bluuebunny/crossref_metadata_2025_split huggingface dataset:
Carbon Starvation Can Induce Energy Deprivation and Loss of Fermentative Capacity in
Saccharomyces cerevisiae
Authors: Thomsson Elisabeth , Larsson Christer , Albers Eva , Nilsson Annika , Franzén Carl Johan , Gustafsson Lena 
Published: June 2003

ABSTRACT

Seven different strains of
Saccharomyces cerevisiae
were tested for the ability to maintain their fermentative capacity during 24 h of carbon or nitrogen starvation. Starvation was imposed by transferring cells, exponentially growing in anaerobic batch cultures, to a defined growth medium lacking either a carbon or a nitrogen source. After 24 h of starvation, fermentative capacity was determined by addition of glucose and measurement of the resulting ethanol production rate. The results showed that 24 h of nitrogen starvation reduced the fermentative capacity by 70 to 95%, depending on the strain. Carbon starvation, on the other hand, provoked an almost complete loss of fermentative capacity in all of the strains tested. The absence of ethanol production following carbon starvation occurred even though the cells possessed a substantial glucose transport capacity. In fact, similar uptake capacities were recorded irrespective of whether the cells had been subjected to carbon or nitrogen starvation. Instead, the loss of fermentative capacity observed in carbon-starved cells was almost surely a result of energy deprivation. Carbon starvation drastically reduced the ATP content of the cells to values well below 0.1 μmol/g, while nitrogen-starved cells still contained approximately 6 μmol/g after 24 h of treatment. Addition of a small amount of glucose (0.1 g/liter at a cell density of 1.0 g/liter) at the initiation of starvation or use of stationary-phase instead of log-phase cells enabled the cells to preserve their fermentative capacity also during carbon starvation. The prerequisites for successful adaptation to starvation conditions are probably gradual nutrient depletion and access to energy during the adaptation period.
External pH and Nitrogen Source Affect Secretion of Pectate Lyase by
Colletotrichum gloeosporioides
Authors: Drori N. , Kramer-Haimovich H. , Rollins J. , Dinoor A. , Okon Y. , Pines O. , Prusky D. 
Published: June 2003

ABSTRACT

Accumulation of ammonia and associated tissue alkalinization predispose fruit to attack by
Colletotrichumgloeosporioides.
As the external pH increases from 4.0 to 6.0, pectate lyase (PL) and other extracellular proteins are secreted and accumulate. At pH 4.0 neither
pelB
(encoding PL) transcription nor PL secretion were detected; however, they were detected as the pH increased. Nitrogen assimilation also was required for PL secretion at pH 6.0. Both inorganic and organic nitrogen sources enhanced PL secretion at pH 6.0, but neither was sufficient for PL secretion at pH 4.0. Sequence analysis of the 5′ upstream region of the
pelB
promoter revealed nine putative consensus binding sites for the
Aspergillus
transcription factor PacC. Consistent with this result, the transcript levels of
pac1
(the
C. gloeosporioides pacC
homologue) and
pelB
increased in parallel as a function of pH. Our results suggest that the ambient pH and the nitrogen source are independent regulatory factors for processes linked to PL secretion and virulence of
C. gloeosporioides
.
Identification and Characterization of the Conjugal Transfer Region of the pCg1 plasmid from Naphthalene-Degrading
Pseudomonas putida
Cg1
Authors: Park Woojun , Jeon Che Ok , Hohnstock-Ashe Amy M. , Winans Stephen C. , Zylstra Gerben J. , Madsen Eugene L. 
Published: June 2003

ABSTRACT

Hybridization and restriction fragment length polymorphism data (K. G. Stuart-Keil, A. M. Hohnstock, K. P. Drees, J. B. Herrick, and E. L. Madsen, Appl. Environ. Microbiol. 64:3633-3640, 1998) have shown that pCg1, a naphthalene catabolic plasmid carried by
Pseudomonas putida
Cg1, is homologous to the archetypal naphthalene catabolic plasmid, pDTG1, in
P. putida
NCIB 9816-4. Sequencing of the latter plasmid allowed PCR primers to be designed for amplifying and sequencing the conjugal transfer region in pCg1. The mating pair formation (
mpf
) gene,
mpfA
encoding the putative precursor of the conjugative pilin subunit from pCg1, was identified along with other
trb
-like
mpf
genes. Sequence comparison revealed that the 10
mpf
genes in pCg1 and pDTG1 are closely related (61 to 84% identity) in sequence and operon structure to the putative
mpf
genes of catabolic plasmid pWW0 (TOL plasmid of
P. putida
) and pM3 (antibiotic resistance plasmid of
Pseudomonas.
spp). A polar mutation caused by insertional inactivation in
mpfA
of pCg1 and reverse transcriptase PCR analysis of mRNA showed that this
mpf
region was involved in conjugation and was transcribed from a promoter located upstream of an open reading frame adjacent to
mpfA. lacZ
transcriptional fusions revealed that
mpf
genes of pCg1 were expressed constitutively both in liquid and on solid media. This expression did not respond to host exposure to naphthalene. Conjugation frequency on semisolid media was consistently 10- to 100-fold higher than that in liquid media. Thus, conjugation of pCg1 in
P. putida
Cg1 was enhanced by expression of genes in the
mpf
region and by surfaces where conditions fostering stable, high-density cell-to-cell contact are manifest.
Distribution of Biosurfactant-Producing Bacteria in Undisturbed and Contaminated Arid Southwestern Soils
Authors: Bodour Adria A. , Drees Kevin P. , Maier Raina M. 
Published: June 2003

