bluuebunny/crossref_metadata_2025_split huggingface dataset:
Year-Round Prevalence of Norovirus in the Environment of Catering Companies without a Recently Reported Outbreak of Gastroenteritis
Authors: Boxman Ingeborg L. A. , Verhoef Linda , Dijkman Remco , Hägele Geke , te Loeke Nathalie A. J. M. , Koopmans Marion 
Published: March 2011

ABSTRACT
Food handlers play an important role in the transmission of norovirus (NoV) in food-borne outbreaks of gastroenteritis (GE). In a year-round prevalence study, the prevalence of NoV in catering companies without recently reported outbreaks of GE was investigated and compared to the observed prevalence in catering companies with recently reported outbreaks. Swab samples were collected from surfaces in the kitchens and (staff) bathrooms in 832 randomly chosen companies and analyzed for the presence of NoV RNA. In total, 42 (1.7%) out of 2,496 environmental swabs from 35 (4.2%) catering companies tested positive. In contrast, NoV was detected in 147 (39.7%) of the 370 samples for 44 (61.1%) of the 72 establishments associated with outbreaks of gastroenteritis. NoV-positive swabs were more frequently found in winter, in specific types of companies (elderly homes and lunchrooms), and in establishments with separate bathrooms for staff. We found a borderline association with population density but no relation to the number of employees. Sequence analysis showed that environmental strains were interspersed with strains found in outbreaks of illness in humans. Thus, the presence of NoV in catering companies seemed to mirror the presence in the population but was strongly increased when associated with food-borne GE. Swabs may therefore serve as a valuable tool in outbreak investigations for the identification of the causative agent, although results should be interpreted with care, taking into account all other epidemiological data.
Isolation of Lactobacillus salivarius 1077 (NRRL B-50053) and Characterization of Its Bacteriocin, Including the Antimicrobial Activity Spectrum
Authors: Svetoch Edward A. , Eruslanov Boris V. , Levchuk Vladimir P. , Perelygin Vladimir V. , Mitsevich Evgeny V. , Mitsevich Irina P. , Stepanshin Juri , Dyatlov Ivan , Seal Bruce S. , Stern Norman J. 
Published: March 2011

ABSTRACT

Lactobacillus salivarius
1077 (NRRL B-50053) was isolated from poultry intestinal materials, and
in vitro
anti-
Campylobacter jejuni
activity was demonstrated. The isolate was then used for bacteriocin production and its enrichment. The protein content of the cell-free supernatant from the spent medium was precipitated by ammonium sulfate and dialyzed to produce the crude antimicrobial preparation. A typical bacteriocin-like response of sensitivity to proteolytic enzymes and resistance to lysozyme, lipase, and 100°C was observed with this preparation. The polypeptide was further purified by gel filtration, ion-exchange, and hydrophobic-interaction chromatography. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), Edman degradation, and isoelectrofocusing were used to characterize its 3,454-Da molecular mass, the amino acid sequence of its 37 residue components, and the isoelectric point of pI 9.1 of the bacteriocin. Bacteriocin L-1077 contained the class IIa bacteriocin signature N-terminal sequence YGNGV. MICs of bacteriocin L-1077 against 33 bacterial isolates (both Gram negative and Gram positive) ranged from 0.09 to 1.5 μg/ml. Subsequently, the therapeutic benefit of bacteriocin L-1077 was demonstrated in market-age (40- to 43-day-old) broiler chickens colonized with both
C. jejuni
and
Salmonella enterica
serovar Enteritidis. Compared with untreated control birds, both
C. jejuni
and
S
. Enteritidis counts in colonized ceca were diminished by >4 log
10
and
S
. Enteritidis counts in both the liver and the spleen of treated birds were reduced by 6 to 8 log
10
/g compared with those in the nontreated control birds. Bacteriocin L-1077 appears to hold promise in controlling
C. jejuni
/
S
. Enteritidis among commercial broiler chickens.
Important Role of Class I Heat Shock Genes
hrcA
and
dnaK
in the Heat Shock Response and the Response to pH and NaCl Stress of Group I Clostridium botulinum Strain ATCC 3502
Authors: Selby Katja , Lindström Miia , Somervuo Panu , Heap John T. , Minton Nigel P. , Korkeala Hannu 
Published: March 2011

