bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of the NF-κB Pathway in Human Intestinal Epithelial Cells by Commensal Streptococcus salivarius
Authors: Kaci Ghalia , Lakhdari Omar , Doré Joël , Ehrlich S. Dusko , Renault Pierre , Blottière Hervé M. , Delorme Christine 
Published: May 2011

ABSTRACT

Streptococcus salivarius
exhibited an anti-inflammatory effect on intestinal epithelial cells (IECs) and monocytes. Strains were screened using a reporter clone, HT-29/kB-luc-E, induced by tumor necrosis factor alpha (TNF-α). Supernatant from each strain downregulated NF-κB activation. The two most efficient strains produced an active metabolite (<3 kDa) which was able to downregulate the secretion of the proinflammatory chemokine interleukin-8 (IL-8).
Ccr4 Promotes Resolution of the Endoplasmic Reticulum Stress Response during Host Temperature Adaptation in Cryptococcus neoformans
Authors: Havel Virginia E. , Wool Nathan K. , Ayad David , Downey Kurtis M. , Wilson Christabel F. , Larsen Peter , Djordjevic Julianne T. , Panepinto John C. 
Published: May 2011

ABSTRACT

Adaptation to host temperature is a prerequisite for any pathogen capable of causing deep infection in humans. Our previous studies demonstrated that a
Cryptococcus neoformans ccr4
Δ mutant lacking the major deadenylase involved in regulated mRNA decay was defective in host temperature adaptation and therefore virulence. In this study, the
ccr4
Δ mutant was found to exhibit characteristics of chronic unfolded-protein response (UPR) engagement in both the gene expression profile and phenotype. We demonstrate that host temperature adaptation in
C. neoformans
is accompanied by transient induction of the endoplasmic reticulum (ER) stress response and that Ccr4-dependent posttranscriptional gene regulation contributes to resolution of ER stress during host temperature adaptation.
Characterization of the Periplasmic Region of PomB, a Na
+
-Driven Flagellar Stator Protein in Vibrio alginolyticus
Authors: Li Na , Kojima Seiji , Homma Michio 
Published: May 2011

ABSTRACT

The stator proteins PomA and PomB form a complex that couples Na
+
influx to torque generation in the polar flagellar motor of
Vibrio alginolyticus
. This stator complex is anchored to an appropriate place around the rotor through a putative peptidoglycan-binding (PGB) domain in the periplasmic region of PomB (PomB
C
). To investigate the function of PomB
C
, a series of N-terminally-truncated and in-frame mutants with deletions between the transmembrane (TM) segment and the PGB domain of PomB was constructed. A PomB
C
fragment consisting of residues 135 to 315 (PomB
C5
) formed a stable homodimer and significantly inhibited the motility of wild-type cells when overexpressed in the periplasm. A fragment with an in-frame deletion (PomB
ΔL
) of up to 80 residues retained function, and its overexpression with PomA impaired cell growth. This inhibitory effect was suppressed by a mutation at the functionally critical Asp (D24N) in the TM segment of PomB, suggesting that a high level of Na
+
influx through the mutant stator causes the growth impairment. The overproduction of functional PomA/PomB
ΔL
stators also reduced the motile fractions of the cells. That effect could be slightly relieved by a mutation (L168P) in the putative N-terminal α-helix that connects to the PGB domain without affecting the growth inhibition, suggesting that a conformational change of the region including the PGB domain affects stator assembly. Our results reveal common features of the periplasmic region of PomB/MotB and demonstrate that a flexible linker that contains a “plug” segment is important for the control of Na
+
influx through the stator complex as well as for stator assembly.
Modulation of Rho-Dependent Transcription Termination in Escherichia coli by the H-NS Family of Proteins
Authors: Saxena Shivalika , Gowrishankar J. 
Published: May 2011

