bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exposure ofSaccharomyces cerevisiaeto Acetaldehyde Induces Sulfur Amino Acid Metabolism and Polyamine Transporter Genes, Which Depend on Met4p and Haa1p Transcription Factors, Respectively
Authors: Aranda Agustín , del Olmo Marcel-lí 
Published: April 2004

ABSTRACTAcetaldehyde is a toxic compound produced bySaccharomyces cerevisiaecells under several growth conditions. The adverse effects of this molecule are important, as significant amounts accumulate inside the cells. By means of global gene expression analyses, we have detected the effects of acetaldehyde addition in the expression of about 400 genes. Repressed genes include many genes involved in cell cycle control, cell polarity, and the mitochondrial protein biosynthesis machinery. Increased expression is displayed in many stress response genes, as well as other families of genes, such as those encoding vitamin B1 biosynthesis machinery and proteins for aryl alcohol metabolism. The induction of genes involved in sulfur metabolism is dependent on Met4p and other well-known factors involved in the transcription ofMETgenes under nonrepressing conditions of sulfur metabolism. Moreover, the deletion ofMET4leads to increased acetaldehyde sensitivity.TPOgenes encoding polyamine transporters are also induced by acetaldehyde; in this case, the regulation is dependent on the Haa1p transcription factor. In this paper, we discuss the connections between acetaldehyde and the processes affected by this compound in yeast cells with reference to the microarray data.
Short Fractions of Oligofructose Are Preferentially Metabolized by
Bifidobacterium animalis
DN-173 010
Authors: Van der Meulen Roel , Avonts Lazlo , De Vuyst Luc 
Published: April 2004

ABSTRACT

The growth of
Bifidobacterium animalis
DN-173 010 on different energy sources was studied through small- and large-scale fermentations. Growth on both more common energy sources (glucose, fructose, galactose, lactose, and sucrose) and inulin-type fructans was examined. High-performance liquid chromatography analysis was used to investigate the kinetics. Gas chromatography was used to determine the fructan degradation during the fermentation process.
B. animalis
DN-173 010 was unable to grow on a medium containing glucose as the sole energy source. In general, monosaccharides were poor growth substrates for the
B. animalis
strain. The fermentations with the inulin-type fructans resulted in changes in both growth and metabolite production due to the preferential metabolism of certain fructans, especially the short-chain oligomers. Only after depletion of the shorter chains were the larger fractions also metabolized, although to a lesser extent. Acetic acid was the major metabolite produced during all fermentation experiments. At the beginning of the fermentation, high levels of lactic acid were produced, which were partially replaced by formic acid at later stages. This suggests a shift in sugar metabolism to gain additional ATP that is necessary for growth on oligofructose, which is metabolized more slowly.
The
htrA
(
degP
) Gene of
Listeria monocytogenes
10403S Is Essential for Optimal Growth under Stress Conditions
Authors: Wonderling Laura D. , Wilkinson Brian J. , Bayles Darrell O. 
Published: April 2004

ABSTRACT

This report describes a mutant of
Listeria monocytogenes
strain 10403S (serotype 1/2a) with a defective response to conditions of high osmolarity, an environment that
L. monocytogenes
encounters in some ready-to-eat foods. A library of
L. monocytogenes
clones mutagenized with Tn
917
was generated and scored for sensitivity to 4% NaCl in order to identify genes responsible for growth or survival in elevated-NaCl environments. One of the
L. monocytogenes
Tn
917
mutants, designated strain OSM1, was selected, and the gene interrupted by the transposon was sequenced. A BLAST search with the putative translated amino acid sequence indicated that the interrupted gene product was a homolog of
htrA
(
degP
), a gene coding for a serine protease identified as a stress response protein in several gram-positive and gram-negative bacteria. An
htrA
deletion strain, strain LDW1, was constructed, and the salt-sensitive phenotype of this strain was complemented by introduction of a plasmid carrying the wild-type
htrA
gene, demonstrating that
htrA
is necessary for optimal growth under conditions of osmotic stress. Additionally, strain LDW1 was tested for its response to temperature and H
2
O
2
stresses. The results of these growth assays indicated that strain LDW1 grew at a lower rate than the wild-type strain at 44°C but at a rate similar to that of the wild-type strain when incubated at 4°C. In addition, strain LDW1 was significantly more sensitive to a 52°C heat shock than the wild-type strain. Strain LDW1 was also defective in its response to H
2
O
2
challenge at 37°C, since 100 or 150 μg of H
2
O
2
was more inhibitory for the growth of strain LDW1 than for that of the parent strain. The stress response phenotype observed for strain LDW1 is similar to that observed for other HtrA
−
organisms, which suggests that
L. monocytogenes
HtrA may play a role in degrading misfolded proteins that accumulate under stress conditions.
Prolonged Maltose-Limited Cultivation of
Saccharomyces cerevisiae
Selects for Cells with Improved Maltose Affinity and Hypersensitivity
Authors: Jansen Mickel L. A. , Daran-Lapujade Pascale , de Winde Johannes H. , Piper Matthew D. W. , Pronk Jack T. 
Published: April 2004