ABSTRACT

Class I heat shock genes (HSGs) code for molecular chaperones which play a major role in the bacterial response to sudden increases of environmental temperature by assisting protein folding. Quantitative reverse transcriptase real-time PCR gene expression analysis of the food-borne pathogen
Clostridium botulinum
grown at 37°C showed that the class I HSGs
grpE
,
dnaK
,
dnaJ
,
groEL
, and
groES
and their repressor,
hrcA
, were expressed at constant levels in the exponential and transitional growth phases, whereas strong downregulation of all six genes was observed during stationary phase. After heat shock from 37 to 45°C, all HSGs were transiently upregulated. A mutant with insertionally inactivated
hrcA
expressed higher levels of class I HSGs during exponential growth than the wild type, followed by upregulation of only
groES
and
groES
after heat shock. Inactivation of
hrcA
or of
dnaK
encoding a major chaperone resulted in lower maximum growth temperatures than for the wild type and reduced growth rates under optimal conditions compared to the wild type. The
dnaK
mutant showed growth inhibition under all tested temperature, pH, and NaCl stress conditions. In contrast, the growth of an
hrcA
mutant was unaffected by mild temperature or acid stress compared to the wild-type strain, indicating that induced class I HSGs support growth under moderately nonoptimal conditions. We show that the expression of class I HSGs plays a major role for survival and growth of
C. botulinum
under the stressful environmental conditions that may be encountered during food processing or growth in food products, in the mammalian intestine, or in wounds.
Living Colors in the Gray Mold Pathogen Botrytis cinerea: Codon-Optimized Genes Encoding Green Fluorescent Protein and mCherry, Which Exhibit Bright Fluorescence
Authors: Leroch Michaela , Mernke Dennis , Koppenhoefer Dieter , Schneider Prisca , Mosbach Andreas , Doehlemann Gunther , Hahn Matthias 
Published: March 2011

ABSTRACT

The green fluorescent protein (GFP) and its variants have been widely used in modern biology as reporters that allow a variety of live-cell imaging techniques. So far, GFP has rarely been used in the gray mold fungus
Botrytis cinerea
because of low fluorescence intensity. The codon usage of
B. cinerea
genes strongly deviates from that of commonly used GFP-encoding genes and reveals a lower GC content than other fungi. In this study, we report the development and use of a codon-optimized version of the
B. cinerea
enhanced GFP (eGFP)-encoding gene (Bc
gfp
) for improved expression in
B. cinerea
. Both the codon optimization and, to a smaller extent, the insertion of an intron resulted in higher mRNA levels and increased fluorescence. Bc
gfp
was used for localization of nuclei in germinating spores and for visualizing host penetration. We further demonstrate the use of promoter-Bc
gfp
fusions for quantitative evaluation of various toxic compounds as inducers of the
atrB
gene encoding an ABC-type drug efflux transporter of
B. cinerea
. In addition, a codon-optimized mCherry-encoding gene was constructed which yielded bright red fluorescence in
B. cinerea
.
Characterization of an Obligate Intracellular Bacterium in the Midgut Epithelium of the Bulrush Bug Chilacis typhae (Heteroptera, Lygaeidae, Artheneinae)
Authors: Kuechler Stefan Martin , Dettner Konrad , Kehl Siegfried 
Published: March 2011

