bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coaggregation by the Freshwater Bacterium
Sphingomonas natatoria
Alters Dual-Species Biofilm Formation
Authors: Min K. R. , Rickard A. H. 
Published: April 2009

ABSTRACT

Coaggregation is hypothesized to enhance freshwater biofilm development. To investigate this hypothesis, the ability of the coaggregating bacterium
Sphingomonas natatoria
to form single- and dual-species biofilms was studied and compared to that of a naturally occurring spontaneous coaggregation-deficient variant. Attachment assays using metabolically inactive cells were performed using epifluorescence and confocal laser scanning microscopy. Under static and flowing conditions, coaggregating
S. natatoria
2.1gfp cells adhered to glass surfaces to form diaphanous single-species biofilms. When glass surfaces were precoated with coaggregation partner
Micrococcus luteus
2.13 cells,
S. natatoria
2.1gfp cells formed densely packed dual-species biofilms. The addition of 80 mM galactosamine, which reverses coaggregation, mildly reduced adhesion to glass but inhibited the interaction and attachment to glass-surface-attached
M. luteus
2.13 cells. As opposed to wild-type coaggregating cells, coaggregation-deficient
S. natatoria
2.1COGgfp variant cells were retarded in colonizing glass and did not interact with glass-surface-attached
M. luteus
2.13 cells. To determine if coaggregation enhances biofilm growth and expansion, viable coaggregating
S. natatoria
2.1gfp cells or the coaggregation-deficient variant
S. natatoria
2.1COGgfp cells were coinoculated in flow cells with viable
M. luteus
2.13 cells and allowed to grow together for 96 h. Coaggregating
S. natatoria
2.1gfp cells outcompeted
M. luteus
2.13 cells, and 96-h biofilms were composed predominantly of
S. natatoria
2.1gfp cells. Conversely, when coaggregation-deficient
S. natatoria
2.1COGgfp cells were coinoculated with
M. luteus
2.13 cells, the 96-h biofilm contained few coaggregation-deficient
S. natatoria
2.1 cells. Thus, coaggregation promotes biofilm integration by facilitating attachment to partner species and likely contributes to the expansion of coaggregating
S. natatoria
2.1 populations in dual-species biofilms through competitive interactions.
Mutations in Domain I Interhelical Loops Affect the Rate of Pore Formation by the
Bacillus thuringiensis
Cry1Aa Toxin in Insect Midgut Brush Border Membrane Vesicles
Authors: Lebel Geneviève , Vachon Vincent , Préfontaine Gabrielle , Girard Frédéric , Masson Luke , Juteau Marc , Bah Aliou , Larouche Geneviève , Vincent Charles , Laprade Raynald , Schwartz Jean-Louis 
Published: April 2009

ABSTRACT

Pore formation in the apical membrane of the midgut epithelial cells of susceptible insects constitutes a key step in the mode of action of
Bacillus thuringiensis
insecticidal toxins. In order to study the mechanism of toxin insertion into the membrane, at least one residue in each of the pore-forming-domain (domain I) interhelical loops of Cry1Aa was replaced individually by cysteine, an amino acid which is normally absent from the activated Cry1Aa toxin, using site-directed mutagenesis. The toxicity of most mutants to
Manduca sexta
neonate larvae was comparable to that of Cry1Aa. The ability of each of the activated mutant toxins to permeabilize
M. sexta
midgut brush border membrane vesicles was examined with an osmotic swelling assay. Following a 1-h preincubation, all mutants except the V150C mutant were able to form pores at pH 7.5, although the W182C mutant had a weaker activity than the other toxins. Increasing the pH to 10.5, a procedure which introduces a negative charge on the thiol group of the cysteine residues, caused a significant reduction in the pore-forming abilities of most mutants without affecting those of Cry1Aa or the I88C, T122C, Y153C, or S252C mutant. The rate of pore formation was significantly lower for the F50C, Q151C, Y153C, W182C, and S252C mutants than for Cry1Aa at pH 7.5. At the higher pH, all mutants formed pores significantly more slowly than Cry1Aa, except the I88C mutant, which formed pores significantly faster, and the T122C mutant. These results indicate that domain I interhelical loop residues play an important role in the conformational changes leading to toxin insertion and pore formation.
Composition of Bacterial Communities Associated with Natural and Laboratory Populations of
Asobara tabida
Infected with
Wolbachia
Authors: Zouache Karima , Voronin Denis , Tran-Van Van , Mavingui Patrick 
Published: April 2009

