bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological Analysis of the Expression of the Styrene Degradation Gene Cluster in
Pseudomonas fluorescens
ST
Authors: Santos Pedro Miguel , Blatny Janet Martha , Di Bartolo Ilaria , Valla Svein , Zennaro Elisabetta 
Published: July 2002

ABSTRACT

The effects of different carbon sources on expression of the styrene catabolism genes in
Pseudomonas fluorescens
ST were analyzed by using a promoter probe vector, pPR9TT, which contains transcription terminators upstream and downstream of the β-galactosidase reporter system. Expression of the promoter of the
stySR
operon, which codes for the styrene two-component regulatory system, was found to be constitutive and not subject to catabolite repression. This was confirmed by the results of an analysis of the
stySR
transcript in
P. fluorescens
ST cells grown on different carbon sources. The promoter of the operon of the upper pathway, designated P
styA
, was induced by styrene and repressed to different extents by organic acids or carbohydrates. In particular, cells grown on succinate or lactate in the presence of styrene started to exhibit β-galactosidase activity during the mid-exponential growth phase, before the preferred carbon sources were depleted, indicating that there is a threshold succinate and lactate concentration which allows induction of styrene catabolic genes. In contrast, cells grown on glucose, acetate, or glutamate and styrene exhibited a diauxic growth curve, and β-galactosidase activity was detected only after the end of the exponential growth phase. In each experiment the reliability of the reporter system constructed was verified by comparing the β-galactosidase activity and the activity of the styrene monooxygenase encoded by the first gene of the styrene catabolic operon.
The Chromosomal Arsenic Resistance Genes of
Thiobacillus ferrooxidans
Have an Unusual Arrangement and Confer Increased Arsenic and Antimony Resistance to
Escherichia coli
Authors: Butcher Bronwyn G. , Deane Shelly M. , Rawlings Douglas E. 
Published: July 2002

ABSTRACT

The chromosomal arsenic resistance genes of the acidophilic, chemolithoautotrophic, biomining bacterium
Thiobacillus ferrooxidans
were cloned and sequenced. Homologues of four arsenic resistance genes,
arsB
,
arsC
,
arsH
, and a putative
arsR
gene, were identified. The
T. ferrooxidans arsB
(arsenite export) and
arsC
(arsenate reductase) gene products were functional when they were cloned in an
Escherichia coli ars
deletion mutant and conferred increased resistance to arsenite, arsenate, and antimony. Therefore, despite the fact that the
ars
genes originated from an obligately acidophilic bacterium, they were functional in
E. coli
. Although
T. ferrooxidans
is gram negative, its ArsC was more closely related to the ArsC molecules of gram-positive bacteria. Furthermore, a functional
trxA
(thioredoxin) gene was required for ArsC-mediated arsenate resistance in
E. coli
; this finding confirmed the gram-positive ArsC-like status of this resistance and indicated that the division of ArsC molecules based on Gram staining results is artificial. Although
arsH
was expressed in an
E. coli
-derived in vitro transcription-translation system, ArsH was not required for and did not enhance arsenic resistance in
E. coli
. The
T. ferrooxidans ars
genes were arranged in an unusual manner, and the putative
arsR
and
arsC
genes and the
arsBH
genes were translated in opposite directions. This divergent orientation was conserved in the four
T. ferrooxidans
strains investigated.
Increased Killing of
Bacillus subtilis
on the Hair Roots of Transgenic T4 Lysozyme-Producing Potatoes
Authors: Ahrenholtz Ingrid , Harms Klaus , de Vries Johann , Wackernagel Wilfried 
Published: July 2002

ABSTRACT

Transgenic potato plants expressing the phage T4 lysozyme gene which are resistant to the plant-pathogenic enterobacterium
Erwinia carotovora
subsp.
carotovora
have been constructed. The agricultural growth of these potatoes might have harmful effects on soil microbiota as a result of T4 lysozyme release into the rhizosphere. To assess the bactericidal effect of roots, we have developed a novel method to associate the cells of
Bacillus subtilis
with hair roots of plants and to quantify the survival of cells directly on the root surface by appropriate staining and fluorescence microscopy. With this technique, we found that the roots of potato plants (Désirée and transgenic control lines) without T4 lysozyme gene display measurable killing activity on root-adsorbed
B. subtilis
cells. Killing was largely independent of the plant age and growth of plants in greenhouse or field plots. Roots from potato lines expressing the T4 lysozyme gene always showed significantly (1.5- to 3.5-fold) higher killing. It is concluded that T4 lysozyme is released from the root epidermis cells and is active in the fluid film on the root surface. We discuss why strong negative effects of T4 lysozyme-producing potatoes on soil bacteria in field trials may not be observed. We propose that the novel method presented here to study interactions of bacteria with roots can be applied not only to bacterial killing but also to interactions leading to growth-sustaining effects of plants on bacteria.
Cospeciation of Psyllids and Their Primary Prokaryotic Endosymbionts
Authors: Thao MyLo L. , Moran Nancy A. , Abbot Patrick , Brennan Eric B. , Burckhardt Daniel H. , Baumann Paul 
Published: July 2002

