bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methodologies for Salmonella enterica subsp. enterica Subtyping: Gold Standards and Alternatives
Authors: Wattiau Pierre , Boland Cécile , Bertrand Sophie 
Published: August 2011

ABSTRACT

For more than 80 years, subtyping of
Salmonella enterica
has been routinely performed by serotyping, a method in which surface antigens are identified based on agglutination reactions with specific antibodies. The serotyping scheme, which is continuously updated as new serovars are discovered, has generated over time a data set of the utmost significance, allowing long-term epidemiological surveillance of
Salmonella
in the food chain and in public health control. Conceptually, serotyping provides no information regarding the phyletic relationships inside the different
Salmonella enterica
subspecies. In epidemiological investigations, identification and tracking of salmonellosis outbreaks require the use of methods that can fingerprint the causative strains at a taxonomic level far more specific than the one achieved by serotyping. During the last 2 decades, alternative methods that could successfully identify the serovar of a given strain by probing its DNA have emerged, and molecular biology-based methods have been made available to address phylogeny and fingerprinting issues. At the same time, accredited diagnostics have become increasingly generalized, imposing stringent methodological requirements in terms of traceability and measurability. In these new contexts, the hand-crafted character of classical serotyping is being challenged, although it is widely accepted that classification into serovars should be maintained. This review summarizes and discusses modern typing methods, with a particular focus on those having potential as alternatives for classical serotyping or for subtyping
Salmonella
strains at a deeper level.
Four-Year Evaluation of the Effect of Vaccination against Coxiella burnetii on Reduction of Animal Infection and Environmental Contamination in a Naturally Infected Dairy Sheep Flock
Authors: Astobiza Ianire , Barandika Jesús F. , Ruiz-Fons Francisco , Hurtado Ana , Povedano Inés , Juste Ramón A. , García-Pérez Ana L. 
Published: August 2011

ABSTRACTVaccination is considered one of the best options for controllingCoxiella burnetiiinfection in livestock. The efficacy of a phase I vaccine was investigated over 4 years in a sheep flock with confirmedC. burnetiiinfection. Shedding was not detected in ewes and yearlings in the last 2 years, butC. burnetiistill persisted in the environment.
Microbial Inactivation for Safe and Rapid Diagnostics of Infectious Samples
Authors: Sagripanti Jose-Luis , Hülseweh Birgit , Grote Gudrun , Voß Luzie , Böhling Katrin , Marschall Hans-Jürgen 
Published: August 2011

ABSTRACT

The high risk associated with biological threat agents dictates that any suspicious sample be handled under strict surety and safety controls and processed under high-level containment in specialized laboratories. This study attempted to find a rapid, reliable, and simple method for the complete inactivation of a wide range of pathogens, including spores, vegetative bacteria, and viruses, while preserving microbial nucleic acid fragments suitable for PCRs and proteinaceous epitopes for detection by immunoassays. Formaldehyde, hydrogen peroxide, and guanidium thiocyanate did not completely inactivate high titers of bacterial spores or viruses after 30 min at 21°C. Glutaraldehyde and sodium hypochlorite showed high microbicidal activity but obliterated the PCR or enzyme-linked immunosorbent assay (ELISA) detection of bacterial spores or viruses. High-level inactivation (more than 6 log
10
) of bacterial spores (
Bacillus atrophaeus
), vegetative bacteria (
Pseudomonas aeruginosa
), an RNA virus (the alphavirus Pixuna virus), or a DNA virus (the orthopoxvirus vaccinia virus) was attained within 30 min at 21°C by treatment with either peracetic acid or cupric ascorbate with minimal hindrance of subsequent PCR tests and immunoassays. The data described here should provide the basis for quickly rendering field samples noninfectious for further analysis under lower-level containment and considerably lower cost.
Identification of a Perchlorate Reduction Genomic Island with Novel Regulatory and Metabolic Genes
Authors: Melnyk Ryan A. , Engelbrektson Anna , Clark Iain C. , Carlson Hans K. , Byrne-Bailey Kathy , Coates John D. 
Published: August 2011

ABSTRACT
A comparative analysis of the genomes of four dissimilatory (per)chlorate-reducing bacteria has revealed a genomic island associated with perchlorate reduction. In addition to the characterized metabolic genes for perchlorate reductase and chlorite dismutase, the island contains multiple conserved uncharacterized genes possibly involved in electron transport and regulation.
Norovirus Infectivity in Humans and Persistence in Water
Authors: Seitz Scot R. , Leon Juan S. , Schwab Kellogg J. , Lyon G. Marshall , Dowd Melissa , McDaniels Marisa , Abdulhafid Gwen , Fernandez Marina L. , Lindesmith Lisa C. , Baric Ralph S. , Moe Christine L. 
Published: August 2011

