bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of Genomic Array Footprinting for Identification of Conditionally Essential Genes inStreptococcus pneumoniae
Authors: Bijlsma Jetta J. E. , Burghout Peter , Kloosterman Tomas G. , Bootsma Hester J. , de Jong Anne , Hermans Peter W. M. , Kuipers Oscar P. 
Published: January 2007

ABSTRACTStreptococcus pneumoniaeis a major cause of serious infections such as pneumonia and meningitis in both children and adults worldwide. Here, we describe the development of a high-throughput, genome-wide technique, genomic array footprinting (GAF), for the identification of genes essential for this bacterium at various stages during infection. GAF enables negative screens by means of a combination of transposon mutagenesis and microarray technology for the detection of transposon insertion sites. We tested several methods for the identification of transposon insertion sites and found that amplification of DNA adjacent to the insertion site by PCR resulted in nonreproducible results, even when combined with an adapter. However, restriction of genomic DNA followed directly by in vitro transcription circumvented these problems. Analysis of parallel reactions generated with this method on a largemarinertransposon library showed that it was highly reproducible and correctly identified essential genes. Comparison of amarinerlibrary to one generated with the in vivo transposition plasmid pGh:ISS1showed that both have an equal degree of saturation but that 9% of the genome is preferentially mutated by either one. The usefulness of GAF was demonstrated in a screen for genes essential for surviving zinc stress. This identified a gene encoding a putative cation efflux transporter, and its deletion resulted in an inability to grow under high-zinc conditions. In conclusion, we developed a fast, versatile, specific, and high-throughput method for the identification of conditionally essential genes inS. pneumoniae.
Erythromycin Resistance-Conferring Plasmid pRSB105, Isolated from a Sewage Treatment Plant, Harbors a New Macrolide Resistance Determinant, an Integron-Containing Tn
402
-Like Element, and a Large Region of Unknown Function
Authors: Schlüter A. , Szczepanowski R. , Kurz N. , Schneiker S. , Krahn I. , Pühler A. 
Published: January 2007

ABSTRACT

The erythromycin resistance plasmid pRSB105 was previously isolated from an activated sludge bacterial community of a municipal wastewater treatment plant. Compilation of the complete pRSB105 nucleotide sequence revealed that the plasmid is 57,137 bp in size and has a mean G+C content of 56.66 mol%. The pRSB105 backbone is composed of two different replication and/or partitioning modules and a functional mobilization region encoding the mobilization genes
mobCDE
and
mobBA
. The first replicon (Rep1) is nearly identical to the corresponding replication module of the multiresistance plasmid pRSB101 isolated from an unknown activated sludge bacterium. Accordingly, pRSB101 and pRSB105 are sister plasmids belonging to a new plasmid family. The second replicon (Rep2) of pRSB105 was classified as a member of the IncP-6 group. While Rep1 confers replication ability only in γ-proteobacteria, Rep2 extents the host range of the plasmid since it is also functional in the β-proteobacterium
Ralstonia eutropha
. Plasmid pRSB105 harbors the macrolide resistance genes
mel
and
mph
, encoding, respectively, a predicted ABC-type efflux permease and a macrolide-2′-phosphotransferase. Erythromycin resistance is mainly attributed to
mel
, whereas
mph
contributes to erythromycin resistance to a lesser extent. The second resistance region, represented by an integron-containing Tn
402
-like element, includes a β-lactam (
oxa10
) and a trimethoprim (
dfrB2
) resistance gene cassette. In addition to antibiotic resistance modules, pRSB105 encodes a functional restriction/modification system and two nonresistance regions of unknown function. The presence of different mobile genetic elements that flank resistance and nonresistance modules on pRSB105 indicates that these elements were involved in acquisition of accessory plasmid modules. Comparative genomics of pRSB105 and related plasmids elucidated that pRSB105 evolved by integration of distinct modules from different plasmid sources, including
Pseudomonas aeruginosa
plasmids, and thus represents a mosaic plasmid.
Methane Oxidation in Termite Hindguts: Absence of Evidence and Evidence of Absence
Authors: Pester Michael , Tholen Anne , Friedrich Michael W. , Brune Andreas 
Published: January 2007

