bluuebunny/crossref_metadata_2025_split huggingface dataset:
Previously Unknown Virus Infects Marine Diatom
Authors: Nagasaki Keizo , Tomaru Yuji , Takao Yoshitake , Nishida Kensho , Shirai Yoko , Suzuki Hidekazu , Nagumo Tamotsu 
Published: July 2005

ABSTRACT

Diatoms are a major phytoplankton group that play important roles in maintaining oxygen levels in the atmosphere and sustaining the primary nutritional production of the aquatic environment. Among diatoms, the genus
Chaetoceros
is one of the most abundant and widespread. Temperature, climate, salinity, nutrients, and predators were regarded as important factors controlling the abundance and population dynamics of diatoms. Here we show that a viral infection can occur in the genus
Chaetoceros
and should therefore be considered as a potential mortality source.
Chaetoceros salsugineum
nuclear inclusion virus (CsNIV) is a 38-nm icosahedral virus that replicates within the nucleus of
C. salsugineum.
The latent period was estimated to be between 12 and 24 h, with a burst size of 325 infectious units per host cell. CsNIV has a genome structure unlike that of other viruses that have been described. It consists of a single molecule of covalently closed circular single-stranded DNA (ssDNA; 6,005 nucleotides), as well as a segment of linear ssDNA (997 nucleotides). The linear segment is complementary to a portion of the closed circle creating a partially double-stranded genome. Sequence analysis reveals a low but significant similarity to the replicase of circoviruses that have a covalently closed circular ssDNA genome. This new host-virus system will be useful for investigating the ecological relationships between bloom-forming diatoms and other viruses in the marine system. Our study supports the view that, given the diversity and abundance of plankton, the ocean is a treasury of undiscovered viruses.
Survey of Bovine Enterovirus in Biological and Environmental Samples by a Highly Sensitive Real-Time Reverse Transcription-PCR
Authors: Jiménez-Clavero Miguel Angel , Escribano-Romero Estela , Mansilla Carmen , Gómez Nuria , Córdoba Laura , Roblas Neftal , Ponz Fernando , Ley Victoria , Sáiz Juan-Carlos 
Published: July 2005

ABSTRACT
Animal enteroviruses shed in the feces of infected animals are likely environmental contaminants and thus can be used as indicators of animal fecal pollution. Previous work has demonstrated that bovine enterovirus (BEV) present in bovine feces contaminates waters adjacent to cattle herds and that BEV-like sequences are also present in shellfish and in deer feces from the same geographical area. However, little information is available about the prevalence, molecular epidemiology, and genomic sequence variation of BEV field isolates. Here we describe an optimized highly sensitive real-time reverse transcription-PCR method to detect BEV RNA in biological and environmental samples. A combination of the amplification procedure with a previously described filtration step with electropositive filters allowed us to detect up to 12 BEV RNA molecules per ml of water. The feasibility of using the method to detect BEV in surface waters at a high risk of fecal pollution was confirmed after analysis of water samples obtained from different sources. The method was also used to study the prevalence of BEV in different cattle herds around Spain, and the results revealed that 78% (78 of 100) of the fecal samples were BEV positive. BEV-like sequences were also detected in feces from sheep, goats, and horses. Nucleotide sequence analyses showed that BEV isolates are quite heterogeneous and suggested the presence of species-specific BEV-like variants. Detection of BEV-like sequences may help in the differentiation and characterization of animal sources of contamination.
Amino Acid Catabolism by an
areA
-Regulated Gene Encoding an
l
-Amino Acid Oxidase with Broad Substrate Specificity in
Aspergillus nidulans
Authors: Davis Meryl A. , Askin Marion C. , Hynes Michael J. 
Published: July 2005