ABSTRACT

To examine the long-term infectivity of human norovirus in water, 13 study subjects were challenged at different time points with groundwater spiked with the prototype human norovirus, Norwalk virus. Norwalk virus spiked in groundwater remained infectious after storage at room temperature in the dark for 61 days (the last time point tested). The Norwalk virus-seeded groundwater was stored for 1,266 days and analyzed, after RNase treatment, by reverse transcription-quantitative PCR (RT-qPCR) to detect Norwalk virus RNA contained within intact capsids. Norwalk virus RNA within intact capsids was detected in groundwater for 1,266 days, with no significant log
10
reduction throughout 427 days and a significant 1.10-log
10
reduction by day 1266. Purified Norwalk virus RNA (extracted from Norwalk virus virions) persisted for 14 days in groundwater, tap water, and reagent-grade water. This study demonstrates that Norwalk virus in groundwater can remain detectable for over 3 years and can remain infectious for at least 61 days. (ClinicalTrials.gov identifier NCT00313404.)
Effect of Sodium Bisulfite Injection on the Microbial Community Composition in a Brackish-Water-Transporting Pipeline
Authors: Park Hyung Soo , Chatterjee Indranil , Dong Xiaoli , Wang Sheng-Hung , Sensen Christoph W. , Caffrey Sean M. , Jack Thomas R. , Boivin Joe , Voordouw Gerrit 
Published: August 2011

ABSTRACT

Pipelines transporting brackish subsurface water, used in the production of bitumen by steam-assisted gravity drainage, are subject to frequent corrosion failures despite the addition of the oxygen scavenger sodium bisulfite (SBS). Pyrosequencing of 16S rRNA genes was used to determine the microbial community composition for planktonic samples of transported water and for sessile samples of pipe-associated solids (PAS) scraped from pipeline cutouts representing corrosion failures. These were obtained from upstream (PAS-616P) and downstream (PAS-821TP and PAS-821LP, collected under rapid-flow and stagnant conditions, respectively) of the SBS injection point. Most transported water samples had a large fraction (1.8% to 97% of pyrosequencing reads) of
Pseudomonas
not found in sessile pipe samples. The sessile population of PAS-616P had methanogens (
Methanobacteriaceae
) as the main (56%) community component, whereas
Deltaproteobacteria
of the genera
Desulfomicrobium
and
Desulfocapsa
were not detected. In contrast, PAS-821TP and PAS-821LP had lower fractions (41% and 0.6%) of
Methanobacteriaceae
archaea but increased fractions of sulfate-reducing
Desulfomicrobium
(18% and 48%) and of bisulfite-disproportionating
Desulfocapsa
(35% and 22%) bacteria. Hence, SBS injection strongly changed the sessile microbial community populations. X-ray diffraction analysis of pipeline scale indicated that iron carbonate was present both upstream and downstream, whereas iron sulfide and sulfur were found only downstream of the SBS injection point, suggesting a contribution of the bisulfite-disproportionating and sulfate-reducing bacteria in the scale to iron corrosion. Incubation of iron coupons with pipeline waters indicated iron corrosion coupled to the formation of methane. Hence, both methanogenic and sulfidogenic microbial communities contributed to corrosion of pipelines transporting these brackish waters.
Effect of Glucose on the Fatty Acid Composition of Cupriavidus necator JMP134 during 2,4-Dichlorophenoxyacetic Acid Degradation: Implications for Lipid-Based Stable Isotope Probing Methods
Authors: Lerch Thomas Z. , Dignac Marie-France , Barriuso Enrique , Mariotti André 
Published: August 2011

ABSTRACT

Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis,
Cupriavidus necator
JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [
13
C]2,4-D, [
13
C]glucose, or mixtures of both substrates alternatively labeled with
13
C.
C. necator
JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the
13
C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.
Myxococcus xanthus Swarms Are Driven by Growth and Regulated by a Pacemaker
Authors: Kaiser Dale , Warrick Hans 
Published: August 2011

