bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium aviumGenes Associated with the Ability To Form a Biofilm
Authors: Yamazaki Yoshitaka , Danelishvili Lia , Wu Martin , MacNab Molly , Bermudez Luiz E. 
Published: January 2006

ABSTRACTMycobacterium aviumis widely distributed in the environment, and it is chiefly found in water and soil.M. avium, as well asMycobacterium smegmatis, has been recognized to produce a biofilm or biofilm-like structure. We screened anM. aviumgreen fluorescent protein (GFP) promoter library inM. smegmatisfor genes involved in biofilm formation on polyvinyl chloride (PVC) plates. Clones associated with increased GFP expression ≥2.0-fold over the baseline were sequenced. Seventeen genes, most encoding proteins of the tricarboxylic acid (TCA) cycle and GDP-mannose and fatty acid biosynthesis, were identified. Their regulation inM. aviumwas confirmed by examining the expression of a set of genes by real-time PCR after incubation on PVC plates. In addition, screening of 2,000 clones of a transposon mutant bank constructed usingM. aviumstrain A5, a mycobacterial strain with the ability to produce large amounts of biofilm, revealed four mutants with an impaired ability to form biofilm. Genes interrupted by transposons were homologues ofM. tuberculosis6-oxodehydrogenase (sucA), enzymes of the TCA cycle, protein synthetase (pstB), enzymes of glycopeptidolipid (GPL) synthesis, and Rv1565c (a hypothetical membrane protein). In conclusion, it appears that GPL biosynthesis, including the GDP-mannose biosynthesis pathway, is the most important pathway involved in the production ofM. aviumbiofilm.
Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes for Rapid Detection of
Mycobacterium avium
subsp.
avium
and
Mycobacterium avium
subsp.
paratuberculosis
in Potable-Water Biofilms
Authors: Lehtola Markku J. , Torvinen Eila , Miettinen Ilkka T. , Keevil C. William 
Published: January 2006

ABSTRACT

Here, we present for the first time a high-affinity peptide nucleic acid (PNA) oligonucleotide sequence for detecting
Mycobacterium avium
bacteria, including the opportunistically pathogenic subspecies
M. avium
subsp.
avium
,
M. avium
subsp.
paratuberculosis
, and
M. avium
subsp.
silvaticum
, by the fluorescence in situ hybridization (FISH) method. There is evidence that
M. avium
subsp.
avium
especially is able to survive and grow in drinking-water biofilms and possibly transmit via drinking water. The designed PNA probe (MAV148) specificity was tested with several bacterial species, including other mycobacteria and mycolic acid-containing bacteria. From the range of bacterial strains tested, only
M. avium
subsp.
avium
and
M. avium
subsp.
paratuberculosis
strains were hybridized. The PNA FISH method was applied successfully to detect
M. avium
subsp.
avium
spiked in water samples and biofilm established within a Propella biofilm reactor fed with potable water from a distribution supply.
Replication and Long-Term Persistence of Bovine and Human Strains of
Mycobacterium avium
subsp.
paratuberculosis
within
Acanthamoeba polyphaga
Authors: Mura Manuela , Bull Tim J. , Evans Hugh , Sidi-Boumedine Karim , McMinn Liz , Rhodes Glenn , Pickup Roger , Hermon-Taylor John 
Published: January 2006