ABSTRACT

The filamentous fungus
Aspergillus nidulans
can use a wide range of compounds as nitrogen sources. The synthesis of the various catabolic enzymes needed to breakdown these nitrogen sources is regulated by the
areA
gene, which encodes a GATA transcription factor required to activate gene expression under nitrogen-limiting conditions. The
areA102
mutation results in pleiotropic effects on nitrogen source utilization, including better growth on certain amino acids as nitrogen sources. Mutations in the
sarA
gene were previously isolated as suppressors of the strong growth of an
areA102
strain on
l
-histidine as a sole nitrogen source. We cloned the
sarA
gene by complementation of a
sarA
mutant and showed that it encodes an
l
-amino acid oxidase enzyme with broad substrate specificity. Elevated expression of this enzyme activity in an
areA102
background accounts for the strong growth of these strains on amino acids that are substrates for this enzyme. Loss of function
sarA
mutations, which abolish the
l
-amino acid oxidase activity, reverse the
areA102
phenotype. Growth tests with
areA102
and
sarA
mutants show that this enzyme is the primary route of catabolism for some amino acids, while other amino acids are metabolized through alternative pathways that yield either ammonium or glutamate for growth.
Assessment of Heat Resistance of Bacterial Spores from Food Product Isolates by Fluorescence Monitoring of Dipicolinic Acid Release
Authors: Kort Remco , O'Brien Andrea C. , van Stokkum Ivo H. M. , Oomes Suus J. C. M. , Crielaard Wim , Hellingwerf Klaas J. , Brul Stanley 
Published: July 2005

ABSTRACT

This study is aimed at the development and application of a convenient and rapid optical assay to monitor the wet-heat resistance of bacterial endospores occurring in food samples. We tested the feasibility of measuring the release of the abundant spore component dipicolinic acid (DPA) as a probe for heat inactivation. Spores were isolated from the laboratory type strain
Bacillus subtilis
168 and from two food product isolates,
Bacillus subtilis
A163 and
Bacillus sporothermodurans
IC4. Spores from the lab strain appeared much less heat resistant than those from the two food product isolates. The decimal reduction times (
D
values) for spores from strains 168, A163, and IC4 recovered on Trypticase soy agar were 1.4, 0.7, and 0.3 min at 105°C, 120°C, and 131°C, respectively. The estimated
Z
values were 6.3°C, 6.1°C, and 9.7°C, respectively. The extent of DPA release from the three spore crops was monitored as a function of incubation time and temperature. DPA concentrations were determined by measuring the emission at 545 nm of the fluorescent terbium-DPA complex in a microtiter plate fluorometer. We defined spore heat resistance as the critical DPA release temperature (

T
c

), the temperature at which half the DPA content has been released within a fixed incubation time. We found

T
c

values for spores from
Bacillus
strains 168, A163, and IC4 of 108°C, 121°C, and 131°C, respectively. On the basis of these observations, we developed a quantitative model that describes the time and temperature dependence of the experimentally determined extent of DPA release and spore inactivation. The model predicts a DPA release rate profile for each inactivated spore. In addition, it uncovers remarkable differences in the values for the temperature dependence parameters for the rate of spore inactivation, DPA release duration, and DPA release delay.
Relative Importance of Bacteriocin-Like Genes in Antagonism ofXanthomonas perforansTomato Race 3 toXanthomonas euvesicatoriaTomato Race 1 Strains
Authors: Hert A. P. , Roberts P. D. , Momol M. T. , Minsavage G. V. , Tudor-Nelson S. M. , Jones J. B. 
Published: July 2005

ABSTRACTIn a previous study, tomato race 3 (T3) strains ofXanthomonas perforansbecame predominant in fields containing bothX. euvesicatoriaandX. perforansraces T1 and T3, respectively. This apparent ability to take over fields led to the discovery that there are three bacteriocin-like compounds associated with T3 strains. T3 strain 91-118 produces at least three different bacteriocin-like compounds (BCN-A, BCN-B, and BCN-C) antagonistic toward T1 strains. We determined the relative importance of the bacteriocin-like compounds by constructing the following mutant forms of a wild-type (WT) T3 strain to evaluate the antagonism to WT T1 strains: Mut-A (BCN-A−), Mut-B (BCN-B−), Mut-C (BCN-C−), Mut-AB, Mut-BC, and Mut-ABC. Although all mutant and WT T3 strains reduced the T1 populations in in planta growth room experiments, Mut-B and WT T3 were significantly more effective. Mutants expressing BCN-B and either BCN-A or BCN-C reduced T1 populations less than mutants expressing only BCN-A or BCN-C. The triple-knockout mutant Mut-ABC also had a significant competitive advantage over the T1 strain. In pairwise-inoculation field experiments where plants were coinoculated with an individual mutant or WT T3 strain and the T1 strain, the mutant strains and the WT T3 strain were reisolated from more than 70% of the lesions. WT T3 and Mut-B were the most frequently reisolated strains. In field experiments where plants were group inoculated with Mut-A, Mut-B, Mut-C, Mut-ABC, and WT T1 and T3 strains, Mut-B populations dominated all three seasons. In greenhouse and field experiments, the WT and mutant T3 strains had a selective advantage over T1 strains. Bacterial strains expressing both BCN-A and BCN-C appeared to have a competitive advantage over all other mutant and WT strains. Furthermore, BCN-B appeared to be a negative factor, with mutant T3 strains lacking BCN-B having a selective advantage in the field.
Diversity of Bacteria Growing in Natural Mineral Water after Bottling
Authors: Loy Alexander , Beisker Wolfgang , Meier Harald 
Published: July 2005