ABSTRACT

Psyllids are plant sap-feeding insects that harbor prokaryotic endosymbionts in specialized cells within the body cavity. Four-kilobase DNA fragments containing 16S and 23S ribosomal DNA (rDNA) were amplified from the primary (P) endosymbiont of 32 species of psyllids representing three psyllid families and eight subfamilies. In addition, 0.54-kb fragments of the psyllid nuclear gene
wingless
were also amplified from 26 species. Phylogenetic trees derived from 16S-23S rDNA and from the host
wingless
gene are very similar, and tests of compatibility of the data sets show no significant conflict between host and endosymbiont phylogenies. This result is consistent with a single infection of a shared psyllid ancestor and subsequent cospeciation of the host and the endosymbiont. In addition, the phylogenies based on DNA sequences generally agreed with psyllid taxonomy based on morphology. The 3′ end of the 16S rDNA of the P endosymbionts differs from that of other members of the domain
Bacteria
in the lack of a sequence complementary to the mRNA ribosome binding site. The rate of sequence change in the 16S-23S rDNA of the psyllid P endosymbiont was considerably higher than that of other bacteria, including other fast-evolving insect endosymbionts. The lineage consisting of the P endosymbionts of psyllids was given the designation
Candidatus
Carsonella (gen. nov.) with a single species,
Candidatus
Carsonella ruddii (sp. nov.).
A Genomic Sample Sequence of the Entomopathogenic Bacterium
Photorhabdus luminescens
W14: Potential Implications for Virulence
Authors: Ffrench-Constant Richard H. , Waterfield Nicholas , Burland Valerie , Perna Nicole T. , Daborn Phillip J. , Bowen David , Blattner Frederick R. 
Published: July 2002

ABSTRACT

Photorhabdus luminescens
is a pathogenic bacterium that lives in the guts of insect-pathogenic nematodes. After invasion of an insect host by a nematode, bacteria are released from the nematode gut and help kill the insect, in which both the bacteria and the nematodes subsequently replicate. However, the bacterial virulence factors associated with this “symbiosis of pathogens” remain largely obscure. In order to identify genes encoding potential virulence factors, we performed ∼2,000 random sequencing reads from a
P. luminescens
W14 genomic library. We then compared the sequences obtained to sequences in existing gene databases and to the
Escherichia coli
K-12 genome sequence. Here we describe the different classes of potential virulence factors found. These factors include genes that putatively encode Tc insecticidal toxin complexes, Rtx-like toxins, proteases and lipases, colicin and pyocins, and various antibiotics. They also include a diverse array of secretion (e.g., type III), iron uptake, and lipopolysaccharide production systems. We speculate on the potential functions of each of these gene classes in insect infection and also examine the extent to which the invertebrate pathogen
P. luminescens
shares potential antivertebrate virulence factors. The implications for understanding both the biology of this insect pathogen and links between the evolution of vertebrate virulence factors and the evolution of invertebrate virulence factors are discussed.
Expression of a Functional Antizearalenone Single-Chain Fv Antibody in Transgenic
Arabidopsis
Plants
Authors: Yuan Qiaoping , Hu Wenqi , Pestka James J. , He Sheng Yang , Hart L. Patrick 
Published: July 2002