ABSTRACT

Many members of the suborder Heteroptera have symbiotic bacteria, which are usually found extracellularly in specific sacs or tubular outgrowths of the midgut or intracellularly in mycetomes. In this study, we describe the second molecular characterization of a symbiotic bacterium in a monophagous, seed-sucking stink bug of the family Lygaeidae (sensu stricto).
Chilacis typhae
possesses at the end of the first section of the midgut a structure which is composed of circularly arranged, strongly enlarged midgut epithelial cells. It is filled with an intracellular endosymbiont. This “mycetocytic belt” might represent an evolutionarily intermediate stage of the usual symbiotic structures found in stink bugs. Phylogenetic analysis based on the 16S rRNA and the
groEL
genes showed that the bacterium belongs to the
Gammaproteobacteria
, and it revealed a phylogenetic relationship with a secondary bacterial endosymbiont of
Cimex lectularius
and free-living plant pathogens such as
Pectobacterium
and
Dickeya
. The distribution and ultrastructure of the rod-shaped
Chilacis
endosymbiont were studied in adults and nymph stages using fluorescence
in situ
hybridization (FISH) and electron microscopy. The detection of symbionts at the anterior poles of developing eggs indicates that endosymbionts are transmitted vertically. A new genus and species name, “
Candidatus
Rohrkolberia cinguli,” is proposed for this newly characterized clade of symbiotic bacteria.
The YaaA Protein of the Escherichia coli OxyR Regulon Lessens Hydrogen Peroxide Toxicity by Diminishing the Amount of Intracellular Unincorporated Iron
Authors: Liu Yuanyuan , Bauer Sarah C. , Imlay James A. 
Published: March 2011

ABSTRACT

Hydrogen peroxide (H
2
O
2
) is commonly formed in microbial habitats by either chemical oxidation processes or host defense responses. H
2
O
2
can penetrate membranes and damage key intracellular biomolecules, including DNA and iron-dependent enzymes. Bacteria defend themselves against this H
2
O
2
by inducing a regulon that engages multiple defensive strategies. A previous microarray study suggested that
yaaA
, an uncharacterized gene found in many bacteria, was induced by H
2
O
2
in
Escherichia coli
as part of its OxyR regulon. Here we confirm that
yaaA
is a key element of the stress response to H
2
O
2
. In a catalase/peroxidase-deficient (Hpx
−
) background,
yaaA
deletion mutants grew poorly, filamented extensively, and lost substantial viability when they were cultured in aerobic LB medium. The results from a
thyA
forward mutagenesis assay and the growth defect of the
yaaA
deletion in a recombination-deficient (
recA56
) background indicated that
yaaA
mutants accumulated high levels of DNA damage. The growth defect of
yaaA
mutants could be suppressed by either the addition of iron chelators or mutations that slowed iron import, indicating that the DNA damage was caused by the Fenton reaction. Spin-trapping experiments confirmed that Hpx
−
yaaA
cells had a higher hydroxyl radical (HO
•
) level. Electron paramagnetic resonance spectroscopy analysis showed that the proximate cause was an unusually high level of intracellular unincorporated iron. These results demonstrate that during periods of H
2
O
2
stress the induction of YaaA is a critical device to suppress intracellular iron levels; it thereby attenuates the Fenton reaction and the DNA damage that would otherwise result. The molecular mechanism of YaaA action remains unknown.
Diversity of Expressed
vlhA
Adhesin Sequences and Intermediate Hemagglutination Phenotypes in Mycoplasma synoviae
Authors: May Meghan , Brown Daniel R. 
Published: March 2011