ABSTRACT

The principal social activity of
Myxococcus xanthus
is to organize a dynamic multicellular structure, known as a swarm. Although its cell density is high, the swarm can grow and expand rapidly. Within the swarm, the individual rod-shaped cells are constantly moving, transiently interacting with one another, and independently reversing their gliding direction. Periodic reversal is, in fact, essential for creating a swarm, and the reversal frequency controls the rate of swarm expansion. Chemotaxis toward nutrient has been thought to drive swarming, but here the nature of swarm growth and the impact of genetic deletions of members of the Frz family of proteins suggest otherwise. We find that three cytoplasmic Frz proteins, FrzCD, FrzF, and FrzE, constitute a cyclic pathway that sets the reversal frequency. Within each cell these three proteins appear to be connected in a negative-feedback loop that produces oscillations whose frequencies are finely tuned by methylation and by phosphorylation. This oscillator, in turn, drives MglAB, a small G-protein switch, to oscillate between its GTP- and GDP-bound states that ultimately determine when the cell moves forward or backward. The periodic reversal of interacting rod-shaped cells promotes their alignment. Swarm organization ensures that each cell can move without blocking the movement of others.
Brucella melitensis Cyclic di-GMP Phosphodiesterase BpdA Controls Expression of Flagellar Genes
Authors: Petersen Erik , Chaudhuri Pallab , Gourley Chris , Harms Jerome , Splitter Gary 
Published: August 2011

ABSTRACT

Brucella melitensis
encounters a variety of conditions and stimuli during its life cycle—including environmental growth, intracellular infection, and extracellular dissemination—which necessitates flexibility of bacterial signaling to promote virulence. Cyclic-di-GMP is a bacterial secondary signaling molecule that plays an important role in adaptation to changing environments and altering virulence in a number of bacteria. To investigate the role of cyclic-di-GMP in
B. melitensis
, all 11 predicted cyclic-di-GMP-metabolizing proteins were separately deleted and the effect on virulence was determined. Three of these cyclic-di-GMP-metabolizing proteins were found to alter virulence. Deletion of the
bpdA
and
bpdB
genes resulted in attenuation of virulence of the bacterium, while deletion of the
cgsB
gene produced a hypervirulent strain. In a
Vibrio
reporter system to monitor apparent alteration in levels of cyclic-di-GMP, both BpdA and BpdB displayed a phenotype consistent with cyclic-di-GMP-specific phosphodiesterases, while CgsB displayed a cyclic-di-GMP synthase phenotype. Further analysis found that deletion of
bpdA
resulted in a dramatic decrease in flagellar promoter activities, and a flagellar mutant showed similar phenotypes to the
bpdA
and
bpdB
mutant strains in mouse models of infection. These data indicate a potential role for regulation of flagella in
Brucella melitensis
via cyclic-di-GMP.
The Yersinia enterocolitica Phage Shock Proteins B and C Can Form Homodimers and Heterodimers
In Vivo
with the Possibility of Close Association between Multiple Domains
Authors: Gueguen Erwan , Flores-Kim Josué , Darwin Andrew J. 
Published: August 2011

ABSTRACT

The
Yersinia enterocolitica
phage shock protein (Psp) stress response is essential for virulence and for survival during the mislocalization of outer membrane secretin proteins. The cytoplasmic membrane proteins PspB and PspC are critical components involved in regulating
psp
gene expression and in facilitating tolerance to secretin-induced stress. Interactions between PspB and PspC monomers might be important for their functions and for PspC stability. However, little is known about these interactions and there are conflicting reports about the ability of PspC to dimerize. To address this, we have used a combination of independent approaches to systematically analyze the ability of PspB and PspC to form dimers
in vivo
. Formaldehyde cross-linking of the endogenous chromosomally encoded proteins in
Y. enterocolitica
revealed discrete complexes corresponding in size to PspB-PspB, PspC-PspC, and PspB-PspC. Bacterial two-hybrid analysis corroborated these protein associations, but an important limitation of the two-hybrid approach was uncovered for PspB. A series of PspB and PspC proteins with unique cysteine substitutions at various positions was constructed.
In vivo
disulfide cross-linking experiments with these proteins further supported close association between PspB and PspC monomers. Detailed cysteine substitution analysis of predicted leucine zipper-like amphipathic helices in both PspB and PspC suggested that their hydrophobic faces could form homodimerization interfaces.
A Novel Factor Controlling Bistability in Bacillus subtilis: the YmdB Protein Affects Flagellin Expression and Biofilm Formation
Authors: Diethmaier Christine , Pietack Nico , Gunka Katrin , Wrede Christoph , Lehnik-Habrink Martin , Herzberg Christina , Hübner Sebastian , Stülke Jörg 
Published: August 2011