ABSTRACT

Nascent transcripts in
Escherichia coli
that fail to be simultaneously translated are subject to a factor-dependent mechanism of termination (also termed a polarity) that involves the proteins Rho and NusG. In this study, we found that overexpression of YdgT suppressed the polarity relief phenotypes and restored the efficiency of termination in
rho
or
nusG
mutants. YdgT and Hha belong to the H-NS and StpA family of proteins that repress a large number of genes in Gram-negative bacteria. Variants of H-NS defective in one or the other of its two dimerization domains, but not those defective in DNA binding alone, also conferred a similar suppression phenotype in
rho
and
nusG
mutants. YdgT overexpression was associated with derepression of
proU
, a prototypical H-NS-silenced locus. Polarity relief conferred by
rho
or
nusG
was unaffected in a derivative completely deficient for both H-NS and StpA, although the suppression effects of YdgT or the oligomerization-defective H-NS variants were abolished in this background. Transcription elongation rates
in vivo
were unaffected in any of the suppressor-bearing strains. Finally, the polarity defects of
rho
and
nusG
mutants were exacerbated by Hha and YdgT deficiency. A model is proposed that invokes a novel role for the polymeric architectural scaffold formed on DNA by H-NS and StpA independent of the gene-silencing functions of these nucleoid proteins, in modulating Rho-dependent transcription termination such that interruption of the scaffold (as obtained by expression either of the H-NS oligomerization variants or of YdgT) is associated with improved termination efficiency in the
rho
and
nusG
mutants.
Compromised Factor-Dependent Transcription Termination in a
nusA
Mutant of Escherichia coli: Spectrum of Termination Efficiencies Generated by Perturbations of Rho, NusG, NusA, and H-NS Family Proteins
Authors: Saxena Shivalika , Gowrishankar J. 
Published: May 2011

ABSTRACT

The proteins NusA and NusG, which are essential for the viability of wild-type
Escherichia coli
, participate in various postinitiation steps of transcription including elongation, antitermination, and termination. NusG is required, along with the essential Rho protein, for factor-dependent transcription termination (also referred to as polarity), but the role of NusA is less clear, with conflicting reports that it both promotes and inhibits the process. In this study, we found that a recessive missense
nusA
mutant [
nusA
(
R258C
)] exhibits a transcription termination-defective (that is, polarity-relieved) phenotype, much like missense mutants in
rho
or
nusG
, but is unaffected for either the rate of transcription elongation or antitermination in λ phage. Various combinations of the
rho
,
nusG
, and
nusA
mutations were synthetically lethal, and the lethality was suppressed by expression of the N-terminal half of nucleoid protein H-NS. Our results suggest that NusA function is indeed needed for factor-dependent transcription termination and that an entire spectrum of termination efficiencies can be generated by perturbations of the Rho, NusG, NusA, and H-NS family of proteins, with the corresponding phenotypes extending from polarity through polarity relief to lethality.
Regulon of the
N
-Acetylglucosamine Utilization Regulator NagR in Bacillus subtilis
Authors: Bertram Ralph , Rigali Sébastien , Wood Natalie , Lulko Andrzej T. , Kuipers Oscar P. , Titgemeyer Fritz 
Published: May 2011

ABSTRACT

N
-Acetylglucosamine (GlcNAc) is the most abundant carbon-nitrogen biocompound on earth and has been shown to be an important source of nutrients for both catabolic and anabolic purposes in
Bacillus
species. In this work we show that the GntR family regulator YvoA of
Bacillus subtilis
serves as a negative transcriptional regulator of GlcNAc catabolism gene expression. YvoA represses transcription by binding a 16-bp sequence upstream of
nagP
encoding the GlcNAc-specific EIIBC component of the sugar phosphotransferase system involved in GlcNAc transport and phosphorylation, as well as another very similar 16-bp sequence upstream of the
nagAB-yvoA
locus, wherein
nagA
codes for
N
-acetylglucosamine-6-phosphate deacetylase and
nagB
codes for the glucosamine-6-phosphate (GlcN-6-P) deaminase.
In vitro
experiments demonstrated that GlcN-6-P acts as an inhibitor of YvoA DNA-binding activity, as occurs for its
Streptomyces
ortholog, DasR. Interestingly, we observed that the expression of
nag
genes was still activated upon addition of GlcNAc in a Δ
yvoA
mutant background, suggesting the existence of an auxiliary transcriptional control instance. Initial computational prediction of the YvoA regulon showed a distribution of YvoA binding sites limited to
nag
genes and therefore suggests renaming YvoA to NagR, for
N
-acetylglucosamine utilization regulator. Whole-transcriptome studies showed significant repercussions of
nagR
deletion for several major
B. subtilis
regulators, probably indirectly due to an excess of the crucial molecules acetate, ammonia, and fructose-6-phosphate, resulting from complete hydrolysis of GlcNAc. We discuss a model deduced from NagR-mediated gene expression, which highlights clear connections with pathways for GlcNAc-containing polymer biosynthesis and adaptation to growth under oxygen limitation.
Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution
Authors: Fricke W. Florian , Mammel Mark K. , McDermott Patrick F. , Tartera Carmen , White David G. , LeClerc J. Eugene , Ravel Jacques , Cebula Thomas A. 
Published: May 2011