ABSTRACT

A reservoir of pseudogene alleles encoding the primary adhesin VlhA occurs in the avian pathogen
Mycoplasma synoviae
. Recombination between this reservoir and its single expression site was predicted to result in lineages of
M. synoviae
that each express a different
vlhA
allele as a consequence of host immune responses to those antigens. Such interstrain diversity at the
vlhA
expression site, including major differences in the predicted secondary structures of their expressed adhesins, was confirmed in 14 specimens of
M. synoviae
. Corresponding functional differences in the extent to which they agglutinated erythrocytes, a quantitative proxy for VlhA-mediated cytadherence, were also evident. There was a >20-fold difference between the highest- and lowest-agglutinating strains and a rheostatic distribution of intermediate phenotypes among the others (Tukey-Kramer honestly significant difference [HSD],
P
< 0.001). Coincubation with the sialic acid analog 2-deoxy-2,3-didehydro-
N
-acetylneuraminate inhibited hemagglutination in a pattern correlated with endogenous sialidase activity (
r
= 0.91,
P
< 0.001), although not consistently to the same extent that erythrocyte pretreatment with sialidase purified from
Clostridium perfringens
did (
P
< 0.05). The striking correlation between the ranked hemagglutination and endogenous sialidase activities of these strains (Spearman's
r
= 0.874,
P
< 0.001) is evidence that host-induced
vlhA
allele switching indirectly drives sequence diversity in the passenger sialidase gene of
M. synoviae
.
Whole-Genome Sequencing of Staphylococcus aureus Strain RN4220, a Key Laboratory Strain Used in Virulence Research, Identifies Mutations That Affect Not Only Virulence Factors but Also the Fitness of the Strain
Authors: Nair Dhanalakshmi , Memmi Guido , Hernandez David , Bard Jonathan , Beaume Marie , Gill Steven , Francois Patrice , Cheung Ambrose L. 
Published: March 2011

ABSTRACT

Staphylococcus aureus
RN4220, a cloning intermediate, is sometimes used in virulence, resistance, and metabolic studies. Using whole-genome sequencing, we showed that RN4220 differs from NCTC8325 and contains a number of genetic polymorphisms that affect both virulence and general fitness, implying a need for caution in using this strain for such studies.
Regulation and Characterization of the
dadRAX
Locus for
d
-Amino Acid Catabolism in Pseudomonas aeruginosa PAO1
Authors: He Weiqing , Li Congran , Lu Chung-Dar 
Published: March 2011

ABSTRACT

d
-Amino acids are essential components for bacterial peptidoglycan, and these natural compounds are also involved in cell wall remodeling and biofilm disassembling. In
Pseudomonas aeruginosa
, the
dadAX
operon, encoding the
d
-amino acid dehydrogenase DadA and the amino acid racemase DadX, is essential for
d
- and
l
-Ala catabolism, and its expression requires a transcriptional regulator, DadR. In this study, purified recombinant DadA alone was sufficient to demonstrate the proposed enzymatic activity with very broad substrate specificity; it utilizes all
d
-amino acids tested as substrates except
d
-Glu and
d
-Gln. DadA also showed comparable
k
cat
and

K
m

values on
d
-Ala and several
d
-amino acids.
dadRAX
knockout mutants were constructed and subjected to analysis of their growth phenotypes on amino acids. The results revealed that utilization of
l
-Ala,
l
-Trp,
d
-Ala, and a specific set of
d
-amino acids as sole nitrogen sources was abolished in the
dadA
mutant and/or severely hampered in the
dadR
mutant while growth yield on
d
-amino acids was surprisingly improved in the
dadX
mutant. The
dadA
promoter was induced by several
l
-amino acids, most strongly by Ala, and only by
d
-Ala among all tested
d
-amino acids. Enhanced growth of the
dadX
mutant on
d
-amino acids is consistent with the finding that the
dadA
promoter was constitutively induced in the
dadX
mutant, where exogenous
d
-Ala but not
l
-Ala reduced the expression. Binding of DadR to the
dadA
regulatory region was demonstrated by electromobility shift assays, and the presence of
l
-Ala but not
d
-Ala increased affinity by 3-fold. The presence of multiple DadR-DNA complexes in the
dadA
regulatory region was demonstrated
in vitro
, and the formation of these nucleoprotein complexes exerted a complicated impact on promoter activation
in vivo
. In summary, the results from this study clearly demonstrate DadA to be the enzyme solely responsible for the proposed
d
-amino acid dehydrogenase activity of broad substrate specificity and the physiological functions of DadRAX in catabolism of several
d
-amino acids and support
l
-Ala as the signal molecule for induction of the
dadAX
genes through DadR binding to several putative operator sites.
Natural Transformation of Myxococcus xanthus
Authors: Wang Jing , Hu Wei , Lux Renate , He Xuesong , Li Yuezhong , Shi Wenyuan 
Published: March 2011