ABSTRACT

The efficacy of cloning a recombinant mycotoxin antibody in plants was tested using
Arabidopsis
as a model. An antizearalenone single-chain Fv (scFv) DNA fragment was first cloned in the newly constructed phage display vector (pEY.5) and then recloned in the plant transformation vector pKYLX71::35S
2
. After transformation, constructs of antizearalenone scFv were introduced into immature
Arabidopsis
seeds via
Agrobacterium tumefaciens
mediation by vacuum infiltration. Only plants transformed with the construct containing a PR-1b signal peptide sequence produced transgenic offspring. The antizearalenone scFv “plantibody” from these transgenic plants bound zearalenone with a high affinity (50% inhibitory concentration, 11.2 ng/ml) that was comparable to that of bacterially produced scFv antibody and the parent monoclonal antibody (MAb). By electron microscopic immunogold labeling, the presence of antizearalenone scFv was detected mainly in the cytoplasm and only occasionally outside the cell. Like bacterially produced scFv antibody, antizearalenone scFv plantibody exhibited greater sensitivity to methanol destabilization than did the parent MAb. The sensitivity of antizearalenone scFv plantibody to acidic disassociation was similar to the sensitivities of bacterially produced scFv antibody and MAb. Expression of specific plantibodies in crops might be useful for neutralizing mycotoxins in animal feeds and for reducing mycotoxin-associated plant diseases.
Production of Poly(3-Hydroxybutyrate) by Fed-Batch Culture of Recombinant
Escherichia coli
with a Highly Concentrated Whey Solution
Authors: Ahn Woo Suk , Park Si Jae , Lee Sang Yup 
Published: July 2002

ABSTRACT

Fermentation strategies for the production of poly(3-hydroxybutyrate) (PHB) from whey by recombinant
Escherichia coli
strain CGSC 4401 harboring the
Alcaligenes latus
polyhydroxyalkanoate (PHA) biosynthesis genes were developed. The pH-stat fed-batch cultures of
E. coli
CGSC 4401 harboring pJC4, a stable plasmid containing the
A. latus
PHA biosynthesis genes, were carried out with a concentrated whey solution containing 280 g of lactose equivalent per liter. Final cell and PHB concentrations of 119.5 and 96.2 g/liter, respectively, were obtained in 37.5 h, which resulted in PHB productivity of 2.57 g/liter/h.
Identification of a Novel Metabolite in the Degradation of Pyrene by
Mycobacterium
sp. Strain AP1: Actions of the Isolate on Two- and Three-Ring Polycyclic Aromatic Hydrocarbons
Authors: Vila Joaquim , López Zaira , Sabaté Jordi , Minguillón Cristina , Solanas Anna M. , Grifoll Magdalena 
Published: July 2002

ABSTRACT

Mycobacterium
sp. strain AP1 grew with pyrene as a sole source of carbon and energy. The identification of metabolites accumulating during growth suggests that this strain initiates its attack on pyrene by either monooxygenation or dioxygenation at its C-4, C-5 positions to give
trans-
or
cis-
4,5-dihydroxy-4,5-dihydropyrene, respectively. Dehydrogenation of the latter,
ortho
cleavage of the resulting diol to form phenanthrene 4,5-dicarboxylic acid, and subsequent decarboxylation to phenanthrene 4-carboxylic acid lead to degradation of the phenanthrene 4-carboxylic acid via phthalate. A novel metabolite identified as 6,6′-dihydroxy-2,2′-biphenyl dicarboxylic acid demonstrates a new branch in the pathway that involves the cleavage of both central rings of pyrene. In addition to pyrene, strain AP1 utilized hexadecane, phenanthrene, and fluoranthene for growth. Pyrene-grown cells oxidized the methylenic groups of fluorene and acenaphthene and catalyzed the dihydroxylation and
ortho
cleavage of one of the rings of naphthalene and phenanthrene to give 2-carboxycinnamic and diphenic acids, respectively. The catabolic versatility of strain AP1 and its use of
ortho
cleavage mechanisms during the degradation of polycyclic aromatic hydrocarbons (PAHs) give new insight into the role that pyrene-degrading bacterial strains may play in the environmental fate of PAH mixtures.
Characteristics of a
Streptomyces coelicolor
A3(2) Extracellular Protein Targeting Chitin and Chitosan
Authors: Saito Akihiro , Miyashita Kiyotaka , Biuković Goran , Schrempf Hildgund 
Published: July 2002

ABSTRACT

Upstream of the
Streptomyces coelicolor
A3(2) chitinase G gene, a small gene (named
chb3
) is located whose deduced product shares 37% identical amino acids with the previously described CHB1 protein from
Streptomyces olivaceoviridis
. The
chb3
gene and its upstream region were cloned in a multicopy vector and transformed into the plasmid-free
Streptomyces lividans
TK21 strain. The CHB3 protein (14.9 kDa) was secreted by the
S. lividans
TK21 transformant during growth in the presence of glucose,
N
-acetylglucosamine, yeast extract, and chitin. The protein was purified to homogeneity using anionic exchange, hydrophobic interaction chromatographies, and gel filtration. In contrast to CHB1, CHB3 targets α-chitin, β-chitin, and chitosan at pH 6.0 but does so relatively loosely. The ecological implications of the divergence of substrate specificity of various types of chitin-binding proteins are described.
Quorum-Sensing Genes in
Pseudomonas aeruginosa
Biofilms: Their Role and Expression Patterns
Authors: De Kievit Teresa R. , Gillis Richard , Marx Steve , Brown Chris , Iglewski Barbara H. 
Published: July 2002