ABSTRACT

Bacterial growth occurs in noncarbonated natural mineral waters a few days after filling and storage at room temperature, a phenomenon known for more than 40 years. Using the full-cycle rRNA approach, we monitored the development of the planktonic bacterial community in a noncarbonated natural mineral water after bottling. Seven 16S rRNA gene libraries, comprising 108 clones in total, were constructed from water samples taken at various days after bottling and from two different bottle sizes. Sequence analyses identified 11 operational taxonomic units (OTUs), all but one affiliated with the betaproteobacterial order
Burkholderiales
(6 OTUs) or the class
Alphaproteobacteria
(4 OTUs). Fluorescence in situ hybridization (FISH) was applied in combination with DAPI (4′,6′-diamidino-2-phenylindole) staining, viability staining, and microscopic counting to quantitatively monitor changes in bacterial community composition. A growth curve similar to that of a bacterium grown in a batch culture was recorded. In contrast to the current perception that
Gammaproteobacteria
are the most important bacterial components of natural mineral water in bottles,
Betaproteobacteria
dominated the growing bacterial community and accounted for 80 to 98% of all bacteria detected by FISH in the late-exponential and stationary-growth phases. Using previously published and newly designed genus-specific probes, members of the betaproteobacterial genera
Hydrogenophaga
,
Aquabacterium
, and
Polaromonas
were found to constitute a significant proportion of the bacterial flora (21 to 86% of all bacteria detected by FISH). For the first time, key genera responsible for bacterial growth in a natural mineral water were identified by applying molecular cultivation-independent techniques.
Degradation of Cyanophycin bySedimentibacter hongkongensisStrain KI andCitrobacter amalonaticusStrain G Isolated from an Anaerobic Bacterial Consortium
Authors: Obst Martin , Krug Andreas , Luftmann Heinrich , Steinbüchel Alexander 
Published: July 2005

ABSTRACTUsing a combination of various enrichment techniques, the strictly anaerobic, gram-positive, endospore-forming bacteriumSedimentibacter hongkongensisstrain KI as revealed by 16S rRNA analysis and the gram-negative enterobacteriumCitrobacter amalonaticusstrain G as revealed by physiological tests were isolated from an anaerobic cyanophycin (CGP)-degrading bacterial consortium.S. hongkongensisstrain KI is the first anaerobic bacterium with the ability to hydrolyze CGP to β-Asp-Arg and β-Asp-Lys dipeptides, as revealed by electrospray ionization-mass spectrometry and reversed-phase high-performance liquid chromatography analysis. However, these primary accumulated hydrolysis products were only partially used byS. hongkongensisstrain KI, and significant growth on CGP did not occur. On the other hand,C. amalonaticusstrain G did not degrade CGP but grew on the β-linked iso-dipeptides formed in vitro by enzymatic CGP degradation or in vivo by metabolic activity ofS. hongkongensisstrain KI. Dipeptide utilization occurred at the highest rate if both strains were used in cocultivation experiments with CGP, indicating that cooperation between different bacteria occurs in anaerobic natural environments for complete CGP turnover. The amino acids obtained from the cleavage of dipeptides were fermented to ethanol, acetic acid, and succinic acid, as revealed by gas chromatographic analysis and by spectrophotometric enzyme assays.
Molecular and Biochemical Analysis of the Galactose Phenotype of Dairy
Streptococcus thermophilus
Strains Reveals Four Different Fermentation Profiles
Authors: de Vin Filip , Rådström Peter , Herman Lieve , De Vuyst Luc 
Published: July 2005

