bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence that HumanChlamydia pneumoniaeWas Zoonotically Acquired
Authors: Myers G. S. A. , Mathews S. A. , Eppinger M. , Mitchell C. , O'Brien K. K. , White O. R. , Benahmed F. , Brunham R. C. , Read T. D. , Ravel J. , Bavoil P. M. , Timms P. 
Published: September 2009

ABSTRACTZoonotic infections are a growing threat to global health.Chlamydia pneumoniaeis a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease.C. pneumoniaewas first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species ofChlamydia,C. pecorumandC. pneumoniae. Transmission ofC. pneumoniaebetween animals and humans has not been reported; however, two other chlamydial species,C. psittaciandC. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain ofC. pneumoniae(LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates ofC. pneumoniaeshow that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) ofC. pneumoniaewhich adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.
The Terminal A Domain of the Fibrillar Accumulation-Associated Protein (Aap) of
Staphylococcus epidermidis
Mediates Adhesion to Human Corneocytes
Authors: Macintosh Robin L. , Brittan Jane L. , Bhattacharya Ritwika , Jenkinson Howard F. , Derrick Jeremy , Upton Mathew , Handley Pauline S. 
Published: September 2009

ABSTRACT

The opportunistic pathogen
Staphylococcus epidermidis
colonizes indwelling medical devices by biofilm formation but is primarily a skin resident. In many
S. epidermidis
strains biofilm formation is mediated by a cell wall-anchored protein, the accumulation-associated protein (Aap). Here, we investigate the role of Aap in skin adhesion. Aap is an LPXTG protein with a domain architecture including a terminal A domain and a B-repeat region.
S. epidermidis
NCTC 11047 expresses Aap as localized, lateral tufts of fibrils on one subpopulation of cells (Fib
+
), whereas a second subpopulation does not express these fibrils of Aap (Fib
−
). Flow cytometry showed that 72% of NCTC 11047 cells expressed Aap and that 28% of cells did not. Aap is involved in the adhesion of Fib
+
cells to squamous epithelial cells from the hand (corneocytes), as the recombinant A-domain protein partially blocked binding to corneocytes. To confirm the role of the Aap A domain in corneocyte attachment, Aap was expressed on the surface of
Lactococcus lactis
MG1363 as sparsely distributed, peritrichous fibrils. The expression of Aap increased corneocyte adhesion 20-fold compared to
L. lactis
carrying Aap without an A domain.
S. epidermidis
isolates from catheters, artificial joints, skin, and the nose also used the A domain of Aap to adhere to corneocytes, emphasizing the role of Aap in skin adhesion. In addition,
L. lactis
expressing Aap with different numbers of B repeats revealed a positive correlation between the number of B repeats and adhesion to corneocytes, suggesting an additional function for the B region in enhancing A-domain-dependent attachment to skin. Therefore, in addition to its established role in biofilm formation, Aap can also promote adhesion to corneocytes and is likely to be an important adhesin in
S. epidermidis
skin colonization.
Genetic and Biochemical Analysis of the Interaction ofBacillus subtilisCodY with Branched-Chain Amino Acids
Authors: Villapakkam Anuradha C. , Handke Luke D. , Belitsky Boris R. , Levdikov Vladimir M. , Wilkinson Anthony J. , Sonenshein Abraham L. 
Published: September 2009

ABSTRACTBacillus subtilisCodY protein is a DNA-binding global transcriptional regulator that responds to branched-chain amino acids (isoleucine, leucine, and valine) and GTP. Crystal structure studies have shown that the N-terminal region of the protein includes a GAF domain that contains a hydrophobic pocket within which isoleucine and valine bind. This region is well conserved in CodY homologs. Site-directed mutagenesis was employed to understand the roles of some of the residues in the GAF domain and hydrophobic pocket in interaction with isoleucine and GTP. The F40A, F71E, and F98A forms of CodY were inactive in vivo. They were activatable by GTP but to a much lesser extent by branched-chain amino acids in vitro. The CodY mutant R61A retained partial repression of target promoters in vivo and was able to respond to GTP in vitro but also responded poorly to branched-chain amino acids in vitro unless GTP was simultaneously present. Thus, the GAF domain includes residues essential for full activation of CodY by branched-chain amino acids, but these residues are not critical for activation by GTP. Binding studies with branched-chain amino acids and their analogs revealed that an amino group at position 2 and a methyl group at position 3 of valine are critical components of the recognition of the amino acids by CodY.
Motility and Flagellar Glycosylation in
Clostridium difficile
Authors: Twine Susan M. , Reid Christopher W. , Aubry Annie , McMullin David R. , Fulton Kelly M. , Austin John , Logan Susan M. 
Published: September 2009