ABSTRACT

Despite extensive surveillance, food-borne
Salmonella enterica
infections continue to be a significant burden on public health systems worldwide. As the
S. enterica
species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of
S. enterica
sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal
S. enterica
strains to 11 previously sequenced
S. enterica
genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known
S. enterica
sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between
S. enterica
clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of
S. enterica
sublineages and aid in the prediction and prevention of future
S. enterica
outbreaks.
Antiparallel and Interlinked Control of Cellular Iron Levels by the Irr and RirA Regulators of Agrobacterium tumefaciens
Authors: Hibbing Michael E. , Fuqua Clay 
Published: May 2011

ABSTRACT

The plant pathogen
Agrobacterium tumefaciens
encodes predicted iron-responsive regulators, Irr and RirA, that function in several other bacteria to control the response to environmental iron levels. Deletion mutations of
irr
and
rirA
, alone and in combination, were evaluated for their impact on cellular iron response. Growth was severely diminished in the Δ
irr
mutant under iron-limiting conditions, but reversed to wild-type levels in an Δ
irr
Δ
rirA
mutant. The level of uncomplexed iron in the Δ
irr
mutant was decreased, whereas the Δ
rirA
mutant exhibited elevated iron levels. Sensitivity of the Δ
irr
and Δ
rirA
mutants to iron-activated antimicrobial compounds generally reflected their uncomplexed-iron levels. Expression of genes that encode iron uptake systems was decreased in the Δ
irr
mutant, whereas that of iron utilization genes was increased. Irr function required a trihistidine repeat likely to mediate interactions with heme. Iron uptake genes were derepressed in the Δ
rirA
mutant. In the Δ
irr
Δ
rirA
mutant, iron uptake and utilization genes were derepressed, roughly combining the phenotypes of the single mutants. Siderophore production was elevated in the
rirA
mutant, but most strongly regulated by an RirA-controlled sigma factor. Expression of
rirA
itself was regulated by Irr, RirA, and iron availability, in contrast to
irr
expression, which was relatively stable in the different mutants. These studies suggest that in
A. tumefaciens
, the Irr protein is most active under low-iron conditions, inhibiting iron utilization and activating iron acquisition, while the RirA protein is active under high-iron conditions, repressing iron uptake.
Role of Dihydrolipoamide Dehydrogenase in Regulation of Raffinose Transport in Streptococcus pneumoniae
Authors: Tyx Robert E. , Roche-Hakansson Hazeline , Hakansson Anders P. 
Published: May 2011