ABSTRACT

Acylated homoserine lactone molecules are used by a number of gram-negative bacteria to regulate cell density-dependent gene expression by a mechanism known as quorum sensing (QS). In
Pseudomonas aeruginosa
, QS or cell-to-cell signaling controls expression of a number of virulence factors, as well as biofilm differentiation. In this study, we investigated the role played by the
las
and
rhl
QS systems during the early stages of static biofilm formation when cells are adhering to a surface and forming microcolonies. These studies revealed a marked difference in biofilm formation between the PAO1 parent and the QS mutants when glucose, but not citrate, was used as the sole carbon source. To further elucidate the contribution of
lasI
and
rhlI
to biofilm maturation, we utilized fusions to unstable green fluorescent protein in concert with confocal microscopy to perform real-time temporal and spatial studies of these genes in a flowing environment. During the course of 8-day biofilm development,
lasI
expression was found to progressively decrease over time. Conversely,
rhlI
expression remained steady throughout biofilm development but occurred in a lower percentage of cells. Spatial analysis revealed that
lasI
and
rhlI
were maximally expressed in cells located at the substratum and that expression decreased with increasing biofilm height. Because QS was shown previously to be involved in biofilm differentiation, these findings have important implications for the design of biofilm prevention and eradication strategies.
Genotypic Analysis of
Escherichia coli
Strains from Poultry Carcasses and Their Susceptibilities to Antimicrobial Agents
Authors: Geornaras Ifigenia , Hastings John W. , von Holy Alexander 
Published: July 2002

ABSTRACT

Plasmid profiling and amplified fragment length polymorphism (AFLP) analysis were used to genotype 50
Escherichia coli
strains from poultry carcasses. Thirty different plasmid profiles were evident, and clustering of the AFLP data showed that they were a distinctly heterogeneous group of strains. Susceptibility testing against five antimicrobial agents used in the South African poultry industry showed all strains to be susceptible to danofloxacin and colistin, while the majority (96%) were resistant to two tetracyclines.
Spontaneous Formation of a Mannitol-Producing Variant of
Leuconostoc pseudomesenteroides
Grown in the Presence of Fructose
Authors: Grobben Gert J. , Peters Sjors W. P. G. , Wisselink H. Wouter , Weusthuis Ruud A. , Hoefnagel Marcel H. N. , Hugenholtz Jeroen , Eggink Gerrit 
Published: July 2002

ABSTRACT

We report the spontaneous formation of a stable mannitol-producing variant of
Leuconostoc pseudomesenteroides
. The mannitol-producing variant showed mannitol dehydrogenase activity which was absent in the parental strain. It was also able to use fructose and glucose simultaneously, whereas the parental strain showed diauxic growth with these sugars. A possible explanation of these observations is discussed.
Chlorine Dioxide Inactivation of
Cryptosporidium parvum
Oocysts and Bacterial Spore Indicators
Authors: Chauret Christian P. , Radziminski Chris Z. , Lepuil Michael , Creason Robin , Andrews Robert C. 
Published: July 2002