ABSTRACT

Free-living protists are ubiquitous in the environment and form a potential reservoir for the persistence of animal and human pathogens.
Mycobacterium avium
subsp.
paratuberculosis
is the cause of Johne's disease, a systemic infection accompanied by chronic inflammation of the intestine that affects many animals, including primates. Most humans with Crohn's disease are infected with this chronic enteric pathogen. Subclinical infection with
M. avium
subsp.
paratuberculosis
is widespread in domestic livestock. Infected animals excrete large numbers of robust organisms into the environment, but little is known about their ability to replicate and persist in protists. In the present study we fed laboratory cultures of
Acanthamoeba polyphaga
with bovine and human strains of
M. avium
subsp.
paratuberculosis
. Real-time PCR showed that the numbers of the pathogens fell over the first 4 to 8 days and recovered by 12 to 16 days. Encystment of the amoebic cultures after 4 weeks resulted in a 2-log reduction in the level of
M. avium
subsp.
paratuberculosis
, which returned to the original level by 24 weeks. Extracts of resection samples of human gut from 39 patients undergoing abdominal surgery were fed to cultures of
A. polyphaga. M. avium
subsp.
paratuberculosis
detected by nested IS
900
PCR with amplicon sequencing and visualized by IS
900
in situ hybridization and auramine-rhodamine staining was found in cultures derived from 13 of the patients and was still present in the cultures after almost 4 years of incubation. Control cultures were negative.
M. avium
subsp.
paratuberculosis
has the potential for long-term persistence in environmental protists.
Rapid Quantification of the Toxic Alga
Prymnesium parvum
in Natural Samples by Use of a Specific Monoclonal Antibody and Solid-Phase Cytometry
Authors: West N. J. , Bacchieri R. , Hansen G. , Tomas C. , Lebaron P. , Moreau H. 
Published: January 2006

ABSTRACT

The increasing incidence of harmful algal blooms around the world and their associated health and economic effects require the development of methods to rapidly and accurately detect and enumerate the target species. Here we describe use of a solid-phase cytometer to detect and enumerate the toxic alga
Prymnesium parvum
in natural samples, using a specific monoclonal antibody and indirect immunofluorescence. The immunoglobulin G antibody 16E4 exhibited narrow specificity in that it recognized several
P. parvum
strains and a
Prymnesium nemamethecum
strain but it did not cross-react with
P. parvum
strains from Scandinavia or any other algal strains, including species of the closely related genus
Chrysochromulina. Prymnesium
sp. cells labeled with 16E4 were readily detected by the solid-phase cytometer because of the large fluorescence signal and the signal/noise ratio. Immunofluorescence detection and enumeration of cultured
P. parvum
cells preserved with different fixatives showed that the highest cell counts were obtained when cells were fixed with either glutaraldehyde or formaldehyde plus the cell protectant Pluronic F-68, whereas the use of formaldehyde alone resulted in significantly lower counts. Immunofluorescence labeling and analysis with the solid-phase cytometer of fixed natural samples from a bloom of
P. parvum
occurring in Lake Colorado in Texas gave cell counts that were close to those obtained by the traditional method of counting using light microscopy. These results show that a solid-phase cytometer can be used to rapidly enumerate natural
P. parvum
cells and that it could be used to detect other toxic algae, with an appropriate antibody or DNA probe.
Novel Surface Display System for Proteins on Non-Genetically Modified Gram-Positive Bacteria
Authors: Bosma Tjibbe , Kanninga Rolf , Neef Jolanda , Audouy Sandrine A. L. , van Roosmalen Maarten L. , Steen Anton , Buist Girbe , Kok Jan , Kuipers Oscar P. , Robillard George , Leenhouts Kees 
Published: January 2006

ABSTRACT

A novel display system is described that allows highly efficient immobilization of heterologous proteins on bacterial surfaces in applications for which the use of genetically modified bacteria is less desirable. This system is based on nonliving and non-genetically modified gram-positive bacterial cells, designated gram-positive enhancer matrix (GEM) particles, which are used as substrates to bind externally added heterologous proteins by means of a high-affinity binding domain. This binding domain, the protein anchor (PA), was derived from the
Lactococcus lactis
peptidoglycan hydrolase AcmA. GEM particles were typically prepared from the innocuous bacterium
L. lactis
, and various parameters for the optimal preparation of GEM particles and binding of PA fusion proteins were determined. The versatility and flexibility of the display and delivery technology were demonstrated by investigating enzyme immobilization and nasal vaccine applications.
Cellular Response of
Shewanella oneidensis
to Strontium Stress
Authors: Brown Steven D. , Martin Madhavi , Deshpande Sameer , Seal Sudipta , Huang Katherine , Alm Eric , Yang Yunfeng , Wu Liyou , Yan Tingfen , Liu Xueduan , Arkin Adam , Chourey Karuna , Zhou Jizhong , Thompson Dorothea K. 
Published: January 2006