ABSTRACT

Streptococcus pneumoniae
strains lacking the enzyme dihydrolipoamide dehydrogenase (DLDH) show markedly reduced ability to grow on raffinose and stachyose as sole carbon sources. Import of these sugars occurs through the previously characterized raffinose ATP-binding cassette (ABC) transport system, encoded by the
raf
operon, that lacks the necessary ATP-binding protein. In this study, we identified the raffinose ATP-binding protein RafK and showed that it was directly involved in raffinose and stachyose import. RafK carries a C-terminal regulatory domain present in a subset of ATP-binding proteins that has been involved in both direct regulation of transporter activity (inducer exclusion) and transcription of transporter genes. Pneumococci lacking RafK showed a 50- to 80-fold reduction in expression of the
raf
operon genes
aga
(alpha-galactosidase) and
rafEFG
(raffinose substrate binding and permease genes), and both glucose and sucrose inhibited raffinose uptake through inducer exclusion. Like RafK, the presence of DLDH also activated the expression of
raf
operon genes, as DLDH-negative pneumococci showed a significantly decreased expression of
aga
and
rafEFG
, but DLDH did not regulate
rafK
or the putative regulatory genes
rafR
and
rafS
. DLDH also bound directly to RafK both
in vitro
and
in vivo
, indicating the possibility that DLDH regulates raffinose transport by a direct interaction with the regulatory domain of the transporter. Finally, although not as attenuated as DLDH-negative bacteria, pneumococci lacking RafK were significantly outcompeted by wild-type bacteria in colonization experiments of murine lung and nasopharynx, indicating a role for raffinose and stachyose transport
in vivo
.
Reliability of Acugraph System for Measuring Skin Conductance at Acupoints
Authors: Mist Scott D , Aickin Mikel , Kalnins Paul , Cleaver Jim , Batchelor Roger , Thorne Tracy , Chamberlin Steve , Tippens Kim , Colbert Agatha P 
Published: May 2011

Objective There are many commercially available instruments for measuring electrical conductance, but there is little information about their reliability. The aim of this study was to quantify measurement variability and assess reliability of the AcuGraph system—a commonly used electrodermal screening device. Methods Four experiments were conducted to measure variability in electrical conductance readings obtained by the AcuGraph system. The first involved measuring known resistors. The second measured non-human organic matter. The third was a test–retest assessment of the Yuan-Source and Jing-Well points in 30 healthy volunteers who were measured by a single operator. The fourth was an interoperator reliability evaluation of seven acupuncturists at the Yuan-Source and Jing-Well acupoints on four individuals at two time points. Results Against known resistors, the AcuGraph had an average coefficient of variability (CV) of 1.8% between operators and test–retests. On non-human organic material the AcuGraph had an average CV of 0.9% and 2.8%. When a single operator tested 30 participants, the average reliability for the Yuan-Source points was 0.86 and 0.76 for Jing-Well points with a CV of 23.2% and 25.9% respectively. The average CV for the seven acupuncturists was 24.5% on Yuan-Source points and 23.7% on Jing-Well points. Conclusions The AcuGraph measures known resistors and organic matter accurately and reliably. Skin conductance at acupoints recorded by one operator was also reliable. There was less consistency in electrodermal recordings obtained by seven different operators. Operator training and technical improvements to the AcuGraph may improve consistency among operators.
Carcinogenic tobacco-specificN-nitrosamines in US cigarettes: three decades of remarkable neglect by the tobacco industry
Authors: Stepanov Irina , Knezevich Aleksandar , Zhang Liqin , Watson Clifford H , Hatsukami Dorothy K , Hecht Stephen S 
Published: May 2011

BackgroundModification of tobacco curing methods and other changes in cigarette manufacturing techniques could substantially reduce the levels of tobacco-specific nitrosamines (TSNA), a group of potent carcinogens, in cigarette smoke. In 1999, two major US cigarette manufacturers stated their intent to move towards using tobaccos low in TSNA. There is no information available on current TSNA levels in tobacco of various cigarettes available in the US, particularly in the newer varieties introduced over the past decade.MethodsSeventeen brands of cigarettes were purchased in April of 2010 from retail stores in Minnesota. TSNA levels were measured in the tobacco filler and smoke of these cigarettes.ResultsIn all brands, the sum of two potent carcinogenic TSNA - 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone andN'-nitrosonornicotine - in cigarette filler averaged 2.54 (±1.05) μg/g tobacco. This value is virtually identical to the sum of these two carcinogens reported for the tobacco of a US filtered cigarette in 1979. TSNA levels in smoke positively correlated with those in tobacco filler of the same cigarettes.ConclusionWe found no indication that any meaningful attempt was made to reduce or at least control TSNA levels in the new varieties of the popular brands Marlboro and Camel introduced over the last decade. In light of the recently granted regulatory authority to the FDA over tobacco products, regulation of TSNA levels in cigarette tobacco should be strongly considered to reduce the levels of these potent carcinogens in cigarette smoke.
Combination of PI3K/mTOR Inhibitors: Antitumor Activity and Molecular Correlates
Authors: Mazzoletti Marco , Bortolin Francesca , Brunelli Laura , Pastorelli Roberta , Di Giandomenico Silvana , Erba Eugenio , Ubezio Paolo , Broggini Massimo 
Published: May 2011