ABSTRACT

Biosurfactants are a unique class of compounds that have been shown to have a variety of potential applications in the remediation of organic- and metal-contaminated sites, in the enhanced transport of bacteria, in enhanced oil recovery, as cosmetic additives, and in biological control. However, little is known about the distribution of biosurfactant-producing bacteria in the environment. The goal of this study was to determine how common culturable surfactant-producing bacteria are in undisturbed and contaminated sites. A series of 20 contaminated (i.e., with metals and/or hydrocarbons) and undisturbed soils were collected and plated on R
2
A agar. The 1,305 colonies obtained were screened for biosurfactant production in mineral salts medium containing 2% glucose. Forty-five of the isolates were positive for biosurfactant production, representing most of the soils tested. The 45 isolates were grouped by using repetitive extragenic palindromic (REP)-PCR analysis, which yielded 16 unique isolates. Phylogenetic relationships were determined by comparing the 16S rRNA gene sequence of each unique isolate with known sequences, revealing one new biosurfactant-producing microbe, a
Flavobacterium
sp. Sequencing results indicated only 10 unique isolates (in comparison to the REP analysis, which indicated 16 unique isolates). Surface tension results demonstrated that isolates that were similar according to sequence analysis but unique according to REP analysis in fact produced different surfactant mixtures under identical growth conditions. These results suggest that the 16S rRNA gene database commonly used for determining phylogenetic relationships may miss diversity in microbial products (e.g., biosurfactants and antibiotics) that are made by closely related isolates. In summary, biosurfactant-producing microorganisms were found in most soils even by using a relatively limited screening assay. Distribution was dependent on soil conditions, with gram-positive biosurfactant-producing isolates tending to be from heavy metal-contaminated or uncontaminated soils and gram-negative isolates tending to be from hydrocarbon-contaminated or cocontaminated soils.
Assessment of Bioavailability of Soil-Sorbed Atrazine
Authors: Park Jeong-Hun , Feng Yucheng , Ji Pingsheng , Voice Thomas C. , Boyd Stephen A. 
Published: June 2003

ABSTRACT

Bioavailability of pesticides sorbed to soils is an important determinant of their environmental fate and impact. Mineralization of sorbed atrazine was studied in soil and clay slurries, and a desorption-biodegradation-mineralization (DBM) model was developed to quantitatively evaluate the bioavailability of sorbed atrazine. Three atrazine-degrading bacteria that utilized atrazine as a sole N source (
Pseudomonas
sp. strain ADP,
Agrobacterium radiobacter
strain J14a, and
Ralstonia
sp. strain M91-3) were used in the bioavailability assays. Assays involved establishing sorption equilibrium in sterile soil slurries, inoculating the system with organisms, and measuring the CO
2
production over time. Sorption and desorption isotherm analyses were performed to evaluate distribution coefficients and desorption parameters, which consisted of three desorption site fractions and desorption rate coefficients. Atrazine sorption isotherms were linear for mineral and organic soils but displayed some nonlinearity for K-saturated montmorillonite. The desorption profiles were well described by the three-site desorption model. In many instances, the mineralization of atrazine was accurately predicted by the DBM model, which accounts for the extents and rates of sorption/desorption processes and assumes biodegradation of liquid-phase, but not sorbed, atrazine. However, for the Houghton muck soil, which manifested the highest sorbed atrazine concentrations, enhanced mineralization rates, i.e., greater than those expected on the basis of aqueous-phase atrazine concentration, were observed. Even the assumption of instantaneous desorption could not account for the elevated rates. A plausible explanation for enhanced bioavailability is that bacteria access the localized regions where atrazine is sorbed and that the concentrations found support higher mineralization rates than predicted on the basis of aqueous-phase concentrations. Characteristics of high sorbed-phase concentration, chemotaxis, and attachment of cells to soil particles seem to contribute to the bioavailability of soil-sorbed atrazine.
Consensus-Degenerate Hybrid Oligonucleotide Primers for Amplification of Priming Glycosyltransferase Genes of the Exopolysaccharide Locus in Strains of the
Lactobacillus casei
Group
Authors: Provencher Cathy , LaPointe Gisèle , Sirois Stéphane , Van Calsteren Marie-Rose , Roy Denis 
Published: June 2003