ABSTRACTMyxococcus xanthusbelongs to the delta class of the proteobacteria and is notable for its complex life-style with social behaviors and relatively large genome. Although previous observations have suggested the existence of horizontal gene transfer inM. xanthus, its ability to take up exogenous DNA via natural transformation has not been experimentally demonstrated. In this study, we achieved natural transformation inM. xanthususing the autonomously replicating myxobacterial plasmid pZJY41 as donor DNA.M. xanthusexopolysaccharide (EPS) was shown to be an extracellular barrier for transformation. Cells deficient in EPS production, e.g., mutant strains carrying ΔdifAor ΔepsA, became naturally transformable. Among the inner barriers to transformation were restriction-modification systems inM. xanthus, which could be partially overcome by methylating DNAin vitrousing cell extracts ofM. xanthusprior to transformation. In addition, the incubation time of DNA with cells and the presence of divalent magnesium ion affected transformation frequency ofM. xanthus. Furthermore, we also observed a potential involvement of the type IV pilus system in the DNA uptake machinery ofM. xanthus. The natural transformation was totally eliminated in the ΔpilQ/epsAand Δtgl/epsAmutants, and null mutation ofpilBorpilCin an ΔepsAbackground diminished the transformation rate. Our study, to the best of our knowledge, provides the first example of a naturally transformable species among deltaproteobacteria.
Identification of a Glycosyltransferase from Mycobacterium marinum Involved in Addition of a Caryophyllose Moiety in Lipooligosaccharides
Authors: Sarkar Debasmita , Sidhu Mandeep , Singh Albel , Chen Jiemin , Lammas David A. , van der Sar Astrid M. , Besra Gurdyal S. , Bhatt Apoorva 
Published: March 2011

ABSTRACT

Deletion of
Mycobacterium marinum MMAR2333
resulted in the loss of three of four subclasses of lipooligosaccharides (LOSs). The mutant was unable to extend an intermediate (LOS-II*) by addition of caryophyllose. These data and the predicted domain structure suggest that MMAR2333 is a glycosyltransferase involved in the generation of a lipid-linked caryophyllose donor.
Genome Sequence of Neisseria meningitidis Serogroup B Strain H44/76
Authors: Piet J. R. , Huis in 't Veld R. A. G. , van Schaik B. D. C. , van Kampen A. H. C. , Baas F. , van de Beek D. , Pannekoek Y. , van der Ende A. 
Published: March 2011

ABSTRACT

Neisseria meningitidis
is an obligate human pathogen. While it is a frequent commensal of the upper respiratory tract, in some individuals the bacterium spreads to the bloodstream, causing meningitis and/or sepsis, which are serious conditions with high morbidity and mortality. Here we report the availability of the genome sequence of the widely used serogroup B laboratory strain H44/76.
YjbH-Enhanced Proteolysis of Spx by ClpXP in Bacillus subtilis Is Inhibited by the Small Protein YirB (YuzO)
Authors: Kommineni Sushma , Garg Saurabh K. , Chan Chio Mui , Zuber Peter 
Published: March 2011