ABSTRACT

A steep oxygen gradient and the presence of methane render the hindgut internal periphery of termites a potential habitat for aerobic methane-oxidizing bacteria. However, methane emissions of various termites increased, if at all, only slightly when termites were exposed to an anoxic (nitrogen) atmosphere, and
14
CH
4
added to the air headspace over live termites was not converted to
14
CO
2
. Evidence for the absence of methane oxidation in living termites was corroborated by the failure to detect
pmoA
, the marker gene for particulate methane monooxygenase, in hindgut DNA extracts of all termites investigated. This adds robustness to our concept of the degradation network in the termite hindgut and eliminates the gut itself as a potential sink of this important greenhouse gas.
Risk Factors for Contamination of Hotel Water Distribution Systems by
Legionella
Species
Authors: Mouchtouri Varvara , Velonakis Emmanuel , Tsakalof Andreas , Kapoula Christina , Goutziana Georgia , Vatopoulos Alkiviadis , Kremastinou Jenny , Hadjichristodoulou Christos 
Published: January 2007

ABSTRACT

The
Legionella
colonization frequency at 385 Greek hotel hot and cold water distribution systems was 20.8%.
Legionella
contamination was associated with the presence of an oil heater (odds ratio [OR] = 2.04, 95% confidence interval [CI] = 1.12 to 3.70), with the sample temperature (OR = 0.26, 95% CI = 0.1 to 0.5), with seasonal operation (OR = 3.23, 95% CI = 1.52 to 6.87), and with the presence of an independent disinfection system (OR = 0.30, 95% CI = 0.15 to 0.62). The same water temperatures, free-chlorine levels, and pHs differently affect the survival of various
Legionella
spp.
Does the Antibacterial Activity of Silver Nanoparticles Depend on the Shape of the Nanoparticle? A Study of the Gram-Negative Bacterium
Escherichia coli
Authors: Pal Sukdeb , Tak Yu Kyung , Song Joon Myong 
Published: January 2007

ABSTRACT

In this work we investigated the antibacterial properties of differently shaped silver nanoparticles against the gram-negative bacterium
Escherichia coli
, both in liquid systems and on agar plates. Energy-filtering transmission electron microscopy images revealed considerable changes in the cell membranes upon treatment, resulting in cell death. Truncated triangular silver nanoplates with a {111} lattice plane as the basal plane displayed the strongest biocidal action, compared with spherical and rod-shaped nanoparticles and with Ag
+
(in the form of AgNO
3
). It is proposed that nanoscale size and the presence of a {111} plane combine to promote this biocidal property. To our knowledge, this is the first comparative study on the bactericidal properties of silver nanoparticles of different shapes, and our results demonstrate that silver nanoparticles undergo a shape-dependent interaction with the gram-negative organism
E. coli
.
High-Level Production of the Low-Calorie Sugar Sorbitol by
Lactobacillus plantarum
through Metabolic Engineering
Authors: Ladero Victor , Ramos Ana , Wiersma Anne , Goffin Philippe , Schanck André , Kleerebezem Michiel , Hugenholtz Jeroen , Smid Eddy J. , Hols Pascal 
Published: January 2007

ABSTRACT

Sorbitol is a low-calorie sugar alcohol that is largely used as an ingredient in the food industry, based on its sweetness and its high solubility. Here, we investigated the capacity of
Lactobacillus plantarum
, a lactic acid bacterium found in many fermented food products and in the gastrointestinal tract of mammals, to produce sorbitol from fructose-6-phosphate by reverting the sorbitol catabolic pathway in a mutant strain deficient for both
l
- and
d
-lactate dehydrogenase activities. The two sorbitol-6-phosphate dehydrogenase (Stl6PDH) genes (
srlD1
and
srlD2
) identified in the genome sequence were constitutively expressed at a high level in this mutant strain. Both Stl6PDH enzymes were shown to be active, and high specific activity could be detected in the overexpressing strains. Using resting cells under pH control with glucose as a substrate, both Stl6PDHs were capable of rerouting the glycolytic flux from fructose-6-phosphate toward sorbitol production with a remarkably high efficiency (61 to 65% glucose conversion), which is close to the maximal theoretical value of 67%. Mannitol production was also detected, albeit at a lower level than the control strain (9 to 13% glucose conversion), indicating competition for fructose-6-phosphate rerouting by natively expressed mannitol-
1
-phosphate dehydrogenase. By analogy, low levels of this enzyme were detected in both the wild-type and the lactate dehydrogenase-deficient strain backgrounds. After optimization, 25% of sugar conversion into sorbitol was achieved with cells grown under pH control. The role of intracellular NADH pools in the determination of the maximal sorbitol production is discussed.
Production of Dehydroamino Acid-Containing Peptides by
Lactococcus lactis
Authors: Rink Rick , Wierenga Jenny , Kuipers Anneke , Kluskens Leon D. , Driessen Arnold J. M. , Kuipers Oscar P. , Moll Gert N. 
Published: January 2007

