bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of the Gonococcal Global Regulatory Protein Fur and Genes Encompassing the Fur and Iron Regulon during In Vitro and In Vivo Infection in Women
Authors: Agarwal Sarika , Sebastian Shite , Szmigielski Borys , Rice Peter A. , Genco Caroline A. 
Published: March 2008

ABSTRACT

The ferric uptake regulatory protein, Fur, functions as a global regulatory protein of gene transcription in the mucosal pathogen
Neisseria gonorrhoeae
. We have shown previously that several
N. gonorrhoeae
Fur-repressed genes are expressed in vivo during mucosal gonococcal infection in men, which suggests that this organism infects in an iron-limited environment and that Fur is expressed under these conditions. In this study we have demonstrated expression of the gonococcal
fur
gene in vitro, in human cervical epithelial cells, and in specimens from female subjects with uncomplicated gonococcal infection. In vitro studies confirmed that the expression of the gonococcal
fur
gene was repressed during growth under iron-replete growth conditions but that a basal level of the protein was maintained. Using GFP transcriptional fusions constructed from specific Fur binding sequences within the
fur
promoter/operator region, we determined that this operator region was functional during
N. gonorrhoeae
infection of cervical epithelial cells. Furthermore, reverse transcription-PCR analysis, as well as microarray analysis, using a custom
Neisseria
Fur and iron regulon microarray revealed that several Fur- and iron-regulated genes were expressed during
N. gonorrhoeae
infection of cervical epithelial cells. Microarray analysis of specimens obtained from female subjects with uncomplicated gonococcal infection corroborated our in vitro findings and point toward a key role of gonococcal Fur- and iron-regulated genes in gonococcal disease.
Deficiency of the Rgg Regulator Promotes H2O2Resistance, AhpCF-Mediated H2O2Decomposition, and Virulence inStreptococcus pyogenes
Authors: Pulliainen Arto Tapio , Hytönen Jukka , Haataja Sauli , Finne Jukka 
Published: March 2008

ABSTRACTStreptococcus pyogenes(group A streptococcus [GAS]), a catalase-negative gram-positive bacterium, is aerotolerant and survives H2O2exposures that kill many catalase-positive bacteria. The molecular basis of the H2O2resistance is poorly known. Here, we demonstrate that serotype M49 GAS lacking the Rgg regulator is more resistant to H2O2and also decomposes more H2O2than the parental strain. Subgenomic transcriptional profiling and genome-integrated green fluorescent protein reporters showed that a bicistronic operon, a homolog of theStreptococcus mutans ahpCFoperon, is transcriptionally up-regulated in the absence of Rgg. Phenotypic assays withahpCFoperon knockouts demonstrated that the gene products decompose H2O2and protect GAS against peroxide stress. In a murine intraperitoneal-infection model, Rgg deficiency increased the virulence of GAS, although in anahpCF-independent manner. Rgg-mediated repression of H2O2resistance is divergent from the previously characterized peroxide resistance repressor PerR. Moreover, Rgg-mediated repression of H2O2resistance is inducible by cellular stresses of diverse natures—ethanol, organic hydroperoxide, and H2O2. Rgg is thus identified as a novel sensoregulator of streptococcal H2O2resistance with potential implications for the virulence of the catalase-negative GAS.
Sustained Axenic Metabolic Activity by the Obligate Intracellular Bacterium
Coxiella burnetii
Authors: Omsland Anders , Cockrell Diane C. , Fischer Elizabeth R. , Heinzen Robert A. 
Published: March 2008

ABSTRACT

Growth of
Coxiella burnetii
, the agent of Q fever, is strictly limited to colonization of a viable eukaryotic host cell. Following infection, the pathogen replicates exclusively in an acidified (pH 4.5 to 5) phagolysosome-like parasitophorous vacuole. Axenic (host cell free) buffers have been described that activate
C. burnetii
metabolism in vitro, but metabolism is short-lived, with bacterial protein synthesis halting after a few hours. Here, we describe a complex axenic medium that supports sustained (>24 h)
C. burnetii
metabolic activity. As an initial step in medium development, several biological buffers (pH 4.5) were screened for
C. burnetii
metabolic permissiveness. Based on [
35
S]Cys-Met incorporation,
C. burnetii
displayed optimal metabolic activity in citrate buffer. To compensate for
C. burnetii
auxotrophies and other potential metabolic deficiencies, we developed a citrate buffer-based medium termed complex
Coxiella
medium (CCM) that contains a mixture of three complex nutrient sources (neopeptone, fetal bovine serum, and RPMI cell culture medium). Optimal
C. burnetii
metabolism occurred in CCM with a high chloride concentration (140 mM) while the concentrations of sodium and potassium had little effect on metabolism. CCM supported prolonged de novo protein and ATP synthesis by
C. burnetii
(>24 h). Moreover,
C. burnetii
morphological differentiation was induced in CCM as determined by the transition from small-cell variant to large-cell variant. The sustained in vitro metabolic activity of
C. burnetii
in CCM provides an important tool to investigate the physiology of this organism including developmental transitions and responses to antimicrobial factors associated with the host cell.
Putative Quorum-Sensing Regulator BlxR ofBrucella melitensisRegulates Virulence Factors Including the Type IV Secretion System and Flagella
Authors: Rambow-Larsen Amy A. , Rajashekara Gireesh , Petersen Erik , Splitter Gary 
Published: March 2008