ABSTRACT

Asobara tabida
wasps are fly endoparasitoids that naturally harbor three
Wolbachia
strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild
A. tabida
populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods.
Proteobacteria
and
Firmicutes
were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera
Acetobacter
,
Acidomonas
,
Bacillus
,
Brevibacillus
,
Duganella
,
Herbaspirillum
,
Pseudomonas
,
Staphylococcus
, and
Streptococcus
. In addition to
Wolbachia
, wild individuals harbored
Rickettsia
, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with
Wolbachia
also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family
Enterobacteriaceae
. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only
Wolbachia
being consistently found in wasp ovaries.
Identification and Characterization of a Novel Gene Involved in the
trans
-Specific Nematicidal Activity of
Photorhabdus luminescens
LN2
Authors: Qiu Xuehong , Han Richou , Yan Xun , Liu Mingxing , Cao Li , Yoshiga Toyoshi , Kondo Eizo 
Published: April 2009

ABSTRACT

Photorhabdus luminescens
subsp.
akhurstii
LN2 from
Heterorhabditis indica
LN2 showed nematicidal activity against axenic
Heterorhabditis bacteriophora
H06 infective juveniles (IJs). Transposon mutagenesis identified an LN2 mutant that supports the growth of H06 nematodes. Tn
5
disrupted the
namA
gene, encoding a novel 364-residue protein and involving the nematicidal activity. The green fluorescent protein-labeled
namA
mutant was unable to colonize the intestines of H06 IJs.
Sonicated Diagnostic Immunoblot for Bartonellosis
Authors: Mallqui Vania , Speelmon Emily C. , Verástegui Manuela , Maguiña-Vargas Ciro , Pinell-Salles Paula , Lavarello Rosa , Delgado Jose , Kosek Margaret , Romero Sofia , Arana Yanina , Gilman Robert H. 
Published: April 2009

ABSTRACT

Two simple
Bartonella bacilliformis
immunoblot preparation methods were developed. Antigen was prepared by two different methods: sonication of whole organisms or glycine extraction. Both methods were then tested for sensitivity and specificity. Well-defined control sera were utilized in the development of these diagnostic immunoblots, and possible cross-reactions were thoroughly examined. Sera investigated for cross-reaction with these diagnostic antigens were drawn from patients with brucellosis, chlamydiosis, Q fever, and cat scratch disease, all of whom were from regions where bartonellosis is not endemic. While both immunoblots yielded reasonable sensitivity and high specificity, we recommend the use of the sonicated immunoblot, which has a higher sensitivity when used to detect acute disease and produces fewer cross-reactions. The sonicated immunoblot reported here is 94% sensitive to chronic bartonellosis and 70% sensitive to acute bartonellosis. In a healthy group, it is 100% specific. This immunoblot preparation requires a simple sonication protocol for the harvesting of
B. bacilliformis
antigens and is well suited for use in regions of endemicity.
Serum Cytokine Responses during Acute Human Granulocytic Ehrlichiosis
Authors: Dumler J. S. , Trigiani E. R. , Bakken J. S. , Aguero-Rosenfeld M. E. , Wormser G. P. 
Published: April 2009