ABSTRACT

The physiology and transcriptome dynamics of the metal ion-reducing bacterium
Shewanella oneidensis
strain MR-1 in response to nonradioactive strontium (Sr) exposure were investigated. Studies indicated that MR-1 was able to grow aerobically in complex medium in the presence of 180 mM SrCl
2
but showed severe growth inhibition at levels above that concentration. Temporal gene expression profiles were generated from aerobically grown, mid-exponential-phase MR-1 cells shocked with 180 mM SrCl
2
and analyzed for significant differences in mRNA abundance with reference to data for nonstressed MR-1 cells. Genes with annotated functions in siderophore biosynthesis and iron transport were among the most highly induced (>100-fold [
P
< 0.05]) open reading frames in response to acute Sr stress, and a mutant (SO3032::pKNOCK) defective in siderophore production was found to be hypersensitive to SrCl
2
exposure, compared to parental and wild-type strains. Transcripts encoding multidrug and heavy metal efflux pumps, proteins involved in osmotic adaptation, sulfate ABC transporters, and assimilative sulfur metabolism enzymes also were differentially expressed following Sr exposure but at levels that were several orders of magnitude lower than those for iron transport genes. Precipitate formation was observed during aerobic growth of MR-1 in broth cultures amended with 50, 100, or 150 mM SrCl
2
but not in cultures of the SO3032::pKNOCK mutant or in the abiotic control. Chemical analysis of this precipitate using laser-induced breakdown spectroscopy and static secondary ion mass spectrometry indicated extracellular solid-phase sequestration of Sr, with at least a portion of the heavy metal associated with carbonate phases.
Role of Tryptophan Residues in Toxicity of Cry1Ab Toxin from
Bacillus thuringiensis
Authors: Padilla Cristopher , Pardo-López Liliana , de la Riva Gustavo , Gómez Isabel , Sánchez Jorge , Hernandez Georgina , Nuñez Maria Eugenia , Carey Marianne P. , Dean Donald H. , Alzate Oscar , Soberón Mario , Bravo Alejandra 
Published: January 2006

ABSTRACT

Bacillus thuringiensis
produces insecticidal proteins (Cry protoxins) during the sporulation phase as parasporal crystals. During intoxication, the Cry protoxins must change from insoluble crystals into membrane-inserted toxins which form ionic pores. The structural changes of Cry toxins during oligomerization and insertion into the membrane are still unknown. The Cry1Ab toxin has nine tryptophan residues; seven are located in domain I, the pore-forming domain, and two are located in domain II, which is involved in receptor recognition. Eight Trp residues are highly conserved within the whole family of three-domain Cry proteins, suggesting an essential role for these residues in the structural folding and function of the toxin. In this work, we analyzed the role of Trp residues in the structure and function of Cry1Ab toxin. We replaced the Trp residues with phenylalanine or cysteine using site-directed mutagenesis. Our results show that W65 and W316 are important for insecticidal activity of the toxin since their replacement by Phe reduced the toxicity against
Manduca sexta
. The presence of hydrophobic residue is important at positions 117, 219, 226, and 455 since replacement by Cys affected either the crystal formation or the insecticidal activity of the toxin in contrast to replacement by Phe in these positions. Additionally, some mutants in positions 219, 316, and 455 were also affected in binding to brush border membrane vesicles (BBMV). This is the first report that studies the role of Trp residues in the activity of Cry toxins.
Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization Allows for Enrichment-Independent Detection of Microcolony-Forming Soil Bacteria
Authors: Ferrari Belinda C. , Tujula Niina , Stoner Kate , Kjelleberg Staffan 
Published: January 2006