ABSTRACT

Prolonged cultivation (>25 generations) of
Saccharomyces cerevisiae
in aerobic, maltose-limited chemostat cultures led to profound physiological changes. Maltose hypersensitivity was observed when cells from prolonged cultivations were suddenly exposed to excess maltose. This substrate hypersensitivity was evident from massive cell lysis and loss of viability. During prolonged cultivation at a fixed specific growth rate, the affinity for the growth-limiting nutrient (i.e., maltose) increased, as evident from a decreasing residual maltose concentration. Furthermore, the capacity of maltose-dependent proton uptake increased up to 2.5-fold during prolonged cultivation. Genome-wide transcriptome analysis showed that the increased maltose transport capacity was not primarily due to increased transcript levels of maltose-permease genes upon prolonged cultivation. We propose that selection for improved substrate affinity (ratio of maximum substrate consumption rate and substrate saturation constant) in maltose-limited cultures leads to selection for cells with an increased capacity for maltose uptake. At the same time, the accumulative nature of maltose-proton symport in
S. cerevisiae
leads to unrestricted uptake when maltose-adapted cells are exposed to a substrate excess. These changes were retained after isolation of individual cell lines from the chemostat cultures and nonselective cultivation, indicating that mutations were involved. The observed trade-off between substrate affinity and substrate tolerance may be relevant for metabolic engineering and strain selection for utilization of substrates that are taken up by proton symport.
Stratification of Activity and Bacterial Community Structure in Biofilms Grown on Membranes Transferring Oxygen
Authors: Cole Alina C. , Semmens Michael J. , LaPara Timothy M. 
Published: April 2004

ABSTRACT

Previous studies have shown that membrane-aerated biofilm (MAB) reactors can simultaneously remove carbonaceous and nitrogenous pollutants from wastewater in a single reactor. Oxygen is provided to MABs through gas-permeable membranes such that the region nearest the membrane is rich in oxygen but low in organic carbon, whereas the outer region of the biofilm is void of oxygen but rich in organic carbon. In this study, MABs were grown under similar conditions but at two different fluid velocities (2 and 14 cm s
−1
) across the biofilm. MABs were analyzed for changes in biomass density, respiratory activity, and bacterial community structure as functions of biofilm depth. Biomass density was generally highest near the membrane and declined with distance from the membrane. Respiratory activity exhibited a hump-shaped profile, with the highest activity occurring in the middle of the biofilm. Community analysis by PCR cloning and PCR-denaturing gradient gel electrophoresis of 16S rRNA genes demonstrated substantial stratification of the community structure across the biofilm. Population profiles were also generated by competitive quantitative PCR of gene fragments specific for ammonia-oxidizing bacteria (AOB) (
amoA
) and denitrifying bacteria (
nirK
and
nirS
). At a flow velocity of 14 cm s
−1
, AOB were found only near the membrane, whereas denitrifying bacteria proliferated in the anoxic outer regions of the biofilm. In contrast, at a flow velocity of 2 cm s
−1
, AOB were either not detected or detected at a concentration near the detection limit. This study suggests that, under the appropriate conditions, both AOB and denitrifying bacteria can coexist within an MAB.
Cross Talk between 2,4-Diacetylphloroglucinol-Producing Biocontrol Pseudomonads on Wheat Roots
Authors: Maurhofer Monika , Baehler Eric , Notz Regina , Martinez Vicente , Keel Christoph 
Published: April 2004