ABSTRACT

Nisin is a pentacyclic peptide antibiotic produced by some
Lactococcus lactis
strains. Nisin contains dehydroresidues and thioether rings that are posttranslationally introduced by a membrane-associated enzyme complex, composed of a serine and threonine dehydratase NisB and the cyclase NisC. In addition, the transporter NisT is necessary for export of the modified peptide. We studied the potential of
L. lactis
expressing NisB and NisT to produce peptides whose serines and threonines are dehydrated.
L. lactis
containing the
nisBT
genes and a plasmid coding for a specific leader peptide fusion construct efficiently produced peptides with a series of non-naturally occurring multiple flanking dehydrobutyrines. We demonstrated NisB-mediated dehydration of serines and threonines in a C-terminal nisin(1-14) extension of nisin, which implies that also residues more distant from the leader peptide than those occurring in prenisin or any other lantibiotic can be modified. Furthermore, the feasibility and efficiency of generating a library of peptides containing dehydroresidues were demonstrated. In view of the particular shape and reactivity of dehydroamino acids, such a library provides a novel source for screening for peptides with desired biological and physicochemical properties.
Adaptation of
Pseudomonas
sp. Strain 7-6 to Quaternary Ammonium Compounds and Their Degradation via Dual Pathways
Authors: Takenaka Shinji , Tonoki Takashi , Taira Kazuya , Murakami Shuichiro , Aoki Kenji 
Published: January 2007

ABSTRACT

Pseudomonas
sp. strain 7-6, isolated from active sludge obtained from a wastewater facility, utilized a quaternary ammonium surfactant,
n
-dodecyltrimethylammonium chloride (DTAC), as its sole carbon, nitrogen, and energy source. When initially grown in the presence of 10 mM DTAC medium, the isolate was unable to degrade DTAC. The strain was cultivated in gradually increasing concentrations of the surfactant until continuous exposure led to high tolerance and biodegradation of the compound. Based on the identification of five metabolites by gas chromatography-mass spectrometry analysis, two possible pathways for DTAC metabolism were proposed. In pathway 1, DTAC is converted to lauric acid via
n
-dodecanal with the release of trimethylamine; in pathway 2, DTAC is converted to lauric acid via
n
-dodecyldimethylamine and then
n
-dodecanal with the release of dimethylamine. Among the identified metabolites, the strain precultivated on DTAC medium could utilize
n
-dodecanal and lauric acid as sole carbon sources and trimethylamine and dimethylamine as sole nitrogen sources, but it could not efficiently utilize
n
-dodecyldimethylamine. These results indicated pathway 1 is the main pathway for the degradation of DTAC.
Genetic Relatedness of
Escherichia coli
Isolates in Interstitial Water from a Lake Huron (Canada) Beach
Authors: Kon Tatiana , Weir Susan C. , Howell E. Todd , Lee Hung , Trevors Jack T. 
Published: January 2007

ABSTRACT

Research was undertaken to characterize
Escherichia coli
isolates in interstitial water samples of a sandy beach on the southeastern shore of Lake Huron, Ontario, Canada. A survey of the beach area revealed the highest abundance of
E. coli
in interstitial water of the foreshore beach sand next to the swash zone. Higher concentrations of
E. coli
(up to 1.6 × 10
6
CFU/100 ml of water) were observed in the interstitial water from the sampling holes on the beach itself compared to lake water and sediment. Repetitive extragenic palindromic PCR (REP-PCR) was used to characterize the genetic diversity of
E. coli
isolates from interstitial water samples on the beach.
E. coli
isolates from the same sampling location frequently exhibited the same REP-PCR pattern or were highly similar to each other. In contrast,
E. coli
isolates from different sampling locations represented populations distinct from each other. This study has identified a unique ecological niche within the foreshore area of the beach where
E. coli
may survive and possibly multiply outside of host organisms. The results are of interest as increasing concentrations of
E. coli
in recreational waters are often considered to be an indication of recent fecal pollution.
Biofilm Formation by and Antifungal Susceptibility of
Candida
Isolates from Urine
Authors: Jain N. , Kohli R. , Cook E. , Gialanella P. , Chang T. , Fries B. C. 
Published: January 2007

