in Model Fish Media and in Vacuum-Packaged Hot-Smoked Fish Products
Authors: Lindström Miia , Nevas Mari , Hielm Sebastian , Lähteenmäki Liisa , Peck Michael W. , Korkeala Hannu 
Published: July 2003

ABSTRACT

Thermal inactivation of nonproteolytic
Clostridium botulinum
type E spores was investigated in rainbow trout and whitefish media at 75 to 93°C. Lysozyme was applied in the recovery of spores, yielding biphasic thermal destruction curves. Approximately 0.1% of the spores were permeable to lysozyme, showing an increased measured heat resistance. Decimal reduction times for the heat-resistant spore fraction in rainbow trout medium were 255, 98, and 4.2 min at 75, 85, and 93°C, respectively, and those in whitefish medium were 55 and 7.1 min at 81 and 90°C, respectively. The
z
values were 10.4°C in trout medium and 10.1°C in whitefish medium. Commercial hot-smoking processes employed in five Finnish fish-smoking companies provided reduction in the numbers of spores of nonproteolytic
C. botulinum
of less than 10
3
. An inoculated-pack study revealed that a time-temperature combination of 42 min at 85°C (fish surface temperature) with >70% relative humidity (RH) prevented growth from 10
6
spores in vacuum-packaged hot-smoked rainbow trout fillets and whole whitefish stored for 5 weeks at 8°C. In Finland it is recommended that hot-smoked fish be stored at or below 3°C, further extending product safety. However, heating whitefish for 44 min at 85°C with 10% RH resulted in growth and toxicity in 5 weeks at 8°C. Moist heat thus enhanced spore thermal inactivation and is essential to an effective process. The sensory qualities of safely processed and more lightly processed whitefish were similar, while differences between the sensory qualities of safely processed and lightly processes rainbow trout were observed.
Development of Reverse Transcription (RT)-PCR and Real-Time RT-PCR Assays for Rapid Detection and Quantification of Viable Yeasts and Molds Contaminating Yogurts and Pasteurized Food Products
Authors: Bleve Gianluca , Rizzotti Lucia , Dellaglio Franco , Torriani Sandra 
Published: July 2003

ABSTRACT

Reverse transcriptase PCR (RT-PCR) and real-time RT-PCR assays have been used to detect and quantify actin mRNA from yeasts and molds. Universal primers were designed based on the available fungal actin sequences, and by RT-PCR they amplified a specific 353-bp fragment from fungal species involved in food spoilage. From experiments on heat-treated cells, actin mRNA was a good indicator of cell viability: viable cells and cells in a nonculturable state were detected, while no signal was observed from dead cells. The optimized RT-PCR assay was able to detect 10 CFU of fungi ml
−1
in pure culture and 10
3
and 10
2
CFU ml
−1
in artificially contaminated yogurts and pasteurized fruit-derived products, respectively. Real-time RT-PCR, performed on a range of spoiled commercial food products, validated the suitability of actin mRNA detection for the quantification of naturally contaminating fungi. The specificity and sensitivity of the procedure, combined with its speed, its reliability, and the potential automation of the technique, offer several advantages to routine analysis programs that assess the presence and viability of fungi in food commodities.
Production of a Polyunsaturated Isoprenoid Wax Ester during Aerobic Metabolism of Squalene by
Marinobacter squalenivorans
sp. nov
Authors: Rontani Jean-François , Mouzdahir Abdelkrim , Michotey Valerie , Caumette Pierre , Bonin Patricia 
Published: July 2003

ABSTRACT

This paper describes the production of 5,9,13-trimethyltetradeca-4
E
,8
E
,12-trienyl-5,9,13-trimethyltetradeca-4
E
,8
E
,12-trienoate during the aerobic degradation of squalene by a
Marinobacter
strain, 2Asq64, isolated from the marine environment. A pathway involving initial cleavage of the C
10
-C
11
or C
14
-C
15
double bonds of the squalene molecule is proposed to explain the formation of this polyunsaturated isoprenoid wax ester. The isoprenoid wax ester content reached 1.1% of the degraded squalene at the mid-exponential growth phase and then decreased during the stationary phase. The wax ester content increased by approximately threefold in N-limited cultures, in which the ammonium concentration corresponds to conditions often found in marine sediments. This suggests that the bacterial formation of isoprenoid wax esters might be favored in such environments. The bacterial strain is then characterized as a member of a new species, for which we propose the name
Marinobacter squalenivorans
sp. nov.