ABSTRACT

A primer design strategy named CODEHOP (consensus-degenerate hybrid oligonucleotide primer) for amplification of distantly related sequences was used to detect the priming glycosyltransferase (GT) gene in strains of the
Lactobacillus casei
group. Each hybrid primer consisted of a short 3′ degenerate core based on four highly conserved amino acids and a longer 5′ consensus clamp region based on six sequences of the priming GT gene products from exopolysaccharide (EPS)-producing bacteria. The hybrid primers were used to detect the priming GT gene of 44 commercial isolates and reference strains of
Lactobacillus rhamnosus
,
L. casei
,
Lactobacillus zeae
, and
Streptococcus thermophilus
. The priming GT gene was detected in the genome of both non-EPS-producing (EPS
−
) and EPS-producing (EPS
+
) strains of
L. rhamnosus
. The sequences of the cloned PCR products were similar to those of the priming GT gene of various gram-negative and gram-positive EPS
+
bacteria. Specific primers designed from the
L. rhamnosus
RW-9595M GT gene were used to sequence the end of the priming GT gene in selected EPS
+
strains of
L. rhamnosus
. Phylogenetic analysis revealed that
Lactobacillus
spp. form a distinctive group apart from other lactic acid bacteria for which GT genes have been characterized to date. Moreover, the sequences show a divergence existing among strains of
L. rhamnosus
with respect to the terminal region of the priming GT gene. Thus, the PCR approach with consensus-degenerate hybrid primers designed with CODEHOP is a practical approach for the detection of similar genes containing conserved motifs in different bacterial genomes.
Characterization of Urease-Positive Thermophilic
Campylobacter
Subspecies by Multilocus Enzyme Electrophoresis Typing
Authors: Matsuda Motoo , Kaneko Aki , Stanley Timothy , Millar B. Cherie , Miyajima M. , Murphy Philip G. , Moore John E. 
Published: June 2003

ABSTRACT

Thirty-one urease-positive thermophilic
Campylobacter
(UPTC) isolates, including three reference strains (NCTC12892, NCTC12895 and NCTC12896), and three
Campylobacter lari
isolates, which were isolated from several countries and sources, were compared genotypically by using multilocus enzyme electrophoresis (MLEE). We examined allelic variation around seven enzyme loci, including the adenylate kinase, alkaline phosphatase, catalase, fumarase, malic enzyme, malate dehydrogenase, and
l
-phenylalanyl-
l
-leucine peptidase loci. MLEE typing revealed the presence of 23 different electrophoretic types (ETs) among the 31 UPTC isolates, and 14 isolates shared six electrophoretic profiles. Three different ETs were identified for the three
C. lari
isolates examined, and no ETs were shared by UPTC and
C. lari
isolates. Quantitative analyses were subsequently performed by using allelic variation data, and the results demonstrated that the mean genetic diversity was 0.655. In conclusion, MLEE demonstrated that the UPTC isolates examined are genetically hypervariable and form a cluster separate from the
C. lari
cluster.
Microbiological Evaluation of a Range of Disinfectant Products To Control Mixed-Species Biofilm Contamination in a Laboratory Model of a Dental Unit Water System
Authors: Walker J. T. , Bradshaw D. J. , Fulford M. R. , Marsh P. D. 
Published: June 2003