ABSTRACT

The performance of
Pseudomonas
biocontrol agents may be improved by applying mixtures of strains which are complementary in their capacity to suppress plant diseases. Here, we have chosen the combination of
Pseudomonas fluorescens
CHA0 with another well-characterized biocontrol agent,
P. fluorescens
Q2-87, as a model to study how these strains affect each other's expression of a biocontrol trait. In both strains, production of the antimicrobial compound 2,4-diacetylphloroglucinol (DAPG) is a crucial factor contributing to the suppression of root diseases. DAPG acts as a signaling compound inducing the expression of its own biosynthetic genes. Experimental setups were developed to investigate whether, when combining strains CHA0 and Q2-87, DAPG excreted by one strain may influence expression of DAPG-biosynthetic genes in the other strain in vitro and on the roots of wheat. DAPG production was monitored by observing the expression of
lacZ
fused to the biosynthetic gene
phlA
of the respective strain. Dual-culture assays in which the two strains were grown in liquid medium physically separated by a membrane revealed that Q2-87 but not its DAPG-negative mutant Q2-87::Tn
5
-1 strongly induced
phlA
expression in a Δ
phlA
mutant of strain CHA0. In the same way,
phlA
expression in a Q2-87 background was induced by DAPG produced by CHA0. When coinoculated onto the roots of wheat seedlings grown under gnotobiotic conditions, strains Q2-87 and CHA0, but not their respective DAPG-negative mutants, were able to enhance
phlA
expression in each other. In summary, we have established that two nonrelated pseudomonads may stimulate each other in the expression of an antimicrobial compound important for biocontrol. This interpopulation communication occurs in the rhizosphere, i.e., at the site of pathogen inhibition, and is mediated by the antimicrobial compound itself acting as a signal exchanged between the two pseudomonads.
Evolution of the Core Genome of
Pseudomonassyringae
, a Highly Clonal, Endemic PlantPathogen
Authors: Sarkar Sara F. , Guttman David S. 
Published: April 2004

ABSTRACT

Pseudomonas
syringae
is a common foliar bacterium responsible for many
important plant diseases. We studied the population structure and
dynamics of the core genome of
P. syringae
via multilocus
sequencing typing (MLST) of 60 strains, representing 21 pathovars and 2
nonpathogens, isolated from a variety of plant hosts. Seven
housekeeping genes, dispersed around the
P. syringae
genome,
were sequenced to obtain 400 to 500 nucleotides per gene. Forty unique
sequence types were identified, with most strains falling into one of
four major clades. Phylogenetic and maximum-likelihood analyses
revealed a remarkable degree of congruence among the seven genes,
indicating a common evolutionary history for the seven loci. MLST and
population genetic analyses also found a very low level of
recombination. Overall, mutation was found to be approximately four
times more likely than recombination to change any single nucleotide. A
skyline plot was used to study the demographic history of
P.
syringae
. The species was found to have maintained a constant
population size over time. Strains were also found to remain
genetically homogeneous over many years, and when isolated from sites
as widespread as the United States and Japan. An analysis of molecular
variance found that host association explains only a small proportion
of the total genetic variation in the sample. These analyses reveal
that with respect to the core genome,
P. syringae
is a highly
clonal and stable species that is endemic within plant populations, yet
the genetic variation seen in these genes only weakly predicts host
association.
Size and UV Germicidal Irradiation Susceptibility of
Serratia marcescens
when Aerosolized from Different Suspending Media
Authors: Lai Ka M. , Burge Harriet A. , First Melvin W. 
Published: April 2004