ABSTRACT

Lactose-limited fermentations of 49 dairy
Streptococcus thermophilus
strains revealed four distinct fermentation profiles with respect to galactose consumption after lactose depletion. All the strains excreted galactose into the medium during growth on lactose, except for strain IMDOST40, which also displayed extremely high galactokinase (GalK) activity. Among this strain collection eight galactose-positive phenotypes sensu stricto were found and their fermentation characteristics and Leloir enzyme activities were measured. As the
gal
promoter seems to play an important role in the galactose phenotype, the
galR-galK
intergenic region was sequenced for all strains yielding eight different nucleotide sequences (NS1 to NS8). The
gal
promoter played an important role in the Gal-positive phenotype but did not determine it exclusively. Although GalT and GalE activities were detected for all Gal-positive strains, GalK activity could only be detected for two out of eight Gal-positive strains. This finding suggests that the other six
S. thermophilus
strains metabolize galactose via an alternative route. For each type of fermentation profile obtained, a representative strain was chosen and four complete Leloir gene clusters were sequenced. It turned out that Gal-positive strains contained more amino acid differences within their
gal
genes than Gal-negative strains. Finally, the biodiversity regarding lactose-galactose utilization among the different
S. thermophilus
strains used in this study was shown by RAPD-PCR. Five Gal-positive strains that contain nucleotide sequence NS2 in their
galR-galK
intergenic region were closely related.
pH and Peptide Supply Can Radically Alter Bacterial Populations and Short-Chain Fatty Acid Ratios within Microbial Communities from the Human Colon
Authors: Walker Alan W. , Duncan Sylvia H. , McWilliam Leitch E. Carol , Child Matthew W. , Flint Harry J. 
Published: July 2005

ABSTRACTThe effects of changes in the gut environment upon the human colonic microbiota are poorly understood. The response of human fecal microbial communities from two donors to alterations in pH (5.5 or 6.5) and peptides (0.6 or 0.1%) was studied here in anaerobic continuous cultures supplied with a mixed carbohydrate source. Final butyrate concentrations were markedly higher at pH 5.5 (0.6% peptide mean, 24.9 mM; 0.1% peptide mean, 13.8 mM) than at pH 6.5 (0.6% peptide mean, 5.3 mM; 0.1% peptide mean, 7.6 mM). At pH 5.5 and 0.6% peptide input, a high butyrate production coincided with decreasing acetate concentrations. The highest propionate concentrations (mean, 20.6 mM) occurred at pH 6.5 and 0.6% peptide input. In parallel, major bacterial groups were monitored by using fluorescence in situ hybridization with a panel of specific 16S rRNA probes.Bacteroideslevels increased from ca. 20 to 75% of total eubacteria after a shift from pH 5.5 to 6.5, at 0.6% peptide, coinciding with high propionate formation. Conversely, populations of the butyrate-producingRoseburiagroup were highest (11 to 19%) at pH 5.5 but fell at pH 6.5, a finding that correlates with butyrate formation. When tested in batch culture, threeBacteroidesspecies grew well at pH 6.7 but poorly at pH 5.5, which is consistent with the behavior observed for the mixed community. TwoRoseburiaisolates grew equally well at pH 6.7 and 5.5. These findings suggest that a lowering of pH resulting from substrate fermentation in the colon may boost butyrate production and populations of butyrate-producing bacteria, while at the same time curtailing the growth ofBacteroidesspp.
Identification of a Positive Transcription Regulatory Element within the Coding Region of the
nifLA
Operon in
Azotobacter vinelandii
Authors: Mitra Ranjana , Das Hirendra K. , Dixit Aparna 
Published: July 2005

ABSTRACT

Nitrogen fixation in
Azotobacter vinelandii
is regulated by the
nifLA
operon. NifA activates the transcription of
nif
genes, while NifL antagonizes the transcriptional activator NifA in response to fixed nitrogen and molecular oxygen levels. However, transcriptional regulation of the
nifLA
operon of
A. vinelandii
itself is not fully understood. Using the S1 nuclease assay, we mapped the transcription start site of the
nifLA
operon, showing it to be similar to the σ
54
-dependent promoters. We also identified a positive
cis-
acting regulatory element (+134 to +790) of the
nifLA
operon within the coding region of the
nifL
gene of
A. vinelandii
. Deletion of this element results in complete loss of promoter activity. Several protein factors bind to this region, and the specific binding sites have been mapped by DNase I foot printing. Two of these sites, namely dR1 (+134 to +204) and dR2 (+745 to +765), are involved in regulating the
nifLA
promoter activity. The absence of NtrC-like binding sites in the upstream region of the
nifLA
operon in
A. vinelandii
makes the identification of these downstream elements a highly significant finding. The interaction of the promoter with the proteins binding to the dR2 region spanning +745 to +765 appears to be dependent on the face of the helix as introduction of 4 bases just before this region completely disrupts promoter activity. Thus, the positive regulatory element present within the BglII-BglII fragment may play, in part; an important role in
nifLA
regulation in
A. vinelandii
.
Dehalogenation of the Herbicides Bromoxynil (3,5-Dibromo-4-Hydroxybenzonitrile) and Ioxynil (3,5-Diiodino-4-Hydroxybenzonitrile) by
Desulfitobacterium chlororespirans
Authors: Cupples Alison M. , Sanford Robert A. , Sims Gerald K. 
Published: July 2005

