bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and Genetic Diversity ofCampylobacterspp. in Environmental Water Samples from a 100-Square-Kilometer Predominantly Dairy Farming Area
Authors: Kemp R. , Leatherbarrow A. J. H. , Williams N. J. , Hart C. A. , Clough H. E. , Turner J. , Wright E. J. , French N. P. 
Published: April 2005

ABSTRACTWater samples were taken systematically from a 100-km2area of mainly dairy farmland in northwestern England and examined forCampylobacterspp. Pulsed-field gel electrophoresis-restriction fragment length polymorphism (PFGE-RFLP) andflaAstrain typing ofCampylobacter jejuniandCampylobacter coliisolates were done. Data on the water source and the adjacent environment were recorded and examined as explanatory variables.Campylobacterspp. were isolated from 40.5% (n= 119) of the water samples tested.C. jejuniwas isolated from 14.3%,C. coliwas isolated from 18.5%, andCampylobacter lariwas isolated from 4.2% of the samples.Campylobacter hyointestinaliswas not isolated from any water source. The difference in prevalence between water types (trough, running, and standing) was significant (P= 0.001).C. jejuniwas the species most commonly isolated from trough-water and running-water sources, whileC. coliwas the most frequently isolated from standing water (P< 0.001). No association was found between the presence ofEscherichia coliand that ofCampylobacterspp. The final multivariable logistic regression model forCampylobacterspp. included the following variables: water source, soil type, aspect, and amount of cattle fecal material in the environment (fecal pat count). Strain typing demonstrated a diverse population ofC. jejuniand the presence of a commonC. coli flaAtype that was widely distributed throughout the area. Most of the isolates within the commonflaAtype were discriminated by PFGE-RFLP. These findings suggest a possible role for environmental water in the epidemiology ofCampylobacterspp. in a farming environment.
Biphasic Behavior of Anammox Regulated by Nitrite and Nitrate in an Estuarine Sediment
Authors: Trimmer Mark , Nicholls Joanna C. , Morley Nicholas , Davies Christian A. , Aldridge John 
Published: April 2005

ABSTRACT

The production of N
2
gas via anammox was investigated in sediment slurries at in situ NO
2
−
concentrations in the presence and absence of NO
3
−
. With single enrichment above 10 μM
14
NO
2
−
or
14
NO
3
−
and
15
NH
4
+
, anammox activity was always linear (
P
< 0.05), in agreement with previous findings. In contrast, anammox exhibited a range of activity below 10 μM NO
2
−
or NO
3
−
, including an elevated response at lower concentrations. With 100 μM NO
3
−
, no significant transient accumulation of NO
2
−
could be measured, and the starting concentration of NO
2
−
could therefore be regulated. With dual enrichment (1 to 20 μM NO
2
−
plus 100 μM NO
3
−
), there was a pronounced nonlinear response in anammox activity. Maximal activity occurred between 2 and 5 μM NO
2
−
, but the amplitude of this peak varied across the study (November 2003 to June 2004). Anammox accounted for as much as 82% of the NO
2
−
added at 1 μM in November 2003 but only for 15% in May 2004 and for 26 and 5% of the NO
2
−
added at 5 μM for these two months, respectively. Decreasing the concentration of NO
3
−
but holding NO
2
−
at 5 μM decreased the significance of anammox as a sink for NO
2
−
. The behavior of anammox was explored by use of a simple anammox-denitrification model, and the concept of a biphasic system for anammox in estuarine sediments is proposed. Overall, anammox is likely to be regulated by the availability of NO
3
−
and NO
2
−
and the relative size or activity of the anammox population.
Elimination of Botulinum Neurotoxin (BoNT) Type B from Drinking Water by Small-Scale (Personal-Use) Water Purification Devices and Detection of BoNT in Water Samples
Authors: Hörman Ari , Nevas Mari , Lindström Miia , Hänninen Marja-Liisa , Korkeala Hannu 
Published: April 2005