ABSTRACTHuman granulocytic ehrlichiosis (HGE) is caused by obligate intracellular bacteria in theEhrlichia phagocytophilagroup. The disease ranges from subclinical to fatal. We speculated that cell-mediated immunity would be important for recovery from and potentially in the clinical manifestations of HGE; thus, serum tumor necrosis factor alpha (TNF-α), interleukin 1β (IL-1β), gamma interferon (IFN-γ), IL-10, and IL-4 concentrations were studied. IFN-γ (1,035 ± 235 pg/ml [mean ± standard error of the mean]) and IL-10 (118 ± 46 pg/ml) concentrations were elevated in acute-phase sera versus convalescent sera and normal subjects (P ≤ 0.013 andP ≤ 0.018, respectively). TNF-α, IL-1β, and IL-4 levels were not elevated. Cytokine levels in severely and mildly affected patients were not different. HGE leads to induction of IFN-γ-dominated cell-mediated immunity associated with clinical manifestations, recovery from infection, or both.
Altered Expression of TAP-1 and Major Histocompatibility Complex Class I in Laryngeal Papillomatosis: Correlation of TAP-1 with Disease
Authors: Vambutas Andrea , Bonagura Vincent R. , Steinberg Bettie M. 
Published: April 2009

ABSTRACTRecurrent respiratory papillomatosis (RRP) is an insidious disease caused by human papillomavirus (HPV) infection. It is characterized by a variable clinical course that can include frequent disease recurrence, significant morbidity, and occasional mortality. The mechanisms responsible for the variability in the clinical course and the persistence of latent HPV infection remain unknown. Effective T-cell-mediated clearance of HPV-infected cells may be defective in patients with RRP, leading to recurrent disease and failure to suppress latent HPV reactivation. This study describes the down-regulation of the transporter associated with antigen presentation (TAP-1) and the major histocompatibility complex (MHC) class I protein expression in laryngeal papilloma tissue biopsies and cell culture of primary explants. There was a statistically significant correlation between reduction of TAP-1 expression in biopsy tissues and rapid recurrence of disease. Patients with RRP had less frequent recurrence if their papillomas expressed TAP-1 at levels close to that of normal tissue, compared with those with very low expression of TAP-1, who had frequent recurrence (32 versus 5 weeks to the next surgical intervention). These findings suggest that HPV may evade immune recognition by down-regulating class I MHC cell surface expression via decreased TAP-1 levels. Expression of TAP-1 could be used for prognostic evaluation of disease severity. Gamma interferon was able to restore class I MHC expression at the surfaces of laryngeal papilloma cells in culture. This up-regulation of class I MHC antigen at the cell surface potentially allows the infected cell to become a target for the immune system again. This finding provides some promise for nonsurgical treatment of laryngeal papillomas.
Molecular Cloning and Nucleotide Sequence Analysis of a Novel Human Papillomavirus (Type 82) Associated with Vaginal Intraepithelial Neoplasia
Authors: Kino Nao , Sata Tetsutaro , Sato Yuko , Sugase Motoyasu , Matsukura Toshihiko 
Published: April 2009

ABSTRACT
The genome of a novel human papillomavirus (HPV-82) was cloned from a vaginal intraepithelial neoplasia grade I. In our series of 291 biopsy specimens, HPV-82 was identified in one case each of cervical intraepithelial neoplasia grade II and grade III by blot hybridization. The histological localization of HPV-82 DNA in the three lesions was confirmed by in situ hybridization. The results indicated that HPV-82 is an etiologic agent for vaginal and cervical intraepithelial neoplasia. By nucleotide sequence similarity of L1 open reading frame (ORF), HPV-82 was closely related to HPV-26, -51, and -69. To know the precise relationship between the HPVs, we determined the complete sequence of HPV-82, as well as that of HPV-69. Sequencing revealed that the four HPVs had no initiation codon in the E5 ORF and had extensive nucleotide sequence similarities in all ORFs. In addition, they exhibited unique frame position patterns for ORFs, different from those of the other genital HPVs.
Cocaine Differentially Modulates Chemokine Production by Mononuclear Cells from Normal Donors and Human Immunodeficiency Virus Type 1-Infected Patients
Authors: Nair Madhavan P. N. , Chadha Kailash C. , Hewitt Ross G. , Mahajan Supriya , Sweet Ann , Schwartz Stanley A. 
Published: April 2009