ABSTRACTCells ofBacillus subtiliscan either be motile or sessile, depending on the expression of mutually exclusive sets of genes that are required for flagellum or biofilm formation, respectively. Both activities are coordinated by the master regulator SinR. We have analyzed the role of the previously uncharacterizedymdBgene for bistable gene expression inB. subtilis. We observed a strong overexpression of thehaggene encoding flagellin and of other genes of the σD-dependent motility regulon in theymdBmutant, whereas the two major operons for biofilm formation,tapA-sipW-tasAandepsA-O, were not expressed. As a result, theymdBmutant is unable to form biofilms. An analysis of the individual cells of a population revealed that theymdBmutant no longer exhibited bistable behavior; instead, all cells are short and motile. The inability of theymdBmutant to form biofilms is suppressed by the deletion of thesinRgene encoding the master regulator of biofilm formation, indicating that SinR-dependent repression of biofilm genes cannot be relieved in aymdBmutant. Our studies demonstrate that lack of expression of SlrR, an antagonist of SinR, is responsible for the observed phenotypes. Overexpression of SlrR suppresses the effects of aymdBmutation.
Structure and Host Recognition of Serotype 13 Glycopeptidolipid from Mycobacterium intracellulare
Authors: Naka Takashi , Nakata Noboru , Maeda Shinji , Yamamoto Reina , Doe Matsumi , Mizuno Seiko , Niki Mamiko , Kobayashi Kazuo , Ogura Hisashi , Makino Masahiko , Fujiwara Nagatoshi 
Published: August 2011

ABSTRACTTheMycobacterium avium-M. intracellularecomplex (MAIC) is divided into 28 serotypes by a species-specific glycopeptidolipid (GPL). Previously, we clarified the structures of serotype 7 GPL and two methyltransferase genes (orfAandorfB) in serotype 12 GPL. This study elucidated the chemical structure, biosynthesis gene, and host innate immune response of serotype 13 GPL. The oligosaccharide (OSE) structure of serotype 13 GPL was determined to be 4-2′-hydroxypropanoyl-amido-4,6-dideoxy-β-hexose-(1→3)-4-O-methyl-α-l-rhamnose-(1→3)-α-l-rhamnose-(1→3)-α-l-rhamnose-(1→2)-α-l-6-deoxy-talose by using chromatography, mass spectrometry, and nuclear magnetic resonance (NMR) analyses. The structure of the serotype 13 GPL was different from those of serotype 7 and 12 GPLs only inO-methylations. We found a relationship between the structure and biosynthesis gene cluster.M. intracellulareserotypes 12 and 13 have a 1.95-kborfA-orfBgene responsible for 3-O-methylation at the terminal hexose,orfB, and 4-O-methylation at the rhamnose next to the terminal hexose,orfA. The serotype 13orfBhad a nonfunctional one-base missense mutation that modifies serotype 12 GPL to serotype 13 GPL. Moreover, the native serotype 13 GPL was multiacetylated and recognized via Toll-like receptor 2. The findings presented here imply that serotypes 7, 12, and 13 are phylogenetically related and confirm that acetylation of the GPL is necessary for host recognition. This study will promote better understanding of the structure-function relationships of GPLs and may open a new avenue for the prevention of MAIC infections.
Hydrogen-Stimulated Carbon Acquisition and Conservation in Salmonella enterica Serovar Typhimurium
Authors: Lamichhane-Khadka Reena , Frye Jonathan G. , Porwollik Steffen , McClelland Michael , Maier Robert J. 
Published: August 2011