ABSTRACT

Seven small-scale drinking water purification devices were evaluated for their capacity to eliminate botulinum neurotoxin (BoNT) type B from drinking water. Influent water inoculated with toxic
Clostridium botulinum
cultures and effluent purified water samples were tested for the presence of BoNT by using a standard mouse bioassay and two commercial rapid enzyme immunoassays (EIAs). The water purification devices based on filtration through ceramic or membrane filters with a pore size of 0.2 to 0.4 μm or irradiation from a low-pressure UV-lamp (254 nm) failed to remove BoNT from raw water (reduction of <0.1 log
10
units). A single device based on reverse osmosis was capable of removing the BoNT to a level below the detection limit of the mouse bioassay (reduction of >2.3 log
10
units). The rapid EIAs intended for the detection of BoNT from various types of samples failed to detect BoNT from aqueous samples containing an estimated concentration of BoNT of 396,000 ng/liter.
Efficient Production ofl-Lactic Acid by Metabolically EngineeredSaccharomyces cerevisiaewith a Genome-Integratedl-Lactate Dehydrogenase Gene
Authors: Ishida Nobuhiro , Saitoh Satoshi , Tokuhiro Kenro , Nagamori Eiji , Matsuyama Takashi , Kitamoto Katsuhiko , Takahashi Haruo 
Published: April 2005

ABSTRACTWe developed a metabolically engineered yeast which produces lactic acid efficiently. In this recombinant strain, the coding region for pyruvate decarboxylase 1 (PDC1) on chromosome XII is substituted for that of thel-lactate dehydrogenase gene (LDH) through homologous recombination. The expression of mRNA for the genome-integratedLDHis regulated under the control of the nativePDC1promoter, whilePDC1is completely disrupted. Using this method, we constructed a diploid yeast transformant, with each haploid genome having a single insertion of bovineLDH. Yeast cells expressingLDHwere observed to convert glucose to both lactate (55.6 g/liter) and ethanol (16.9 g/liter), with up to 62.2% of the glucose being transformed into lactic acid under neutralizing conditions. This transgenic strain, which expresses bovineLDHunder the control of thePDC1promoter, also showed high lactic acid production (50.2 g/liter) under nonneutralizing conditions. The differences in lactic acid production were compared among four different recombinants expressing a heterologousLDHgene (i.e., either the bovineLDHgene or theBifidobacterium longum LDHgene): two transgenic strains with 2μm plasmid-based vectors and two genome-integrated strains.
Production of Novel Rapamycin Analogs by Precursor-Directed Biosynthesis
Authors: Ritacco Frank V. , Graziani Edmund I. , Summers Mia Y. , Zabriskie T. Mark , Yu Ker , Bernan Valerie S. , Carter Guy T. , Greenstein Michael 
Published: April 2005

ABSTRACTThe natural product rapamycin, produced during fermentation byStreptomyces hygroscopicus, is known for its potent antifungal, immunosuppressive, and anticancer activities. During rapamycin biosynthesis, the amino acidl-pipecolate is incorporated into the rapamycin molecule. We investigated the use of precursor-directed biosynthesis to create new rapamycin analogs by substitution of unusuall-pipecolate analogs in place of the normal amino acid. Our results suggest that thel-pipecolate analog (±)-nipecotic acid inhibits the biosynthesis ofl-pipecolate, thereby limiting the availability of this molecule for rapamycin biosynthesis. We used (±)-nipecotic acid in our precursor-directed biosynthesis studies to reducel-pipecolate availability and thereby enhance the incorporation of other pipecolate analogs into the rapamycin molecule. We describe here the use of this method for production of two new sulfur-containing rapamycin analogs, 20-thiarapamycin and 15-deoxo-19-sulfoxylrapamycin, and report measurement of their binding to FKBP12.
Expression of
abrB310
and
sinR
, and Effects of Decreased
abrB310
Expression on the Transition from Acidogenesis to Solventogenesis, in
Clostridium acetobutylicum
ATCC 824
Authors: Scotcher Miles C. , Rudolph Frederick B. , Bennett George N. 
Published: April 2005

ABSTRACT

The transcription factors
sinR
and
abrB
are involved in the control of sporulation initiation in
Bacillus subtilis
. We identified a single homologue to
sinR
and three highly similar homologues to
abrB
, designated
abrB310
,
abrB1941
, and
abrB3647
, in
Clostridium acetobutylicum
ATCC 824. Using reporter vectors, we showed that the promoters of
abrB1941
and
abrB3647
were not active under the growth conditions tested. The
abrB310
promoter was strongly active throughout growth and exhibited a transient elevation of expression at the onset of solventogenesis. Primer extension assays showed that two transcripts of
abrB310
and a single, extremely weak transcript for
sinR
are expressed. Potential −35 and −10 consensus motifs are readily identifiable surrounding the transcription start sites of
abrB310
and
sinR
, with a single putative 0A box present within the promoter of
abrB310
. In strains of
C. acetobutylicum
transformed with plasmids to elevate
sinR
expression or decrease
sinR
expression, no significant differences in growth or in acid or solvent production were observed compared to the control strains. In
C. acetobutylicum
strain 824(pAS310), which expressed an antisense RNA construct targeted against
abrB310
, the acids acetate and butyrate accumulated to approximately twice the normal concentration. This accumulation corresponded to a delay and decrease in acetone and butanol production. It was also found that sporulation in strain 824(pAS310) was delayed but that the morphology of sporulating cells and spores was normal. Based upon these observations, we propose that
abrB310
may act as a regulator at the transition between acidogenic and solventogenic growth.
Accumulation of Polyhydroxyalkanoate from Styrene and Phenylacetic Acid by
Pseudomonas putida
CA-3
Authors: Ward Patrick G. , de Roo Guy , O'Connor Kevin E. 
Published: April 2005