ABSTRACT
Dental unit water system (DUWS) tubing harbors complex multispecies biofilms that are responsible for high microbial levels at the distal outlet. The aim of this study was to use an established biofilm laboratory model to simulate biofouling of DUWS to evaluate practical, cost-effective, and evidence-based methods of microbial decontamination. Reproducible biofilms were developed in the model over 14 days; decontamination was assessed using total viable counts (TVC) and microscopic-image analysis techniques to view the inner surface of tubing. Flushing did not reduce the biofilm coverage or TVC. Combizyme and ozone did not completely eliminate the viable bacteria (70 and 65% reduction in biofilm TVC, respectively), nor did they remove the biofilm (45 and 57% reduction in biofilm coverage, respectively). Chlorhexidine and Bio2000 (active agent: ethanol and chlorhexidine), Tegodor and Gigasept Rapid (aldehyde based), and Grotanol (hydroxide based) completely eliminated the TVC but did not completely remove biofilm (31, 53 33, 34, and 64.9% reduction of biofilm coverage, respectively). Other products including Grotanol Flussig (phenol based), Betadine (povidone-iodine based), Alpron (chlorite based), and the hydroxide-containing products Sporklenz, Sterilex Ultra, Dialox, Sterilox, Sanosil, Oxigenal, and Grotanat Bohrerbad resulted in a 100% reduction in the biofilm TVC and a >95% reduction in biofilm coverage. The study demonstrated that while many disinfectants achieve a sufficient reduction in TVC they may not necessarily remove unwanted biofilm from the tubing surfaces as tested in this laboratory-controlled biofilm model.
Interactions of Insecticidal Toxin Gene Products from
Xenorhabdus nematophilus
PMFI296
Authors: Sergeant Martin , Jarrett Paul , Ousley Margaret , Morgan J. Alun W. 
Published: June 2003

ABSTRACT

Four genes on a genomic fragment from
Xenorhabdus nematophilus
PMFI296 were shown to be involved in insecticidal activity towards three commercially important insect species. Each gene was expressed individually and in combinations in
Escherichia coli
, and the insecticidal activity of the lysates was determined. The combined four genes (
xptA1
,
xptA2
,
xptB1
, and
xptC1
), in
E. coli
, showed activity towards
Pieris brassicae
,
Pieris rapae
, and
Heliothis virescens
. The genes
xptA1
,
xptB1
, and
xptC1
were involved in expressing activity towards
P. rapae
and
P. brassicae
, while the genes
xptA2
,
xptB1
, and
xptC1
were needed for activity towards
H. virescens
. When each of these three genes was expressed individually in
E. coli
and the cell lysates were used in insect assays or mixed and then used, insecticidal activity was detected at a very low level. If the genes
xptB1
and
xptC1
were expressed in the same
E. coli
cell and this cell lysate was mixed with cells expressing
xptA1
, activity was restored to
P. rapae
and
P. brassicae
. Similarly mixing XptB1/C1 lysate with XptA2 lysate restored activity towards
H. virescens.
Individual gene disruptions in
X. nematophilus
PMFI296 reduced activity to insects; this activity was restored by complementation with cells expressing either
xptA1
or
xptA2
for their respective disruptions or
E. coli
expressing both
xptB1
and
xptC1
for individual disruptions of either of these genes. The genes
xptA2
,
xptC1
, and
xptB1
were expressed as an operon in PMFI296 and inactivation of
xptA2
or
xptC1
resulted in silencing of downstream gene(s), while
xptA1
was expressed as a single gene. Therefore, the two three gene product combinations interact with each other to produce good insecticidal activity.
Detection and Enumeration of Aromatic Oxygenase Genes by Multiplex and Real-Time PCR
Authors: Baldwin Brett R. , Nakatsu Cindy H. , Nies Loring 
Published: June 2003

ABSTRACT

Our abilities to detect and enumerate pollutant-biodegrading microorganisms in the environment are rapidly advancing with the development of molecular genetic techniques. Techniques based on multiplex and real-time PCR amplification of aromatic oxygenase genes were developed to detect and quantify aromatic catabolic pathways, respectively. PCR primer sets were identified for the large subunits of aromatic oxygenases from alignments of known gene sequences and tested with genetically well-characterized strains. In all, primer sets which allowed amplification of naphthalene dioxygenase, biphenyl dioxygenase, toluene dioxygenase, xylene monooxygenase, phenol monooxygenase, and ring-hydroxylating toluene monooxygenase genes were identified. For each primer set, the length of the observed amplification product matched the length predicted from published sequences, and specificity was confirmed by hybridization. Primer sets were grouped according to the annealing temperature for multiplex PCR permitting simultaneous detection of various genotypes responsible for aromatic hydrocarbon biodegradation. Real-time PCR using SYBR green I was employed with the individual primer sets to determine the gene copy number. Optimum polymerization temperatures for real-time PCR were determined on the basis of the observed melting temperatures of the desired products. When a polymerization temperature of 4 to 5°C below the melting temperature was used, background fluorescence signals were greatly reduced, allowing detection limits of 2 × 10
2
copies per reaction mixture. Improved in situ microbial characterization will provide more accurate assessment of pollutant biodegradation, enhance studies of the ecology of contaminated sites, and facilitate assessment of the impact of remediation technologies on indigenous microbial populations.
Development of a
Listeria monocytogenes
EGDe Partial Proteome Reference Map and Comparison with the Protein Profiles of Food Isolates
Authors: Ramnath Manilduth , Rechinger K. Björn , Jänsch Lothar , Hastings John W. , Knøchel Susanne , Gravesen Anne 
Published: June 2003