ABSTRACT

Biofilm formation (BF) in the setting of candiduria has not been well studied. We determined BF and MIC to antifungals in
Candida
spp. isolates grown from urine samples of patients and performed a retrospective chart review to examine the correlation with risk factors. A total of 67
Candida
spp. isolates were grown from urine samples from 55 patients. The species distribution was
C. albicans
(54%),
C. glabrata
(36%), and
C. tropicalis
(10%). BF varied greatly among individual
Candida
isolates but was stable in sequential isolates during chronic infection. BF also depended on the growth medium and especially in
C. albicans
was significantly enhanced in artificial urine (AU) compared to RPMI medium. In nine of the
C. albicans
strains BF was 4- to 10-fold higher in AU, whereas in three of the
C. albicans
strains and two of the
C. glabrata
strains higher BF was measured in RPMI medium than in AU. Determination of the MICs showed that planktonic cells of all strains were susceptible to amphotericin B (AMB) and caspofungin (CASPO) and that three of the
C. glabrata
strains and two of the
C. albicans
strains were resistant to fluconazole (FLU). In contrast, all biofilm-associated adherent cells were resistant to CASPO and FLU. The biofilms of 14 strains (28%) were sensitive to AMB (MIC
50
of <1 μg/ml). Correlation between degree of BF and MIC of AMB was not seen in RPMI grown biofilms but was present when grown in AU. A retrospective chart review demonstrated no correlation of known risk factors of candiduria with BF in AU or RPMI. We conclude that BF is a stable characteristic of
Candida
strains that varies greatly among clinical strains and is dependent on the growth medium. Resistance to AMB is associated with higher BF in AU, which may represent the more physiologic medium to test BF. Future studies should address whether in vitro BF can predict treatment failure in vivo.
Simple Method for Repurification of Endotoxins for Biological Use
Authors: Tirsoaga Alina , Novikov Alexey , Adib-Conquy Minou , Werts Catherine , Fitting Catherine , Cavaillon Jean-Marc , Caroff Martine 
Published: January 2007

ABSTRACT
A method for obtaining highly purified endotoxin (lipopolysaccharide [LPS]) in a few hours by repurification of commercial or laboratory preparations was devised. It avoids the use of phenol, which is not suitable for phenol-soluble lipopolysaccharides nor for some industrial purposes. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization mass spectrometry analysis confirmed the integrity of the purified LPSs. The purified products did not activate Toll-like receptor 2 (TLR2), nuclear oligomerization domain 1 (NOD1), or NOD2 but did activate TLR4. Applied to different lipopolysaccharides, the method also improved their mass spectra, thus facilitating their structural analysis.
Biochemical Characterization of an
l
-Xylulose Reductase from
Neurospora crassa
Authors: Nair Nikhil , Zhao Huimin 
Published: January 2007

ABSTRACT

An
l
-xylulose reductase identified from the genome sequence of the filamentous fungus
Neurospora crassa
was heterologously expressed in
Escherichia coli
as a His
6
tag fusion protein, purified, and characterized. The enzyme may be used in the production of xylitol from the major pentose components of hemicellulosic waste,
d
-xylose and
l
-arabinose.
Se(VI) Reduction and the Precipitation of Se(0) by the Facultative Bacterium
Enterobacter cloacae
SLD1a-1 Are Regulated by FNR
Authors: Yee N. , Ma J. , Dalia A. , Boonfueng T. , Kobayashi D. Y. 
Published: January 2007

ABSTRACT

The fate of selenium in the environment is controlled, in part, by microbial selenium oxyanion reduction and Se(0) precipitation. In this study, we identified a genetic regulator that controls selenate reductase activity in the Se-reducing bacterium
Enterobacter cloacae
SLD1a-1. Heterologous expression of the global anaerobic regulatory gene
fnr
(fumarate nitrate reduction regulator) from
E. cloacae
in the non-Se-reducing strain
Escherichia coli
S17-1 activated the ability to reduce Se(VI) and precipitate insoluble Se(0) particles. Se(VI) reduction by
E. coli
S17-1 containing the
fnr
gene occurred at rates similar to those for
E. cloacae
, with first-order reaction constants of
k
= 2.07 × 10
−2
h
−1
and
k
= 3.36 × 10
−2
h
−1
, respectively, and produced elemental selenium particles with identical morphologies and short-range atomic orders. Mutation of the
fnr
gene in
E. cloacae
SLD1a-1 resulted in derivative strains that were deficient in selenate reductase activity and unable to precipitate elemental selenium. Complementation by the wild-type
fnr
sequence restored the ability of mutant strains to reduce Se(VI). Our findings suggest that Se(VI) reduction and the precipitation of Se(0) by facultative anaerobes are regulated by oxygen-sensing transcription factors and occur under suboxic conditions.
Melanin Biosynthesis in the Maize PathogenCochliobolus heterostrophusDepends on Two Mitogen-Activated Protein Kinases, Chk1 and Mps1, and the Transcription Factor Cmr1
Authors: Eliahu Noa , Igbaria Aeid , Rose Mark S. , Horwitz Benjamin A. , Lev Sophie 
Published: January 2007