ABSTRACT

Pseudomonas putida
CA-3 is capable of converting the aromatic hydrocarbon styrene, its metabolite phenylacetic acid, and glucose into polyhydroxyalkanoate (PHA) when a limiting concentration of nitrogen (as sodium ammonium phosphate) is supplied to the growth medium. PHA accumulation occurs to a low level when the nitrogen concentration drops below 26.8 mg/liter and increases rapidly once the nitrogen is no longer detectable in the growth medium. The depletion of nitrogen and the onset of PHA accumulation coincided with a decrease in the rate of substrate utilization and biochemical activity of whole cells grown on styrene, phenylacetic acid, and glucose. However, the efficiency of carbon conversion to PHA dramatically increased once the nitrogen concentration dropped below 26.8 mg/liter in the growth medium. When supplied with 67 mg of nitrogen/liter, the carbon-to-nitrogen (C:N) ratios that result in a maximum yield of PHA (grams of PHA per gram of carbon) for styrene, phenylacetic acid, and glucose are 28:1, 21:1, and 18:1, respectively. In cells grown on styrene and phenylacetic acid, decreasing the carbon-to-nitrogen ratio below 28:1 and 21:1, respectively, by increasing the nitrogen concentration and using a fixed carbon concentration leads to lower levels of PHA per cell and lower levels of PHA per batch of cells. Increasing the carbon-to-nitrogen ratio above 28:1 and 21:1 for cells grown on styrene and phenylacetic acid, respectively, by decreasing the nitrogen concentration and using a fixed carbon concentration increases the level of PHA per cell but results in a lower level of PHA per batch of cells. Increasing the carbon and nitrogen concentrations but maintaining the carbon-to-nitrogen ratio of 28:1 and 21:1 for cells grown on styrene and phenylacetic acid, respectively, results in an increase in the total PHA per batch of cells. The maximum yields for PHA from styrene, phenylacetic acid, and glucose are 0.11, 0.17, and 0.22 g of PHA per g of carbon, respectively.
Characterization of a MobileclpLGene fromLactobacillus rhamnosus
Authors: Suokko Aki , Savijoki Kirsi , Malinen Erja , Palva Airi , Varmanen Pekka 
Published: April 2005

ABSTRACTTwo genes encoding ClpL ATPase proteins were identified in a probioticLactobacillus rhamnosusstrain, E-97800. Sequence analyses revealed that the genes, designatedclpL1andclpL2, share 80% identity. TheclpL2gene showed the highest degree of identity (98.5%) to aclpLgene fromLactobacillus plantarumWCFSI, while it was not detected in three otherL. rhamnosusstrains studied. According to Northern analyses, the expression ofclpL1and theclpL2were induced during heat shock by >20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and theclpL1promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating thatclpL1belongs to the HrcA regulon inL. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in theclpL2promoter region. Interestingly, theclpL2gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1fromL. plantarumHN38. Furthermore,clpL2was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical toclpL2inL. plantarumand its absence in otherL. rhamnosusstrains suggest that theL. rhamnosusE-97800 has acquired theclpL2gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed.
Spatial Distribution and Transcriptional Activity of an Uncultured Clade of Planktonic Diazotrophic γ-Proteobacteria in the Arabian Sea
Authors: Bird Clare , Martinez Martinez Joaquín , O'Donnell Anthony G. , Wyman Michael 
Published: April 2005