ABSTRACT

In this study, intact flagellin proteins were purified from strains of
Clostridium difficile
and analyzed using quadrupole time of flight and linear ion trap mass spectrometers. Top-down studies showed the flagellin proteins to have a mass greater than that predicted from the corresponding gene sequence. These top-down studies revealed marker ions characteristic of glycan modifications. Additionally, diversity in the observed masses of glycan modifications was seen between strains. Electron transfer dissociation mass spectrometry was used to demonstrate that the glycan was attached to the flagellin protein backbone in O linkage via a HexNAc residue in all strains examined. Bioinformatic analysis of
C. difficile
genomes revealed diversity with respect to glycan biosynthesis gene content within the flagellar biosynthesis locus, likely reflected by the observed flagellar glycan diversity. In
C. difficile
strain 630, insertional inactivation of a glycosyltransferase gene (CD0240) present in all sequenced genomes resulted in an inability to produce flagellar filaments at the cell surface and only minor amounts of unmodified flagellin protein.
Laboratory Strains ofBacillus subtilisDo Not Exhibit Swarming Motility
Authors: Patrick Joyce E. , Kearns Daniel B. 
Published: September 2009

ABSTRACTWe redemonstrate that SwrA is essential for swarming motility inBacillus subtilis, and we reassert that laboratory strains ofB. subtilisdo not swarm. Additionally, we find that a number of other genes, previously reported to be required for swarming in laboratory strains, are dispensable for robust swarming motility in an undomesticated strain. We attribute discrepancies in the literature to a lack of reproducible standard experimental conditions, selection for spontaneous swarming suppressors, inadvertent genetic linkage to swarming mutations, and auxotrophy.
Identification of Functional LsrB-Like Autoinducer-2 Receptors
Authors: Pereira Catarina S. , de Regt Anna K. , Brito Patrícia H. , Miller Stephen T. , Xavier Karina B. 
Published: September 2009

ABSTRACTAlthough a variety of bacterial species have been reported to use the interspecies communication signal autoinducer-2 (AI-2) to regulate multiple behaviors, the molecular mechanisms of AI-2 recognition and signal transduction remain poorly understood. To date, two types of AI-2 receptors have been identified: LuxP, present inVibriospp., and LsrB, first identified inSalmonella entericaserovar Typhimurium. InS.Typhimurium, LsrB is the ligand binding protein of a transport system that enables the internalization of AI-2. Here, using both sequence analysis and structure prediction, we establish a set of criteria for identifying functional AI-2 receptors. We test our predictions experimentally, assaying key species for their abilities to import AI-2 in vivo, and test their LsrB orthologs for AI-2 binding in vitro. Using these experimental approaches, we were able to identify AI-2 receptors in organisms belonging to phylogenetically distinct families such as theEnterobacteriaceae,Rhizobiaceae, andBacillaceae. Phylogenetic analysis of LsrB orthologs indicates that this pattern could result from one single origin of the functional LsrB gene in a gammaproteobacterium, suggesting possible posterior independent events of lateral gene transfer to theAlphaproteobacteriaandFirmicutes. Finally, we used mutagenesis to show that two AI-2-interacting residues are essential for the AI-2 binding ability. These two residues are conserved in the binding sites of all the functional AI-2 binding proteins but not in the non-AI-2-binding orthologs. Together, these results strongly support our ability to identify functional LsrB-type AI-2 receptors, an important step in investigations of this interspecies signal.
Archaeal Intrinsic Transcription Termination In Vivo
Authors: Santangelo Thomas J. , Cubonová L'ubomíra , Skinner Katherine M. , Reeve John N. 
Published: September 2009