ABSTRACTEarlier studies have supported a significant role for cocaine in the susceptibility to and the progression of human immunodeficiency virus type 1 (HIV-1) infection. Recently, several unique HIV-1 entry coreceptors (e.g., CCR5 and CCR3) and a trio of HIV-1-specific suppressor chemokines, namely, RANTES (regulated-upon-activation T expressed and secreted), macrophage inflammatory protein 1α (MIP-1α) and MIP-1β, were identified. Although cocaine has been linked to the immunopathogenesis of HIV-1 infection, the corresponding cellular and molecular mechanism(s) have not been well defined. We hypothesize that cocaine mediates these pathologic effects through the downregulation of HIV-1-suppressing chemokines and/or upregulating HIV-1 entry coreceptors in HIV-1-infected subjects, resulting in disease progression to AIDS. Our results show that cocaine selectively downregulates endogenous MIP-1β secretion by normal peripheral blood mononuclear cells (PBMC), while cocaine did not affect the MIP-1β production by PBMC from AIDS patients. Cocaine also selectively suppresses lipopolysaccharide-induced MIP-1β production by PBMC from HIV-infected patients. Further, cocaine significantly downregulates endogenous MIP-1β gene expression, while it upregulates HIV-1 entry coreceptor CCR5 by normal PBMC. These studies suggests a role for cocaine as a cofactor in the pathogenesis of HIV infection and support the premise that cocaine increases susceptibility to and progression of HIV-1 infection by inhibiting the synthesis of HIV-1 protective chemokines and/or upregulating the HIV-1 entry coreceptor, CCR5.
Using Morpholinos for Gene Knockdown in
Giardia intestinalis
Authors: Carpenter Meredith L. , Cande W. Zacheus 
Published: April 2009

ABSTRACT

We used translation-blocking morpholinos to reduce protein levels in
Giardia intestinalis
. Twenty-four hours after electroporation with morpholinos targeting either green fluorescent protein or kinesin-2b, levels of these proteins were reduced by 60%. An epitope-tagged transgene can also be used as a reporter for morpholino efficacy with targets lacking specific antibodies.
Functional Domains of ExsA, the Transcriptional Activator of the
Pseudomonas aeruginosa
Type III Secretion System
Authors: Brutinel Evan D. , Vakulskas Christopher A. , Yahr Timothy L. 
Published: April 2009

ABSTRACT

The opportunistic pathogen
Pseudomonas aeruginosa
utilizes a type III secretion system (T3SS) to evade phagocytosis and damage eukaryotic cells. Transcription of the T3SS regulon is controlled by ExsA, a member of the AraC/XylS family of transcriptional regulators. These family members generally consist of an ∼100-amino acid carboxy-terminal domain (CTD) with two helix-turn-helix DNA binding motifs and an ∼200-amino acid amino-terminal domain (NTD) with known functions including oligomerization and ligand binding. In the present study, we show that the CTD of ExsA binds to ExsA-dependent promoters in vitro and activates transcription from ExsA-dependent promoters both in vitro and in vivo. Despite possessing these activities, the CTD lacks the cooperative binding properties observed for full-length ExsA at the P

exsC

promoter. In addition, the CTD is unaffected by the negative regulatory activity of ExsD, an inhibitor of ExsA activity. Binding studies confirm that ExsD interacts directly with the NTD of ExsA. Our data are consistent with a model in which a single ExsA molecule first binds to a high-affinity site on the P

exsC

promoter. Protein-protein interactions mediated by the NTD then recruit an additional ExsA molecule to a second site on the promoter to form a complex capable of stimulating wild-type levels of transcription. These findings provide important insight into the mechanisms of transcriptional activation by ExsA and inhibition of ExsA activity by ExsD.
Functional Genomics Reveals Extended Roles of the
Mycobacterium tuberculosis
Stress Response Factor σ
H
Authors: Mehra Smriti , Kaushal Deepak 
Published: April 2009