ABSTRACT
Advances in the growth of hitherto unculturable soil bacteria have emphasized the requirement for rapid bacterial identification methods. Due to the slow-growing strategy of microcolony-forming soil bacteria, successful fluorescence in situ hybridization (FISH) requires an rRNA enrichment step for visualization. In this study, catalyzed reporter deposition (CARD)-FISH was employed as an alternative method to rRNA enhancement and was found to be superior to conventional FISH for the detection of microcolonies that are cultivated by using the soil substrate membrane system. CARD-FISH enabled real-time identification of oligophilic microcolony-forming soil bacteria without the requirement for enrichment on complex media and the associated shifts in community composition.
The
Bifidobacterium longum
NCIMB 702259
T
ctr
Gene Codes for a Novel Cholate Transporter
Authors: Price Claire E. , Reid Sharon J. , Driessen Arnold J. M. , Abratt Valerie R. 
Published: January 2006

ABSTRACT

Preexposure of
Bifidobacterium longum
NCIMB 702259
T
to cholate caused increased resistance to cholate, chloramphenicol, and erythromycin. The
B. longum ctr
gene, encoding a cholate efflux transporter, was transformed into the efflux-negative mutant
Escherichia coli
KAM3, conferring resistance to bile salts and other antimicrobial compounds and causing the efflux of [
14
C]cholate.
Immobilization of Cells with Surface-Displayed Chitin-Binding Domain
Authors: Wang Jen-You , Chao Yun-Peng 
Published: January 2006

ABSTRACT

To explore chitin-binding domain (ChBD)-based cell immobilization, a tripartite gene fusion consisting of an in-frame fusion of ChBD to
lpp
and
ompA
was constructed and expressed in
Escherichia coli
. ChBD-displayed cells exhibited highly specific and stable binding to chitin within a wide range of pHs (5 to 8) and temperatures (15 to 37°C). These results illustrate the promising use of this approach for engineering applications.
Naturally Transformable
Acinetobacter
sp. Strain ADP1 Belongs to the Newly Described Species
Acinetobacter baylyi
Authors: Vaneechoutte Mario , Young David M. , Ornston L. Nicholas , De Baere Thierry , Nemec Alexandr , Van Der Reijden Tanny , Carr Emma , Tjernberg Ingela , Dijkshoorn Lenie 
Published: January 2006

ABSTRACT

Genotypic and phenotypic analyses were carried out to clarify the taxonomic position of the naturally transformable
Acinetobacter
sp. strain ADP1. Transfer tDNA-PCR fingerprinting, 16S rRNA gene sequence analysis, and selective restriction fragment amplification (amplified fragment length polymorphism analysis) indicate that strain ADP1 and a second transformable strain, designated 93A2, are members of the newly described species
Acinetobacter baylyi
. Transformation assays demonstrate that the
A. baylyi
type strain B2
T
and two other originally identified members of the species (C5 and A7) also have the ability to undergo natural transformation at high frequencies, confirming that these five strains belong to a separate species of the genus
Acinetobacter
, characterized by the high transformability of its strains that have been cultured thus far.
Autoinducer 2 Affects Biofilm Formation byBacillus cereus
Authors: Auger Sandrine , Krin Evelyne , Aymerich Stéphane , Gohar Michel 
Published: January 2006

ABSTRACTCell-free supernatants from growingBacillus cereusstrain ATCC 10987 induced luminescence in aPhotorhabdus luminescensΔluxSmutant, indicating the production of functional autoinducer 2 (AI-2). The exogenous addition of in vitro synthesized AI-2 had an inhibitory effect on biofilm formation byB. cereusand promoted release of the cells from a preformed biofilm.
Multiphasic Approach To Study the Bacterial Ecology of Fermented Sausages Inoculated with a Commercial Starter Culture
Authors: Cocolin Luca , Urso Rosalinda , Rantsiou Kalliopi , Cantoni Carlo , Comi Giuseppe 
Published: January 2006

ABSTRACT

In this paper, the ability of a commercial starter culture to perform a sausage fermentation is evaluated. Molecular analysis revealed the presence of several strains of the same species contained in the starter culture with different behavior during the fermentation, and the contribution of
Lactobacillus curvatus
, which was only marginally isolated during the transformation.
Butyrate Specifically Down-Regulates
Salmonella
Pathogenicity Island 1 Gene Expression
Authors: Gantois I. , Ducatelle R. , Pasmans F. , Haesebrouck F. , Hautefort I. , Thompson A. , Hinton J. C. , Van Immerseel F. 
Published: January 2006