ABSTRACT

Thermococcus kodakarensis
(formerly
Thermococcus kodakaraensis
) strains have been constructed with synthetic and natural DNA sequences, predicted to function as archaeal transcription terminators, identically positioned between a constitutive promoter and a β-glycosidase-encoding reporter gene (TK1761). Expression of the reporter gene was almost fully inhibited by the upstream presence of 5′-TTTTTTTT (T
8
) and was reduced >70% by archaeal intergenic sequences that contained oligo(T) sequences. An archaeal intergenic sequence (t

mcrA

) that conforms to the bacterial intrinsic terminator motif reduced TK1761 expression ∼90%, but this required only the oligo(T) trail sequence and not the inverted-repeat and loop region. Template DNAs were amplified from each
T. kodakarensis
strain, and transcription in vitro by
T. kodakarensis
RNA polymerase was terminated by sequences that reduced TK1761 expression in vivo. Termination occurred at additional sites on these linear templates, including at a 5′-AAAAAAAA (A
8
) sequence that did not reduce TK1761 expression in vivo. When these sequences were transcribed on supercoiled plasmid templates, termination occurred almost exclusively at oligo(T) sequences. The results provide the first in vivo experimental evidence for intrinsic termination of archaeal transcription and confirm that archaeal transcription termination is stimulated by oligo(T) sequences and is different from the RNA hairpin-dependent mechanism established for intrinsic bacterial termination.
Global Transcriptional Response to Spermine, a Component of the Intramacrophage Environment, Reveals Regulation of
Francisella
Gene Expression through Insertion Sequence Elements
Authors: Carlson Paul E. , Horzempa Joseph , O'Dee Dawn M. , Robinson Cory M. , Neophytou Panayiotis , Labrinidis Alexandros , Nau Gerard J. 
Published: September 2009

ABSTRACT

Tularemia is caused by the category A biodefense agent
Francisella tularensis
. This bacterium is associated with diverse environments and a plethora of arthropod and mammalian hosts. How
F. tularensis
adapts to these different conditions, particularly the eukaryotic intracellular environment in which it replicates, is poorly understood. Here, we demonstrate that the polyamines spermine and spermidine are environmental signals that alter bacterial stimulation of host cells. Genomewide analysis showed that
F. tularensis
LVS undergoes considerable changes in gene expression in response to spermine. Unexpectedly, analysis of gene expression showed that multiple members of two classes of
Francisella
insertion sequence (IS) elements, IS
Ftu1
and IS
Ftu2
, and the genes adjacent to these elements were induced by spermine. Spermine was sufficient to activate transcription of these IS elements and of nearby genes in broth culture and in macrophages. Importantly, the virulent strain of
F. tularensis
, Schu S4, exhibited similar phenotypes of cytokine induction and gene regulation in response to spermine. Distinctions in gene expression changes between Schu S4 and LVS at one orthologous locus, however, correlated with differences in IS element location. Our results indicate that spermine and spermidine are novel triggers to alert
F. tularensis
of its eukaryotic host environment. The results reported here also identify an unexpected mechanism of gene regulation controlled by a spermine-responsive promoter contained within IS elements. Different arrangements of these mobile genetic elements among
Francisella
strains may contribute to virulence by conveying new expression patterns for genes from different strains.
YjhS (NanS) Is Required for
Escherichia coli
To Grow on 9-O-Acetylated
N
-Acetylneuraminic Acid
Authors: Steenbergen Susan M. , Jirik Jamie L. , Vimr Eric R. 
Published: September 2009

ABSTRACT

The
nanATEK
-
yhcH
,
yjhATS
, and
yjhBC
operons in
Escherichia coli
are coregulated by environmental
N
-acetylneuraminic acid, the most prevalent sialic acid in nature. Here we show that YjhS (NanS) is a probable 9-O-acetyl
N
-acetylneuraminic acid esterase required for
E. coli
to grow on this alternative sialic acid, which is commonly found in mammalian host mucosal sites.
Mutualistic Biofilm Communities Develop with
Porphyromonas gingivalis
and Initial, Early, and Late Colonizers of Enamel
Authors: Periasamy Saravanan , Kolenbrander Paul E. 
Published: September 2009