ABSTRACT

The Spx protein of
Bacillus subtilis
is a global regulator of the oxidative stress response. Spx concentration is controlled at the level of proteolysis by the ATP-dependent protease ClpXP and a substrate-binding protein, YjbH, which interacts with Spx. A yeast two-hybrid screen was carried out using
yjbH
as bait to uncover additional substrates or regulators of YjbH activity. Of the several genes identified in the screen, one encoded a small protein, YirB (YuzO), which elevated Spx concentration and activity
in vivo
when overproduced from an isopropyl-β-
d
-thiogalactopyranoside (IPTG)-inducible
yirB
construct. Pulldown experiments using extracts of
B. subtilis
cells producing a His-tagged YirB showed that native YjbH interacts with YirB in
B. subtilis
. Pulldown experiments using affinity-tagged Spx showed that YirB inhibited YjbH interaction with Spx.
In vitro
, YjbH-mediated proteolysis of Spx by ClpXP was inhibited by YirB. The activity of YirB is similar to that of the antiadaptor proteins that were previously shown to reduce proteolysis of a specific ClpXP substrate by interacting with a substrate-binding protein.
Effect of Amino Acid Substitutions in the GerAA Protein on the Function of the Alanine-Responsive Germinant Receptor of Bacillus subtilis Spores
Authors: Mongkolthanaruk Wiyada , Cooper Gareth R. , Mawer Julia S. P. , Allan Raymond N. , Moir Anne 
Published: March 2011

ABSTRACT

Spores of
Bacillus subtilis
require the GerAA, GerAB, and GerAC receptor proteins for
l
-alanine-induced germination. Mutations in
gerAA
, both random and site directed, result in phenotypes that identify amino acid residues important for receptor function in broad terms. They highlight the functional importance of two regions in the central, integral membrane domain of GerAA. A P324S substitution in the first residue of a conserved PFPP motif results in a 10-fold increase in a spore's sensitivity to alanine; a P326S change results in the release of phase-dark spores, in which the receptor may be in an “activated” or “quasigerminated” state. Substitutions in residues 398 to 400, in a short loop between the last two likely membrane-spanning helices of this central domain, all affect the germination response, with the G398S substitution causing a temperature-sensitive defect. In others, there are wider effects on the receptor: if alanine is substituted for conserved residue N146, H304, or E330, a severe defect in
l
-alanine germination results. This correlates with the absence of GerAC, suggesting that the assembly or stability of the entire receptor complex has been compromised by the defect in GerAA. In contrast, severely germination-defective mutants such as E129K, L373F, S400F, and M409N mutants retain GerAC at normal levels, suggesting more local and specific effects on the function of GerAA itself. Further interpretation will depend on progress in structural analysis of the receptor proteins.
Complex Transcriptional Control of the Antibiotic Regulator
afsS
in Streptomyces: PhoP and AfsR Are Overlapping, Competitive Activators
Authors: Santos-Beneit Fernando , Rodríguez-García Antonio , Martín Juan F. 
Published: March 2011

ABSTRACT

The
afsS
gene of several
Streptomyces
species encodes a small sigma factor-like protein that acts as an activator of several pathway-specific regulatory genes (e.g.,
actII
-ORF4 and
redD
in
Streptomyces coelicolor
). The two pleiotropic regulators AfsR and PhoP bind to overlapping sequences in the −35 region of the
afsS
promoter and control its expression. Using mutated
afsS
promoters containing specific point mutations in the AfsR and PhoP binding sequences, we proved that the overlapping recognition sequences for AfsR and PhoP are displaced by 1 nucleotide. Different nucleotide positions are important for binding of AfsR or PhoP, as shown by electrophoretic mobility shift assays and by reporter studies using the
luxAB
gene coupled to the different promoters. Mutant promoter M5 (with a nucleotide change at position 5 of the consensus box) binds AfsR but not PhoP with high affinity (named “superAfsR”). Expression of the
afsS
gene from this promoter led to overproduction of actinorhodin. Mutant promoter M16 binds PhoP with extremely high affinity (“superPhoP”). Studies with Δ
afsR
and Δ
phoP
mutants (lacking AfsR and PhoP, respectively) showed that both global regulators are competitive transcriptional activators of
afsS
. AfsR has greater influence on expression of
afsS
than PhoP, as shown by reverse transcriptase PCR (RT-PCR) and promoter reporter (luciferase) studies. These two high-level regulators appear to integrate different nutritional signals (particularly phosphate limitation sensed by PhoR),
S
-adenosylmethionine, and other still unknown environmental signals (leading to AfsR phosphorylation) for the AfsS-mediated control of biosynthesis of secondary metabolites.