ABSTRACT

A partially annotated proteome reference map of the food pathogen
Listeria monocytogenes
was developed for exponentially growing cells under standardized, optimal conditions by using the sequenced strain EGDe (serotype 1/2a) as a model organism. The map was developed by using a reproducible total protein extraction and two-dimensional (2-D) polyacrylamide gel electrophoresis analysis procedure, and it contained 33 identified proteins representing the four main protein functional classes. In order to facilitate analysis of membrane proteins, a protein compartmentalization procedure was assessed. The method used provided partial fractionation of membrane and cytosolic proteins. The total protein 2-D profiles of three serotype 1/2a strains and one serotype 1/2b strain isolated from food were compared to the
L. monocytogenes
EGDe proteome. An average of 13% of the major protein spots in the food strain proteomes were not matched in the strain EGDe proteome. The variation was greater for the less intense spots, and on average 28% of these spots were not matched. Two of the proteins identified in
L. monocytogenes
EGDe were missing in one or more of the food isolates. These two proteins were proteins involved in the main glycolytic pathway and in metabolism of coenzymes and prosthetic groups. The two corresponding genes were found by PCR amplification to be present in the four food isolates. Our results show that the
L. monocytogenes
EGDe reference map is a valuable starting point for analyses of strains having various origins and could be useful for analyzing the proteomes of different isolates of this pathogen.
Determination of the Domain of the
Lactobacillus delbrueckii
subsp.
bulgaricus
Cell Surface Proteinase PrtB Involved in Attachment to the Cell Wall after Heterologous Expression of the
prtB
Gene in
Lactococcus lactis
Authors: Germond Jacques-Edouard , Delley Michèle , Gilbert Christophe , Atlan Danièle 
Published: June 2003

ABSTRACT

Belonging to the subtilase family, the cell surface proteinase (CSP) PrtB of
Lactobacillus delbrueckii
subsp.
bulgaricus
differs from other CSPs synthesized by lactic acid bacteria. Expression of the
prtB
gene under its own promoter was shown to complement the proteinase-deficient strain MG1363 (PrtP
−
PrtM
−
) of
Lactococcus lactis
subsp.
cremoris
. Surprisingly, the maturation process of PrtB, unlike that of lactococcal CSP PrtPs, does not require a specific PrtM-like chaperone. The carboxy end of PrtB was previously shown to be different from the consensus anchoring region of other CSPs and exhibits an imperfect duplication of 59 amino acids with a high lysine content. By using a deletion strategy, the removal of the last 99 amino acids, including the degenerated anchoring signal (LPKKT), was found to be sufficient to release a part of the truncated PrtB into the culture medium and led to an increase in PrtB activity. This truncated PrtB is still active and enables
L. lactis
MG1363 to grow in milk supplemented with glucose. By contrast, deletion of the last 806 amino acids of PrtB led to the secretion of an inactive proteinase. Thus, the utmost carboxy end of PrtB is involved in attachment to the bacterial cell wall. Proteinase PrtB constitutes a powerful tool for cell surface display of heterologous proteins like antigens.
Increasing the Oxidative Stress Response AllowsEscherichia coliTo Overcome Inhibitory Effects of Condensed Tannins
Authors: Smith Alexandra H. , Imlay James A. , Mackie Roderick I. 
Published: June 2003

ABSTRACTTannins are plant-derived polyphenols with antimicrobial effects. The mechanism of tannin toxicity towardsEscherichia coliwas determined by using an extract fromAcacia mearnsii(Black wattle) as a source of condensed tannins (proanthocyanidins).E. coligrowth was inhibited by tannins only when tannins were exposed to oxygen. Tannins auto-oxidize, and substantial hydrogen peroxide was generated when they were added to aerobic media. The addition of exogenous catalase permitted growth in tannin medium.E. colimutants that lacked HPI, the major catalase, were especially sensitive to tannins, whileoxyRmutants that constitutively overexpress antioxidant enzymes were resistant. A tannin-resistant mutant was isolated in which a promoter-region point mutation increased the level of HPI by 10-fold. Our results indicate that wattle condensed tannins are toxic toE. coliin aerobic medium primarily because they generate H2O2. The oxidative stress response helpsE. colistrains to overcome their inhibitory effect.