ABSTRACT

Porphyromonas gingivalis
is present in dental plaque as early as 4 h after tooth cleaning, but it is also associated with periodontal disease, a late-developing event in the microbial successions that characterize daily plaque development. We report here that
P. gingivalis
ATCC 33277 is remarkable in its ability to interact with a variety of initial, early, middle, and late colonizers growing solely on saliva. Integration of
P. gingivalis
into multispecies communities was investigated by using two in vitro biofilm models. In flow cells, bacterial growth was quantified using fluorescently conjugated antibodies against each species, and static biofilm growth on saliva-submerged polystyrene pegs was analyzed by quantitative real-time PCR using species-specific primers.
P. gingivalis
could not grow as a single species or together with initial colonizer
Streptococcus oralis
but showed mutualistic growth when paired with two other initial colonizers,
Streptococcus gordonii
and
Actinomyces oris
, as well as with
Veillonella
sp. (early colonizer),
Fusobacterium nucleatum
(middle colonizer), and
Aggregatibacter actinomycetemcomitans
(late colonizer). In three-species flow cells,
P. gingivalis
grew with
Veillonella
sp. and
A. actinomycetemcomitans
but not with
S. oralis
and
A. actinomycetemcomitans
. Also, it grew with
Veillonella
sp. and
F. nucleatum
but not with
S. oralis
and
F. nucleatum
, indicating that
P. gingivalis
and
S. oralis
are not compatible. However,
P. gingivalis
grew in combination with
S. gordonii
and
S. oralis
, demonstrating its ability to overcome the incompatibility when cultured with a second initially colonizing species. Collectively, these data help explain the observed presence of
P. gingivalis
at all stages of dental plaque development.
Identification of the UDP-
N
-Acetylglucosamine 4-Epimerase Involved in Exosporium Protein Glycosylation in
Bacillus anthracis
Authors: Dong Shengli , Chesnokova Olga N. , Turnbough Charles L. , Pritchard David G. 
Published: September 2009

ABSTRACT

Spores of
Bacillus anthracis
, the causative agent of anthrax, are enclosed by a loosely fitting exosporium composed of a basal layer and an external hair-like nap. The filaments of the nap are formed by trimers of the collagen-like glycoprotein BclA. The side chains of BclA include multiple copies of two linear rhamnose-containing oligosaccharides, a trisaccharide and a pentasaccharide. The pentasaccharide terminates with the unusual deoxyamino sugar anthrose. Both oligosaccharide side chains are linked to the BclA protein backbone through an
N
-acetylgalactosamine (GalNAc) residue. To identify the gene encoding the epimerase required to produce GalNAc for BclA oligosaccharide biosynthesis, three annotated UDP-glucose 4-epimerase genes of
B. anthracis
were cloned and expressed in
Escherichia coli
. The candidate proteins were purified, and their enzymatic activities were assessed. Only two proteins, encoded by the BAS5114 and BAS5304 genes (
B. anthracis
Sterne designations), exhibited epimerase activity. Both proteins were able to convert UDP-glucose (Glc) to UDP-Gal, but only the BAS5304-encoded protein could convert UDP-GlcNAc to UDP-GalNAc, indicating that BAS5304 was the gene sought. Surprisingly, spores produced by a mutant strain lacking the BAS5304-encoded enzyme still contained normal levels of BclA-attached oligosaccharides. However, monosaccharide analysis of the oligosaccharides revealed that GlcNAc had replaced GalNAc. Thus, while GalNAc appears to be the preferred amino sugar for the linkage of oligosaccharides to the BclA protein backbone, in its absence, GlcNAc can serve as a substitute linker. Finally, we demonstrated that the expression of the BAS5304 gene occurred in a biphasic manner during both the early and late stages of sporulation.
Adverse effects of a social contract smoking prevention program among children in Québec, Canada
Authors: Kairouz S , O’Loughlin J , Laguë J 
Published: September 2009