ABSTRACT

Experimental systems have been built in laboratories worldwide to investigate the influence of various environmental parameters on the efficacy of UV germicidal irradiation (UVGI) for deactivating airborne microorganisms. It is generally recognized that data from different laboratories might vary significantly due to differences in systems and experimental conditions. In this study we looked at the effect of the composition of the suspending medium on the size and UVGI susceptibility of
Serratia marcescens
in an experimental system built in our laboratory.
S. marcescens
was suspended in (i) distilled water, (ii) phosphate buffer, (iii) 10% fetal calf serum, (iv) phosphate-buffered saline (saline, 0.8% sodium chloride), and (v) synthetic saliva (phosphate-buffered saline with 10% fetal calf serum). At low humidity (36%),
S. marcescens
suspended in water-only medium was the most susceptible to UVGI, followed by those in serum-only medium. The count median diameters (CMDs) for culturable particles from water-only and serum-only media were 0.88 and 0.95 μm, respectively, with the measurements based on their aerodynamic behavior. The bacteria suspended in phosphate buffer, synthetic saliva, and phosphate-buffered saline had similar UVGI susceptibility and CMD at 1.0, 1.4, and 1.5 μm, respectively. At high humidity (68%) the CMD of the particles increased by 6 to 16%, and at the same time UVGI susceptibility decreased, with the magnitude of decrease related to the type of suspending medium. In conclusion, the choice of suspending medium influenced both size and UVGI susceptibility of
S. marcescens
. These data are valuable for making comparisons and deciding on the use of an appropriate medium for various applications.
Characterization of Protistan Assemblages in the Ross Sea, Antarctica, by Denaturing Gradient Gel Electrophoresis
Authors: Gast Rebecca J. , Dennett Mark R. , Caron David A. 
Published: April 2004

ABSTRACT
The diversity of protistan assemblages has traditionally been studied using microscopy and morphological characterization, but these methods are often inadequate for ecological studies of these communities because most small protists inherently lack adequate taxonomic characters to facilitate their identification at the species level and many protistan species also do not preserve well. We have therefore used a culture-independent approach (denaturing gradient gel electrophoresis [DGGE]) to obtain an assessment of the genetic composition and distribution of protists within different microhabitats (seawater, meltwater or slush on sea-ice floes, and ice) of the Ross Sea, Antarctica. Samples of the same type (e.g., water) shared more of the same bands than samples of different types (e.g., ice versus water), despite being collected from different sites. These findings imply that samples from the same environment have a similar protistan species composition and that the type of microenvironment significantly influences the protistan species composition of these Antarctic assemblages. It should be noted that a large number of bands among the samples within each microhabitat were distinct, indicating the potential presence of significant genetic diversity within each microenvironment. Sequence analysis of selected DGGE bands revealed sequences that represent diatoms, dinoflagellates, ciliates, flagellates, and several unidentified eukaryotes.
Stationary-Phase Quorum-Sensing Signals Affect Autoinducer-2 and Gene Expression in
Escherichia coli
Authors: Ren Dacheng , Bedzyk Laura A. , Ye Rick W. , Thomas Stuart M. , Wood Thomas K. 
Published: April 2004

ABSTRACT

Quorum sensing via autoinducer-2 (AI-2) has been identified in different strains, including those from
Escherichia
,
Vibrio
,
Streptococcus
, and
Bacillus
species, and previous studies have suggested the existence of additional quorum-sensing signals working in the stationary phase of
Escherichia coli
cultures. To investigate the presence and global effect of these possible quorum-sensing signals other than AI-2, DNA microarrays were used to study the effect of stationary-phase signals on the gene expression of early exponential-phase cells of the AI-2-deficient strain
E. coli
DH5α. For statistically significant differential gene expression (
P
< 0.05), 14 genes were induced by supernatants from a stationary culture and 6 genes were repressed, suggesting the involvement of indole (induction of
tnaA
and
tnaL
) and phosphate (repression of
phoA
,
phoB
, and
phoU
). To study the stability of the signals, the stationary-phase supernatant was autoclaved and was used to study its effect on
E. coli
gene expression. Three genes were induced by autoclaved stationary-phase supernatant, and 34 genes were repressed. In total, three genes (
ompC
,
ptsA
, and
btuB
) were induced and five genes (
nupC
,
phoB
,
phoU
,
argT
, and
ompF
) were repressed by both fresh and autoclaved stationary-phase supernatants. Furthermore, supernatant from
E. coli
DH5α stationary culture was found to repress
E. coli
K-12 AI-2 concentrations by 4.8-fold ± 0.4-fold, suggesting that an additional quorum-sensing system in
E. coli
exists and that gene expression is controlled as a network with different signals working at different growth stages.
Identification of the Bacterial Community of Maple Sap by Using Amplified Ribosomal DNA (rDNA) Restriction Analysis and rDNA Sequencing
Authors: Lagacé L. , Pitre M. , Jacques M. , Roy D. 
Published: April 2004