ABSTRACT

The spatial distribution of an uncultured clade of marine diazotrophic γ-proteobacteria in the Arabian Sea was investigated by the development of a specific primer pair to amplify an internal fragment of
nifH
by PCR. These organisms were most readily detected in highly oligotrophic surface waters but could also be found in deeper waters below the nutricline.
nifH
transcripts originating from this clade were detected in oligotrophic surface waters and, in addition, in the deeper and the more productive near-coastal waters. The
nifH
sequences most closely related to the unidentified marine bacterial group are from environmental clones amplified from the Atlantic and Pacific Oceans. These findings suggest that these γ-proteobacteria are widespread and likely to be an important component of the heterotrophic diazotrophic microbial community of the tropical and subtropical oceans.
Rehydration of the LichenRamalina laceraResults in Production of Reactive Oxygen Species and Nitric Oxide and a Decrease in Antioxidants
Authors: Weissman Lior , Garty Jacob , Hochman Ayala 
Published: April 2005

ABSTRACTLichens are slow-growing associations of fungi and unicellular green algae or cyanobacteria. They are poikilohydric organisms whose lifestyle in many cases consists of alternating periods of desiccation, with low metabolic activity, and hydration, which induces increase in their metabolism. Lichens have apparently adapted to such extreme transitions between desiccation and rehydration, but the mechanisms that govern these adaptations are still poorly understood. In this study, the effect of rehydration on the production of reactive oxygen species and nitric oxide as well as low-molecular-weight antioxidants was investigated with the lichenRamalina lacera. Rehydration ofR. laceraresulted in the initiation of and a rapid increase in photosynthetic activity. Recovery of photosynthesis was accompanied by bursts of intracellular production of reactive oxygen species and nitric oxide. Laser-scanning confocal microscopy using dichlorofluorescein fluorescence revealed that formation of reactive oxygen species following rehydration was associated with both symbiotic partners of the lichen. The rate and extent of reactive oxygen species production were similar in the light and in the dark, suggesting a minor contribution of photosynthesis. Diaminofluorescein fluorescence, indicating nitric oxide formation, was detected only in fungal hyphae. Activities associated with rehydration did not have a deleterious effect on membrane integrity as assessed by measurement of electrolyte leakage, but water-soluble low-molecular-weight antioxidants decreased significantly.
Differential Sunlight Sensitivity of Picophytoplankton from Surface Mediterranean Coastal Waters
Authors: Sommaruga Ruben , Hofer Julia S. , Alonso-Sáez Laura , Gasol Josep M. 
Published: April 2005

ABSTRACT

We tested the sensitivity of coastal picophytoplankton exposed to natural sunlight in short-term experiments. Cell abundance and cell-specific chlorophyll fluorescence were significantly reduced in
Prochlorococcus
spp. but not in
Synechococcus
, whereas picoeukaryotes had an intermediate response. These results are the first direct evidence of a differential sensitivity to sunlight of these ubiquitous marine members of unicellular phytoplankton.
Anaerobic, Nitrate-Dependent Oxidation of U(IV) Oxide Minerals by the Chemolithoautotrophic Bacterium
Thiobacillus denitrificans
Authors: Beller Harry R. 
Published: April 2005

ABSTRACT

Under anaerobic conditions and at circumneutral pH, cells of the widely distributed, obligate chemolithoautotrophic bacterium
Thiobacillus denitrificans
oxidatively dissolved synthetic and biogenic U(IV) oxides (uraninite) in nitrate-dependent fashion: U(IV) oxidation required the presence of nitrate and was strongly correlated with nitrate consumption. This is the first report of anaerobic U(IV) oxidation by an autotrophic bacterium.
Evaluation of 16S rRNA Sequencing and Reevaluation of a Short Biochemical Scheme for Identification of Clinically Significant
Bacteroides
Species
Authors: Song Yuli , Liu Chengxu , Bolaňos Mauricio , Lee Julia , McTeague Maureen , Finegold Sydney M. 
Published: April 2005

ABSTRACT

Sequence analysis of the 16S rRNA gene represents a highly accurate and versatile method for bacterial classification and identification, even when the species in question is notoriously difficult to identify by phenotypic means. In this study, we evaluated the utility of 16S rRNA gene sequencing as a means of identifying clinically important
Bacteroides
species. We sequenced 231 clinical isolates that had been identified by a short biochemical scheme. Based on the sequence analysis, 192 clinical isolates were assigned to an established species, with the other 39 clinical strains revealing five unique sequences that may represent five novel species. This is in contrast to identification obtained from a short biochemical scheme, by which only 73.5% (172 of 231) of isolates were correctly identified to species level. Based on the solid identification obtained from 16S rRNA gene sequencing, the short biochemical scheme was modified and improved to provide clinical laboratories with an inexpensive and simple alternative for the identification of isolates of clinically significant
Bacteroides
species.
Multilocus Variable-Number Tandem Repeat Typing of
Mycobacterium ulcerans
Authors: Ablordey Anthony , Swings Jean , Hubans Christine , Chemlal Karim , Locht Camille , Portaels Françoise , Supply Philip 
Published: April 2005