ABSTRACT

Cryptosporidium parvum
, which is resistant to chlorine concentrations typically used in water treatment, is recognized as a significant waterborne pathogen. Recent studies have demonstrated that chlorine dioxide is a more efficient disinfectant than free chlorine against
Cryptosporidium
oocysts. It is not known, however, if oocysts from different suppliers are equally sensitive to chlorine dioxide. This study used both a most-probable-number–cell culture infectivity assay and in vitro excystation to evaluate chlorine dioxide inactivation kinetics in laboratory water at pH 8 and 21°C. The two viability methods produced significantly different results (
P
< 0.05). Products of disinfectant concentration and contact time (
Ct
values) of 1,000 mg · min/liter were needed to inactivate approximately 0.5 log
10
and 2.0 log
10
units (99% inactivation) of
C. parvum
as measured by in vitro excystation and cell infectivity, respectively, suggesting that excystation is not an adequate viability assay. Purified oocysts originating from three different suppliers were evaluated and showed marked differences with respect to their resistance to inactivation when using chlorine dioxide.
Ct
values of 75, 550, and 1,000 mg · min/liter were required to achieve approximately 2.0 log
10
units of inactivation with oocysts from different sources. Finally, the study compared the relationship between easily measured indicators, including
Bacillus subtilis
(aerobic) spores and
Clostridium sporogenes
(anaerobic) spores, and
C. parvum
oocysts. The bacterial spores were found to be more sensitive to chlorine dioxide than
C. parvum
oocysts and therefore could not be used as direct indicators of
C. parvum
inactivation for this disinfectant. In conclusion, it is suggested that future studies address issues such as oocyst purification protocols and the genetic diversity of
C. parvum
, since these factors might affect oocyst disinfection sensitivity.
Adhesion of Bifidobacteria to Granular Starch and Its Implications in Probiotic Technologies
Authors: Crittenden R. , Laitila A. , Forssell P. , Mättö J. , Saarela M. , Mattila-Sandholm T. , Myllärinen P. 
Published: July 2002

ABSTRACT

Adhesion of 19
Bifidobacterium
strains to native maize, potato, oat, and barley starch granules was examined to investigate links between adhesion and substrate utilization and to determine if adhesion to starch could be exploited in probiotic food technologies. Starch adhesion was not characteristic of all the bifidobacteria tested. Adherent bacteria bound similarly to the different types of starch, and the binding capacity of the starch (number of bacteria per gram) correlated to the surface area of the granules. Highly adherent strains were able to hydrolyze the granular starches, but not all amylolytic strains were adherent, indicating that starch adhesion is not a prerequisite for efficient substrate utilization for all bifidobacteria. Adhesion was mediated by a cell surface protein(s). For the model organisms tested (
Bifidobacterium adolescentis
VTT E-001561 and
Bifidobacterium pseudolongum
ATCC 25526), adhesion appeared to be specific for α-1,4-linked glucose sugars, since adhesion was inhibited by maltose, maltodextrin, amylose, and soluble starch but not by trehalose, cellobiose, or lactose. In an in vitro gastric model, adhesion was inhibited both by the action of protease and at pH values of ≤3. Adhesion was not affected by bile, but the binding capacity of the starch was reduced by exposure to pancreatin. It may be possible to exploit adhesion of probiotic bifidobacteria to starch granules in microencapsulation technology and for synbiotic food applications.
Methane Oxidation and the Competition for Oxygen in the Rice Rhizosphere
Authors: van Bodegom Peter , Stams Fons , Mollema Liesbeth , Boeke Sara , Leffelaar Peter 
Published: July 2002

ABSTRACT

A mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. In flooded rice paddies these methanotrophs compete for available O
2
with other types of bacteria. Soil incubation studies and most-probable-number (MPN) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. MPN counts of methanotrophs showed large spatial and temporal variability. The most abundant methanotrophs (a
Methylocystis
sp.) and heterotrophs (a
Pseudomonas
sp. and a
Rhodococcus
sp.) were isolated and characterized. Growth dynamics of these bacteria under carbon and oxygen limitations are presented. Theoretical calculations based on measured growth dynamics show that methanotrophs were only able to outcompete heterotrophs at low oxygen concentrations (frequently <5 μM). The oxygen concentration at which methanotrophs won the competition from heterotrophs did not depend on methane concentration, but it was highly affected by organic carbon concentrations in the paddy soil. Methane oxidation was severely inhibited at high acetate concentrations. This is in accordance with competition experiments between
Pseudomonas
spp. and
Methylocystis
spp. carried out at different oxygen and carbon concentrations. Likely, methane oxidation mainly occurs at microaerophilic and low-acetate conditions and thus not directly at the root surface. Acetate and oxygen concentrations in the rice rhizosphere are in the critical range for methane oxidation, and a high variability in methane oxidation rates is thus expected.
Effectiveness of Germicidal UV Radiation for Reducing Fungal Contamination within Air-Handling Units
Authors: Levetin Estelle , Shaughnessy Richard , Rogers Christine A. , Scheir Robert 
Published: July 2002

ABSTRACTLevels of fungi growing on insulation within air-handling units (AHUs) in an office building and levels of airborne fungi within AHUs were measured before the use of germicidal UV light and again after 4 months of operation. The fungal levels following UV operation were significantly lower than the levels in control AHUs.