Abstract
The phosphatidylinositol-3-kinase (PI3K)/Akt/mTOR pathway is a major target for cancer therapy. As a strategy to induce the maximal inhibition of this pathway in cancer cells, we combined allosteric mTOR inhibitors (rapamycin and RAD001) with a dual PI3K/mTOR kinase inhibitor (PI-103). Both in vitro and in vivo, the combination exhibited more activity than single agents in human ovarian and prostate cancer cells that harbor alterations in the pathway. At the molecular level, combined inhibition of mTOR prevented the rebound activation of Akt that is seen after treatment with rapamycin and its analogues and caused more sustained inhibition of Akt phosphorylation. Furthermore, the combination strongly inhibited the expression of PI3K/Akt/mTOR downstream proteins. In particular, it showed greater activity than the single agents in inhibiting the phosphorylation of 4EBP1, both in vitro and in vivo, resulting in selective inhibition of CAP-dependent translation. A proteomic approach was used to confirm the identification of c-Myc as the key regulator for the reduction in downstream proteins affected by the combined inhibition of mTOR. In conclusion, the combination of a catalytic and an allosteric inhibitor of mTOR shows greater activity, without a concomitant increase in toxicity, than either drug alone, and this may have therapeutic implications for inhibiting this pathway in the clinical setting. Cancer Res; 71(13); 4573–84. ©2011 AACR.
Curcumin Sensitizes Acute Promyelocytic Leukemia Cells to Unfolded Protein Response–Induced Apoptosis by Blocking the Loss of Misfolded N-CoR Protein
Authors: Ng Angela Ping Ping , Chng Wee Joo , Khan Matiullah 
Published: May 2011

Abstract
Acute promyelocytic leukemia (APL) is characterized by accumulation of apoptosis-resistant immature promyelocytic cells in the bone marrow and peripheral blood. We have shown that endoplasmic reticulum (ER)–associated degradation (ERAD) and protease-mediated degradation of misfolded nuclear receptor corepressor (N-CoR) confer resistance to unfolded protein response (UPR)-induced apoptosis in APL. These findings suggest that therapeutic inhibition of N-CoR misfolding or degradation may promote growth arrest in APL cells by sensitizing them to UPR-induced apoptosis. On the basis of this hypothesis, we tested the effects of several known protein conformation–modifying agents on the growth and survival of APL cells and identified curcumin, a natural component of turmeric, as a potent growth inhibitor of APL cells. Curcumin selectively inhibited the growth and promoted apoptosis in both primary and secondary leukemic cells derived from APL. The curcumin-induced apoptosis of APL cells was triggered by an amplification of ER stress, possibly from the accumulation of misfolded N-CoR protein in the ER. Curcumin promoted this net accumulation of aberrantly phosphorylated misfolded N-CoR protein by blocking its ERAD and protease-mediated degradation, which then led to the activation of UPR-induced apoptosis in APL cells. The activation of UPR by curcumin was manifested by phosphorylation of protein kinase RNA-like endoplasmic reticulum kinase (PERK) and eukaryotic translation initiation factor 2 alpha (eIF2α), and upregulation of C/EBP homologous protein (CHOP) and GADD34, the principal mediators of proapoptotic UPR. These findings identify the therapeutic potential of curcumin in APL and further establish the rationale of misfolded N-CoR protein as an attractive molecular target in APL. Mol Cancer Res; 9(7); 878–88. ©2011 AACR.