ABSTRACT

The apparent genetic homogeneity of
Mycobacterium ulcerans
contributes to the poorly understood epidemiology of
M. ulcerans
infection. Here, we report the identification of variable number tandem repeat (VNTR) sequences as novel polymorphic elements in the genome of this species. A total of 19 potential VNTR loci identified in the closely related
M. marinum
genome sequence were screened in a collection of 23
M. ulcerans
isolates, one
Mycobacterium
species referred to here as an intermediate species, and five
M. marinum
strains. Nine of the 19 loci were polymorphic in the three species (including the intermediate species) and revealed eight
M. ulcerans
and five
M. marinum
genotypes. The results from the VNTR analysis corroborated the genetic relationships of
M. ulcerans
isolates from various geographical origins, as defined by independent molecular markers. Although these results further highlight the extremely high clonal homogeneity within certain geographic regions, we report for the first time the discrimination of the two South American strains from Surinam and French Guyana. These findings support the potential of a VNTR-based genotyping method for strain discrimination within
M. ulcerans
and
M. marinum.
Comparison of an Internally Controlled, Large-Volume LightCycler Assay for Detection of
Mycobacterium tuberculosis
in Clinical Samples with the COBAS AMPLICOR Assay
Authors: Burggraf Siegfried , Reischl Udo , Malik Naeem , Bollwein Markus , Naumann Ludmila , Olgemöller Bernhard 
Published: April 2005

ABSTRACT

We present a sensitive and specific assay for reliable and flexible detection of members of the
Mycobacterium tuberculosis
complex (MTBC) in clinical samples. This real-time PCR assay, which uses the LightCycler 2.0 instrument and 100-μl glass capillaries, can provide a result within 1 h after DNA extraction. The primers amplify a 206-bp fragment of the MTBC 16S rRNA gene. The sensor hybridization probe targets a region highly specific to members of the MTBC. The assay also includes a novel type of internal control that monitors the function of the reaction components and can detect potential inhibitors. Template DNA was extracted by the same procedure used for the COBAS AMPLICOR
M. tuberculosis
assay, so the LightCycler assay could be directly compared to the COBAS AMPLICOR assay. The LightCycler assay was evaluated with 146 clinical samples of various types. Very good agreement (100% sensitivity, 98.6% specificity) could be shown between the LightCycler and COBAS AMPLICOR assays. Specificity was checked with a panel of nontuberculous mycobacteria, as well as a large panel of bacterial and fungal organisms.
Determinants for the Occurrence of Acute Exacerbation of Hepatitis B Virus Infection in Chinese Patients after HBeAg Seroclearance
Authors: Yuan He-Jun , Yuen Man-Fung , Wong Danny Ka-Ho , Sum Siu-Man , Doutreloigne Joke , Sablon Erwin , Lai Ching-Lung 
Published: April 2005

ABSTRACT

This study was performed to determine the factors for predicting the occurrence of acute exacerbation of hepatitis B virus infection in HBeAg-negative patients. Two hundred and sixteen patients with known times of HBeAg seroclearance were recruited. Liver biochemistry and virologic markers were monitored. Precore and core promoter mutations were determined by a line probe assay. The median age at HBeAg seroclearance was 34.5 years. The median follow-up duration was 26.4 months. Fifty-six (27.9%) patients had acute exacerbations. By Cox regression analysis, male gender, older age, and core promoter mutations at the time of HBeAg seroclearance were independently associated with the occurrence of acute exacerbation after HBeAg seroclearance (
P
= 0.025, 0.018, and 0.001, respectively). Fourteen (7.0%) patients had HBeAg seroreversion within a median follow-up period of 11.6 months after HBeAg seroclearance. By Cox regression analysis, older age at HBeAg seroclearance was independently associated with the chance of HBeAg seroreversion (
P
= 0.01). We concluded that male patients with core promoter mutations and delayed HBeAg seroclearance had a higher cumulative chance of acute exacerbation in the HBeAg-negative phase. Patients with delayed HBeAg seroclearance had a higher frequency of HBeAg seroreversion.