ABSTRACT

The bacterial community of maple sap was characterized by analysis of samples obtained at the taphole of maple trees for the 2001 and 2002 seasons. Among the 190 bacterial isolates, 32 groups were formed according to the similarity of the banding patterns obtained by amplified ribosomal DNA restriction analysis (ARDRA). A subset of representative isolates for each ARDRA group was identified by 16S rRNA gene fragment sequencing. Results showed a wide variety of organisms, with 22 different genera encountered.
Pseudomonas
and
Ralstonia
, of the γ
-
and β
-Proteobacteria,
respectively, were the most frequently encountered genera. Gram-positive bacteria were also observed, and
Staphylococcus
,
Plantibacter
, and
Bacillus
were the most highly represented genera. The sampling period corresponding to 50% of the cumulative sap flow percentage presented the greatest bacterial diversity according to its Shannon diversity index value (1.1). γ
-Proteobacteria
were found to be dominant almost from the beginning of the season to the end. These results are providing interesting insights on maple sap microflora that will be useful for further investigation related to microbial contamination and quality of maple products and also for guiding new strategies on taphole contamination control.
Receptor Binding Domain ofEscherichia coliF18 Fimbrial Adhesin FedF Can Be both Efficiently Secreted and Surface Displayed in a Functional Form inLactococcus lactis
Authors: Lindholm Agneta , Smeds Andreas , Palva Airi 
Published: April 2004

ABSTRACTAdherence of F18 fimbrialEscherichia colito porcine intestinal epithelial cells is mediated by the adhesin (FedF) of F18 fimbriae. In a previous study, we demonstrated the specificity of the amino acid residues between 60 and 109 as the receptor binding domain of FedF. In this study, different expression, secretion, and anchoring systems for the receptor binding domain of the FedF adhesin inLactococcus lactiswere evaluated. Two partially overlapping receptor binding domains (42 and 62 amino acid residues) were expressed as fusions withL. lactissubsp.cremorisprotein PrtP for evaluation of secretion efficiency. To evaluate the cell surface display of these FedF-PrtP fusions, they were further combined with different lengths of PrtP spacers fused with either theL. lactisAcmA anchor or the PrtP cell wall binding domain. An HtrA-defectiveL. lactisNZ9000 mutant was constructed to determine its effect on the level of secreted or anchored fusion proteins. RecombinantL. lactisclones secreting the receptor binding domain of F18 fimbriae as a fusion with the H domains ofL. lactisprotein PrtP were first constructed by using two different signal peptides. FedF-PrtP fusions, directed by the signal sequence ofL. brevisSlpA, were throughout found to be secreted at significantly higher quantities than corresponding fusions with the signal peptide ofL. lactisUsp45. In the surface display systems tested, theL. lactisAcmA anchor performed significantly better, particularly in theL. lactisNZ9000ΔhtrAstrain, compared to theL. lactisPrtP anchor region. Of the cell surface display constructs with the AcmA anchor, only those with the longest PrtP spacer regions resulted in efficient binding of recombinantL. lactiscells to porcine intestinal epithelial cells. These results confirmed that it is possible to efficiently produce the receptor binding domain of the F18 adhesin in a functionally active form inL. lactis.
Effect of Trophic Status on the Culturability and Activity of Bacteria from a Range of Lakes in the English Lake District
Authors: Porter Jonathan , Morris Samantha A. , Pickup Roger W. 
Published: April 2004

ABSTRACT
The bacterioplankton from a number of lakes that differed in nutrient status in the English Lake District was examined with a number of techniques for enumeration and activity assessment. Natural water samples showed a clear correlation between total counts and trophic status. Esterase activity measurements with Chemchrome B were able to distinguish high- and low-nutrient-status lakes, whereas tetrazolium salt (5-cyano-2,3-ditoyltetrazolium chloride) reduction, the direct viable count-cell elongation assay, and culturability measurements could not. Tetrazolium salt reduction and esterase activity measurements labeled a significant number of cells from water of all nutrient levels, whereas the direct viable count-cell elongation method was of use only in oligotrophic waters. Size fractionation of samples showed that the culturable cells were retained by the larger filters, especially in nutrient-rich waters. Esterase activity measurements also favored the larger cells. The differences observed between assays using water that differed in trophic status raise questions about the use of these tests as a definitive measure of viability.