Objective:To evaluate the impact of a smoke-free class competition in elementary schools in Québec, Canada before widespread dissemination of the program across the province.Methods:In a quasiexperimental study design, 843 students in 27 schools exposed to “Mission TNT.06” were compared to 1213 students in 57 matched comparison schools. Baseline data were collected in grade 6 prior to implementation of the program. Follow-up data were collected in grade 7 after students had transitioned to secondary school.Results:The program improved knowledge about the harmful effects of second-hand smoke, but had no impact on knowledge about the harmful effects of smoking, attitudes about the acceptability of cigarettes, beliefs about the tobacco industry, or self-efficacy to resist peer pressure to smoke. After exposure to the program, intervention students were more likely to misreport their smoking status and to report unfavourable attitudes about classmates who smoke.Conclusion:Mission TNT.06 may encourage young smokers to misreport their smoking status and to marginalise classmates who smoke. These findings prompted recommendations to conduct more in-depth evaluation of the smoke-free class competition before widespread dissemination of the program across the province.
Smoking-attributable deaths and potential years of life lost from a large, representative study in China
Authors: Jiang Jingmei , Liu Boqi , Sitas Freddy , Li Junyao , Zeng Xianjia , Han Wei , Zou Xiaonong , Wu Yanping , Zhao Ping 
Published: September 2009

ObjectivesTo provide a more accurate estimate of early smoking-attributable mortality and potential years of life lost using data from a representative study of 103 study areas in China.MethodsTwo datasets were employed as follows. Firstly, retrospective national mortality survey data, which included a population of 67 million in 103 study areas, and about 1 million adults who died in 1986–1988; secondly, nationally representative case-control comparative data was extracted from the survey data to measure the effect of smoking on age trends in smoking-attributable mortality. Potential years of life lost, and sex differences in life expectancy in smokers and non-smokers in the total population aged 35 and over were also estimated.ResultsTobacco caused 11.2% (16.0% of men and 3.7% of women) of total deaths in 1987, and more than two-thirds of these excess deaths occurred between the ages of 50 and 74 years, but only less than 5% excess deaths occurred at ages under 50. Although life expectancies varied with region or sex differences, the years of life lost attributable to smoking was almost the same. Smokers at age 35 lost about 3 years of life expectancy in comparison with never smokers. The study also confirmed that more than 50% of the sex difference in life expectancy was accounted for by smoking.ConclusionFully understanding the consequences of smoking in relation to mortality can clarify its effects on the health and longevity of the entire population.
Smoke-free homes in England: prevalence, trends and validation by cotinine in children
Authors: Jarvis M J , Mindell J , Gilmore A , Feyerabend C , West R 
Published: September 2009

Objective:To examine the prevalence of smoke-free homes in England between 1996 and 2007 and their impact on children’s exposure to second-hand smoke via a series of annual cross-sectional surveys: the Health Survey for England. These comprised nationally representative samples of non-smoking children aged 4–15 (n = 13 365) and their parents interviewed in the home. Main outcome measures were cotinine measured in saliva, smoke-free homes defined by “no” response to “Does anyone smoke inside this house/flat on most days?”, self-reported smoking status of parents and self-reported and cotinine validated smoking status in children.Results:The proportion of homes where one parent was a smoker that were smoke free increased from 21% in 1996 to 37% in 2007, and where both parents were smokers from 6% to 21%. The overwhelming majority of homes with non-smoking parents were smoke free (95% in 1996; 99% in 2007). For children with non-smoking parents and living in a smoke-free home the geometric mean cotinine across all years was 0.22 ng/ml. For children with one smoking parent geometric mean cotinine levels were 0.37 ng/ml when the home was smoke free and 1.67 ng/ml when there was smoking in the home; and for those with two smoking parents, 0.71 ng/ml and 2.46 ng/ml. There were strong trends across years for declines in cotinine concentrations in children in smoke-free homes for the children of smokers and non-smokers.Conclusions:There has been a marked secular trend towards smoke-free homes, even when parents themselves are smokers. Living in a smoke-free home offers children a considerable, but not complete, degree of protection against exposure to parental smoking.