ABSTRACT

Mycobacterium tuberculosis
is one of the most successful pathogens of humankind. During infection,
M. tuberculosis
must cope with and survive against a variety of different environmental conditions. Sigma factors likely facilitate the modulation of the pathogen's gene expression in response to changes in its extracellular milieu during infection. σ
H
, an alternate sigma factor encoded by the
M. tuberculosis
genome, is induced by thiol-oxidative stress, heat shock, and phagocytosis. In response to these conditions, σ
H
induces the expression of σ
B
, σ
E
, and the thioredoxin regulon. In order to more effectively characterize the transcriptome controlled by σ
H
, we studied the long-term effects of the induction of σ
H
on global transcription in
M. tuberculosis
. The
M. tuberculosis
isogenic mutant of σ
H
(Δ-σ
H
) is more susceptible to diamide stress than wild-type
M. tuberculosis
. To study the long-term effects of σ
H
induction, we exposed both strains to diamide, rapidly washed it away, and resumed culturing in diamide-free medium (post-diamide stress culturing). Analysis of the effects of σ
H
induction in this experiment revealed a massive temporal programming of the
M. tuberculosis
transcriptome. Immediately after the induction of σ
H
, genes belonging to the functional categories “virulence/detoxification” and “regulatory proteins” were induced in large numbers. Fewer genes belonging to the “lipid metabolism” category were induced, while a larger number of genes belonging to this category were downregulated. σ
H
caused the induction of the ATP-dependent
clp
proteolysis regulon, likely mediated by a transcription factor encoded by Rv2745c, several members of the
mce1
virulence regulon, and the sulfate acquisition/transport network.
Phosphate-Enhanced Stationary-Phase Fitness of
Escherichia coli
Is Related to Inorganic Polyphosphate Level
Authors: Schurig-Briccio Lici A. , Farías Ricardo N. , Rintoul María R. , Rapisarda Viviana A. 
Published: April 2009

ABSTRACT

We found that
Escherichia coli
grown in media with >37 mM phosphate maintained a high polyphosphate level in late stationary phase, which could account for changes in gene expression and enzyme activities that enhance stationary-phase fitness.
Transcriptome and Functional Analysis of the Eukaryotic-Type Serine/Threonine Kinase PknB inStaphylococcus aureus
Authors: Donat Stefanie , Streker Karin , Schirmeister Tanja , Rakette Sonja , Stehle Thilo , Liebeke Manuel , Lalk Michael , Ohlsen Knut 
Published: April 2009

ABSTRACTThe function of theStaphylococcus aureuseukaryotic-like serine/threonine protein kinase PknB was investigated by performing transcriptome analysis using DNA microarray technology and biochemical assays. The transcriptional profile revealed a strong regulatory impact of PknB on the expression of genes encoding proteins which are involved in purine and pyrimidine biosynthesis, cell wall metabolism, autolysis, and glutamine synthesis. Functional activity of overexpressed and purified PknB kinase was demonstrated using the myelin basic protein as a surrogate substrate. Phosphorylation occurred in a time-dependent manner with Mn2+as a preferred cofactor. Furthermore, biochemical characterization revealed regulation of adenylosuccinate synthase (PurA) activity by phosphorylation. Phosphorylated PurA showed a 1.8-fold decrease in enzymatic activity compared to unphosphorylated PurA. Loss of PknB led to formation of larger cell clusters, and apknBdeletion strain showed 32-fold-higher sensitivity to the cell wall-active antibiotic tunicamycin. The results of this study strongly indicate that PknB has a role in regulation of purine biosynthesis, autolysis, and central metabolic processes inS. aureus.
Comparison of the Complete Genome Sequences of
Bifidobacterium animalis
subsp.
lactis
DSM 10140 and Bl-04
Authors: Barrangou Rodolphe , Briczinski Elizabeth P. , Traeger Lindsay L. , Loquasto Joseph R. , Richards Melissa , Horvath Philippe , Coûté-Monvoisin Anne-Claire , Leyer Gregory , Rendulic Snjezana , Steele James L. , Broadbent Jeffery R. , Oberg Taylor , Dudley Edward G. , Schuster Stephan , Romero Dennis A. , Roberts Robert F. 
Published: April 2009

ABSTRACT

Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two
Bifidobacterium animalis
subsp.
lactis
strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three
Bifidobacterium
species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium
B. animalis
subsp.
lactis
provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.