ABSTRACTSalmonella entericaserovar Typhimurium can utilize molecular hydrogen for growth and amino acid transport during anaerobic growth. Via microarray we identified H2gas-affected gene expression changes inSalmonella. The addition of H2caused altered expression of 597 genes, of which 176 genes were upregulated and 421 were downregulated. The significantly H2-upregulated genes include those that encode proteins involved in the transport of iron, manganese, amino acids, nucleosides, and sugars. Genes encoding isocitrate lyase (aceA) and malate synthase (aceB), both involved in the carbon conserving glyoxylate pathway, and genes encoding the enzymes of thed-glucarate andd-glycerate pathways (gudT,gudD,garR,garL,garK) are significantly upregulated by H2. Cells grown with H2showed markedly increased AceA enzyme activity compared to cells without H2. Mutant strains with deletion of eitheraceAoraceBhad reduced H2-dependent growth rates. Genes encoding the glutamine-specific transporters (glnH,glnP,glnQ) were upregulated by H2, and cells grown with H2showed increased [14C]glutamine uptake. Similarly, the mannose uptake system genes (manX,manY) were upregulated by H2,and cells grown with H2showed about 2.0-fold-increased [14C]d-mannose uptake compared to the cells grown without H2. Hydrogen stimulates the expression of genes involved in nutrient and carbon acquisition and carbon-conserving pathways, linking carbon and energy metabolism to sustain H2-dependent growth.
The Bacillus subtilis Extracytoplasmic Function σ Factor σ
V
Is Induced by Lysozyme and Provides Resistance to Lysozyme
Authors: Ho Theresa D. , Hastie Jessica L. , Intile Peter J. , Ellermeier Craig D. 
Published: August 2011

ABSTRACT

Bacteria encounter numerous environmental stresses which can delay or inhibit their growth. Many bacteria utilize alternative σ factors to regulate subsets of genes required to overcome different extracellular assaults. The largest group of these alternative σ factors are the extracytoplasmic function (ECF) σ factors. In this paper, we demonstrate that the expression of the ECF σ factor σ
V
in
Bacillus subtilis
is induced specifically by lysozyme but not other cell wall-damaging agents. A mutation in
sigV
results in increased sensitivity to lysozyme killing, suggesting that σ
V
is required for lysozyme resistance. Using reverse transcription (RT)-PCR, we show that the previously uncharacterized gene
yrhL
(here referred to as
oatA
for
O
-acetyltransferase) is in a four-gene operon which includes
sigV
and
rsiV
. In quantitative RT-PCR experiments, the expression of
oatA
is induced by lysozyme stress. Lysozyme induction of
oatA
is dependent upon σ
V
. Overexpression of
oatA
in a
sigV
mutant restores lysozyme resistance to wild-type levels. This suggests that OatA is required for σ
V
-dependent resistance to lysozyme. We also tested the ability of lysozyme to induce the other ECF σ factors and found that only the expression of
sigV
is lysozyme inducible. However, we found that the other ECF σ factors contributed to lysozyme resistance. We found that
sigX
and
sigM
mutations alone had very little effect on lysozyme resistance but when combined with a
sigV
mutation resulted in significantly greater lysozyme sensitivity than the
sigV
mutation alone. This suggests that
sigV
,
sigX
, and
sigM
may act synergistically to control lysozyme resistance. In addition, we show that two ECF σ factor-regulated genes,
dltA
and
pbpX
, are required for lysozyme resistance. Thus, we have identified three independent mechanisms which
B. subtilis
utilizes to avoid killing by lysozyme.
Neisserial Correia Repeat-Enclosed Elements Do Not Influence the Transcription of
pil
Genes in Neisseria gonorrhoeae and Neisseria meningitidis
Authors: Lin Ya-Hsun , Ryan Catherine S. , Davies John K. 
Published: August 2011

ABSTRACT

Two human-specific neisserial pathogens,
Neisseria gonorrhoeae
and
Neisseria meningitidis
, require the expression of type IV pili (tfp) for initial attachment to the host during infection. However, the mechanisms controlling the assembly and functionality of tfp are poorly understood. It is known that the gonococcal
pilE
gene, encoding the major subunit, is positively regulated by IHF, a multifunctional DNA binding protein. A neisserial specific repetitive DNA sequence, termed the Correia repeat-enclosed element (CREE) is situated upstream of three
pil
loci:
pilHIJKX
(
pilH-X
),
pilGD
, and
pilF
. CREEs have been shown to contain strong promoters, and some CREE variants contain a functional IHF binding site. CREEs might therefore be involved in the regulation of tfp biogenesis in pathogenic
Neisseria
. Site-directed and deletion mutagenesis on promoter::
cat
reporter constructs demonstrated that transcription of
pilH-X
and
pilGD
is from a σ
70
promoter and is independent of the CREE. The insertion of a CREE in the
pilF
promoter region in
N. meningitidis
generated a functional σ
70
promoter. However, there is also a functional promoter at this position in
N. gonorrhoeae
, where there is no CREE. These results suggest CREE insertion in these three
pil
loci does not influence transcription and that IHF does not coordinately regulate tfp biogenesis.