ABSTRACT

Invasion of intestinal epithelial cells by
Salmonella enterica
is decreased after exposure to butyric acid. To understand the molecular mechanisms of this phenomenon, a comparative transcriptomic analysis of
Salmonella enterica
serovar Enteritidis and
Salmonella enterica
serovar Typhimurium grown in medium supplemented with butyrate was performed. We found that butyrate down-regulated the expression of 19 genes common to both serovars by a factor of twofold or more, and 17 of these genes localized to the
Salmonella
pathogenicity island 1 (SPI1). These included the SPI1 regulatory genes
hilD
and
invF
. Of the remaining two genes,
ampH
has 91% homology to an
Escherichia coli
penicillin-binding protein and
sopE2
encodes a type III-secreted effector protein associated with invasion but located at a separate site on the chromosome from SPI1.
Propane and
n
-Butane Oxidation by
Pseudomonas putida
GPo1
Authors: Johnson Erika L. , Hyman Michael R. 
Published: January 2006

ABSTRACT

Propane and
n
-butane inhibit methyl
tertiary
butyl ether oxidation by
n-
alkane-grown
Pseudomonas putida
GPo1. Here we demonstrate that these gases are oxidized by this strain and support cell growth. Both gases induced alkane hydroxylase activity and appear to be oxidized by the same enzyme system used for the oxidation of
n-
octane.
HacA-Independent Induction of Chaperone-Encoding Gene
bipA
in
Aspergillus niger
Strains Overproducing Membrane Proteins
Authors: Davé Anoushka , Jeenes David J. , Mackenzie Donald A. , Archer David B. 
Published: January 2006

ABSTRACT

Transcription of two unfolded protein response genes,
hacA
and
bipA
, was examined in
Aspergillus niger
strains overproducing membrane proteins. Despite elevated
bipA
mRNA levels, no 5′-truncated
hacA
transcript was detected, raising the possibility of a
hacA
-independent induction of
bipA
mRNA under the stress of membrane protein overproduction in
A. niger
.
Emergence of Biofilm-Forming Subpopulations upon Exposure of
Escherichia coli
to Environmental Bacteriophages
Authors: Lacqua Andrea , Wanner Oskar , Colangelo Teresa , Martinotti Maria Giovanna , Landini Paolo 
Published: January 2006

ABSTRACT

Exposure of
Escherichia coli
MG1655 to environmental bacteriophages results in rapid selection for phage-tolerant subpopulations displaying increased biofilm formation. Analysis of one phage-tolerant strain revealed large amounts of the DNA-binding Dps protein in the outer membrane protein and production of fimbria-like structures. In
dps
and
fimA
mutant derivatives of MG1655, no selection of phage-tolerant bacteria upon exposure to bacteriophages occurred, suggesting a role for Dps and type I pili in bacteriophage tolerance.
Microbial Conversion of Glycerol to 1,3-Propanediol: Physiological Comparison of a Natural Producer,
Clostridium butyricum
VPI 3266, and an Engineered Strain,
Clostridium acetobutylicum
DG1(pSPD5)
Authors: González-Pajuelo María , Meynial-Salles Isabelle , Mendes Filipa , Soucaille Philippe , Vasconcelos Isabel 
Published: January 2006