ABSTRACTThe maize pathogenCochliobolus heterostrophusrequires two mitogen-activated protein kinases (MAPKs), Chk1 and Mps1, to produce normal pigmentation. Young colonies ofmps1andchk1deletion mutants have a white and autolytic appearance, which was partially rescued by a hyperosmotic environment. We isolated the transcription factor Cmr1, an ortholog ofColletotrichum lagenariumCmr1 andMagnaporthe griseaPig1, which regulates melanin biosynthesis inC. heterostrophus. Deletion ofCMR1inC. heterostrophusresulted in mutants that lacked dark pigmentation and acquired an orange-pink color. Incmr1deletion strains the expression of putative scytalone dehydratase (SCD1) and hydroxynaphthalene reductase (BRN1andBRN2) genes involved in melanin biosynthesis was undetectable, whereas expression ofPKS18, encoding a polyketide synthase, was only moderately reduced. Inchk1andmps1mutants expression ofPKS18,SCD1,BRN1,BRN2, and the transcription factorCMR1itself was very low in young colonies, slightly up-regulated in aging colonies, and significantly induced in hyperosmotic conditions, compared to invariably high expression in the wild type. These findings indicate that two MAPKs, Chk1 and Mps1, affect Cmr1 at the transcriptional level and this influence is partially overridden in stress conditions including aging culture and hyperosmotic environment. Surprisingly, we found that theCMR1gene was transcribed in both sense and antisense directions, apparently producing mRNA as well as a long noncoding RNA transcript. Expression of the antisenseCMR1was also Chk1 and Mps1 dependent. Analysis of chromosomal location of the melanin biosynthesis genes inC. heterostrophusresulted in identification of a small gene cluster comprisingBRN1,CMR1, andPKS18. Since expression of all three genes depends on Chk1 and Mps1 MAPKs, we suggest their possible epigenetic regulation.
Aspergillus nidulans
Dis1/XMAP215 Protein AlpA Localizes to Spindle Pole Bodies and Microtubule Plus Ends and Contributes to Growth Directionality
Authors: Enke Cathrin , Zekert Nadine , Veith Daniel , Schaaf Carolin , Konzack Sven , Fischer Reinhard 
Published: January 2007

ABSTRACT

The dynamics of cytoplasmic microtubules (MTs) is largely controlled by a protein complex at the MT plus end. In
Schizosaccharomyces pombe
and in filamentous fungi, MT plus end-associated proteins also determine growth directionality. We have characterized the Dis1/XMAP215 family protein AlpA from
Aspergillus nidulans
and show that it determines MT dynamics as well as hyphal morphology. Green fluorescent protein-tagged AlpA localized to MT-organizing centers (centrosomes) and to MT plus ends. The latter accumulation occurred independently of conventional kinesin or the Kip2-familiy kinesin KipA.
alpA
deletion strains were viable and only slightly temperature sensitive. Mitosis, nuclear migration, and nuclear positioning were not affected, but hyphae grew in curves rather than straight, which appeared to be an effect of reduced MT growth and dynamics.
Dictyostelium
Myb Transcription Factors Function at Culmination as Activators of Ancillary Stalk Differentiation
Authors: Tsujioka Masatsune , Zhukovskaya Natasha , Yamada Yoko , Fukuzawa Masashi , Ross Susan , Williams Jeffrey G. 
Published: January 2007

ABSTRACT

ecmB
and
mrrA
are expressed in the cups that cradle
Dictyostelium
spore heads, and MybE is necessary for their expression in lower but not upper cup cells. A Myb site within the
mrrA
promoter is necessary for expression in both cups. Thus, multiple Myb proteins are required for ancillary stalk differentiation.
Aeromonas salmonicidaToxin AexT Has a Rho Family GTPase-Activating Protein Domain
Authors: Litvak Yael , Selinger Zvi 
Published: January 2007

ABSTRACTThe N terminus of theAeromonas salmonicidaADP-ribosylating toxin AexT displays in vitro GTPase-activating protein (GAP) activity for Rac1, CDC42, and RhoA. HeLa cells transfected with the AexT N terminus exhibit rounding and actin disordering. We propose that theAeromonas salmonicidaAexT toxin is a novel member of the growing family of bacterial RhoGAPs.