ABSTRACT

Desulfitobacterium chlororespirans
has been shown to grow by coupling the oxidation of lactate to the metabolic reductive dehalogenation of
ortho
chlorines on polysubstituted phenols. Here, we examine the ability of
D. chlororespirans
to debrominate and deiodinate the polysubstituted herbicides bromoxynil (3,5-dibromo-4-hydroxybenzonitrile), ioxynil (3,5-diiodo-4-hydroxybenzonitrile), and the bromoxynil metabolite 3,5-dibromo-4-hydroxybenzoate (DBHB). Stoichiometric debromination of bromoxynil to 4-cyanophenol and DBHB to 4-hydroxybenzoate occurred. Further, bromoxynil (35 to 75 μM) and DBHB (250 to 260 μM) were used as electron acceptors for growth. Doubling times for growth (means ± standard deviations for triplicate cultures) on bromoxynil (18.4 ± 5.2 h) and DBHB (11.9 ± 1.4 h), determined by rate of [
14
C]lactate uptake into biomass, were similar to those previously reported for this microorganism during growth on pyruvate (15.4 h). In contrast, ioxynil was not deiodinated when added alone or when added with bromoxynil; however, ioxynil dehalogenation, with stoichiometric conversion to 4-cyanophenol, was observed when the culture was amended with 3-chloro-4-hydroxybenzoate (a previously reported electron acceptor). To our knowledge, this is the first direct report of deiodination by a bacterium in the
Desulfitobacterium
genus and the first report of an anaerobic pure culture with the ability to transform bromoxynil or ioxynil. This research provides valuable insights into the substrate range of
D. chlororespirans
.
Hyaluronic Acid Production in
Bacillus subtilis
Authors: Widner Bill , Behr Régine , Von Dollen Steve , Tang Maria , Heu Tia , Sloma Alan , Sternberg Dave , DeAngelis Paul L. , Weigel Paul H. , Brown Steve 
Published: July 2005

ABSTRACT

The
hasA
gene from
Streptococcus equisimilis
, which encodes the enzyme hyaluronan synthase, has been expressed in
Bacillus subtilis
, resulting in the production of hyaluronic acid (HA) in the 1-MDa range. Artificial operons were assembled and tested, all of which contain the
hasA
gene along with one or more genes encoding enzymes involved in the synthesis of the UDP-precursor sugars that are required for HA synthesis. It was determined that the production of UDP-glucuronic acid is limiting in
B. subtilis
and that overexpressing the
hasA
gene along with the endogenous
tuaD
gene is sufficient for high-level production of HA. In addition, the
B. subtilis
-derived material was shown to be secreted and of high quality, comparable to commercially available sources of HA.
Empirical Establishment of Oligonucleotide Probe Design Criteria
Authors: He Zhili , Wu Liyou , Li Xingyuan , Fields Matthew W. , Zhou Jizhong 
Published: July 2005

ABSTRACT
Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide array that contained perfect match (PM) and mismatch probes (50-mers and 70-mers) based upon four genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were tested. Little hybridization was observed at a probe-target identity of ≤85% for both 50-mer and 70-mer probes. PM signal intensities (33 to 48%) were detected at a probe-target identity of 94% for 50-mer oligonucleotides and 43 to 55% for 70-mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a nonstretch probe (≤15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50-mer probes or a 50-base stretch for 70-mer probes had approximately 55% of the PM signal. Little cross-hybridization was observed for probes with a minimal binding free energy greater than −30 kcal/mol for 50-mer probes or −40 kcal/mol for 70-mer probes. Based on the experimental results, a set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and the experimentally established criteria should provide valuable information for new software and algorithms for microarray-based studies.