ABSTRACT

Clostridium acetobutylicum
is not able to grow on glycerol as the sole carbon source since it cannot reoxidize the excess of NADH generated by glycerol catabolism. Nevertheless, when the pSPD5 plasmid, carrying the NADH-consuming 1,3-propanediol pathway from
C. butyricum
VPI 3266, was introduced into
C. acetobutylicum
DG1, growth on glycerol was achieved, and 1,3-propanediol was produced. In order to compare the physiological behavior of the recombinant
C. acetobutylicum
DG1(pSPD5) strain with that of the natural 1,3-propanediol producer
C. butyricum
VPI 3266, both strains were grown in chemostat cultures with glycerol as the sole carbon source. The same “global behavior” was observed for both strains: 1,3-propanediol was the main fermentation product, and the qH
2
flux was very low. However, when looking at key intracellular enzyme levels, significant differences were observed. Firstly, the pathway for glycerol oxidation was different:
C. butyricum
uses a glycerol dehydrogenase and a dihydroxyacetone kinase, while
C. acetobutylicum
uses a glycerol kinase and a glycerol-3-phosphate dehydrogenase. Secondly, the electron flow is differentially regulated: (i) in
C. butyricum
VPI 3266, the in vitro hydrogenase activity is 10-fold lower than that in
C. acetobutylicum
DG1(pSPD5), and (ii) while the ferredoxin-NAD
+
reductase activity is high and the NADH-ferredoxin reductase activity is low in
C. acetobutylicum
DG1(pSPD5), the reverse is observed for
C. butyricum
VPI 3266. Thirdly, lactate dehydrogenase activity is only detected in the
C. acetobutylicum
DG1(pSPD5) culture, explaining why this microorganism produces lactate.
Presence of
Salmonella
and
Campylobacter
spp. in Wild Small Mammals on Organic Farms
Authors: Meerburg B. G. , Jacobs-Reitsma W. F. , Wagenaar J. A. , Kijlstra A. 
Published: January 2006

ABSTRACT

The presence of
Salmonella
and
Campylobacter
spp. in rodents and insectivores (
n
= 282) was investigated on organic farms. Infections were encountered in house mice (8 of 83
Campylobacter
positive and 1 of 83
Salmonella
sp. strain Livingstone positive) and brown rats (1 of 8
Campylobacter
positive) but not in other species. No shared
Campylobacter
genotypes were found between rodent and pig manure isolates. Effective on-farm rodent management is recommended.
Expression of the
ubiE
Gene of
Geobacillus stearothermophilus
V in
Escherichia coli
K-12 Mediates the Evolution of Selenium Compounds into the Headspace of Selenite- and Selenate-Amended Cultures
Authors: Swearingen J. W. , Fuentes D. E. , Araya M. A. , Plishker M. F. , Saavedra C. P. , Chasteen T. G. , Vásquez C. C. 
Published: January 2006

ABSTRACT

The
ubiE
gene of
Geobacillus stearothermophilus
V, with its own promoter, was cloned and introduced into
Escherichia coli
. The cloned gene complemented the
ubiE
gene deficiency of
E. coli
AN70. In addition, the expression of this gene in
E. coli
JM109 resulted in the evolution of volatile selenium compounds when these cells were grown in selenite- or selenate-amended media. These compounds were dimethyl selenide and dimethyl diselenide.
Characterization of a Novel PepF-Like Oligopeptidase Secreted by
Bacillus amyloliquefaciens
23-7A
Authors: Chao Shiou-Huei , Cheng Tzu-Hao , Shaw Chin-Ying , Lee Meng-Hwan , Hsu Yuan-Hsun , Tsai Ying-Chieh 
Published: January 2006

ABSTRACT

An oligopeptidase from
Bacillus amyloliquefaciens
23-7A was characterized along with its biochemical activities and structural gene. The protein's amino acid sequence and enzymatic activities were similar to those of other bacterial PepFs, which belong to metallopeptidase family M3. While most bacterial PepFs are cytoplasmic endopeptidases, the identified PepF
Ba
oligopeptidase is a secreted protein and may facilitate the process of sporulation.
Bilirubin Oxidase Activity of
Bacillus subtilis
CotA
Authors: Sakasegawa Shin-ichi , Ishikawa Hidehiko , Imamura Shigeyuki , Sakuraba Haruhiko , Goda Shuichiro , Ohshima Toshihisa 
Published: January 2006

ABSTRACT

The spore coat protein CotA from
Bacillus subtilis
was previously identified as a laccase. We have now found that CotA also shows strong bilirubin oxidase activity and markedly higher affinity for bilirubin than conventional bilirubin oxidase. This is the first characterization of bilirubin oxidase activity in a bacterial protein.