ABSTRACTBrucella melitensisis an intracellular pathogen that establishes a replicative niche within macrophages. While the intracellular lifestyle ofBrucellais poorly understood and few virulence factors have been identified, components of a quorum-sensing pathway inBrucellahave recently been identified. The LuxR-type regulatory protein, VjbR, and anN-acylhomoserine lactone signaling molecule are both involved in regulating expression of thevirB-encoded type IV secretion system. We have identified a second LuxR-type regulatory protein (BlxR) inBrucella. Microarray analysis of ablxRmutant suggests that BlxR regulates the expression of a number of genes, including those encoding the type IV secretion system and flagella. Confirming these results, deletion ofblxRinB. melitensisreduced the transcriptional activities of promoters for thevirBoperon, flagellar genes, and another putative virulence factor gene,bopA. Furthermore, our data suggested that both BlxR and VjbR are positively autoregulated and cross-regulate the expression of each other. TheblxRdeletion strain exhibited reduced growth in macrophages, similar to that observed for avjbRdeletion strain. However, unlike thevjbRdeletion, theblxRdeletion did not fully attenuate virulence in mice. More strikingly, bioluminescent imaging revealed that dissemination of theblxRmutant was similar to that of wild-typeB. melitensis, while thevjbRmutant was defective for systemic spread in IRF-1−/−mice, suggesting that these regulators are not functionally redundant but that they converge in a common pathway regulating bacterial processes.
The Extracellular Death Factor: Physiological and Genetic Factors Influencing Its Production and Response inEscherichia coli
Authors: Kolodkin-Gal Ilana , Engelberg-Kulka Hanna 
Published: March 2008

ABSTRACTGene pairs specific for a toxin and its antitoxin are called toxin-antitoxin modules and are found on the chromosomes of many bacteria. The most studied of these modules isEscherichia coli mazEF, in whichmazFencodes a stable toxin, MazF, andmazEencodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. In a previous report from this laboratory, it was shown thatmazEF-mediated cell death is a population phenomenon requiring a quorum-sensing peptide called theextracellulardeathfactor (EDF). EDF is the linear pentapeptide NNWNN (32). Here, we further confirm that EDF is a signal molecule in a mixed population. In addition, we characterize some physiological conditions and genes required for EDF production and response. Furthermore, stress response and the gene specifying MazEF, the Zwf (glucose-6-phosphate dehydrogenase) gene, and the protease ClpXP are critical in EDF production. Significant strain differences in EDF production and response explain variations in the induction ofmazEF-mediated cell death.
Campylobacter jejuniCsrA Mediates Oxidative Stress Responses, Biofilm Formation, and Host Cell Invasion
Authors: Fields Joshua A. , Thompson Stuart A. 
Published: March 2008

ABSTRACTThe putative global posttranscriptional regulatorcsrAwas mutated inCampylobacter jejuni81-176. ThecsrAmutant was attenuated in surviving oxidative stress. CsrA also contributed to biofilm formation and adherence to and invasion of INT407 intestinal epithelial cells, suggesting a regulatory role for CsrA inC. jejunipathogenesis.
ThesimOperon Facilitates the Transport and Metabolism of Sucrose Isomers inLactobacillus caseiATCC 334
Authors: Thompson John , Jakubovics Nicholas , Abraham Bindu , Hess Sonja , Pikis Andreas 
Published: March 2008

ABSTRACTInspection of the genome sequence ofLactobacillus caseiATCC 334 revealed two operons that might dissimilate the five isomers of sucrose. To test this hypothesis, cells ofL. caseiATCC 334 were grown in a defined medium supplemented with various sugars, including each of the five isomeric disaccharides. Extracts prepared from cells grown on the sucrose isomers contained high levels of two polypeptides withMrs of ∼50,000 and ∼17,500. Neither protein was present in cells grown on glucose, maltose or sucrose. Proteomic, enzymatic, and Western blot analyses identified the ∼50-kDa protein as an NAD+- and metal ion-dependent phospho-α-glucosidase. The oligomeric enzyme was purified, and a catalytic mechanism is proposed. The smaller polypeptide represented an EIIA component of the phosphoenolpyruvate-dependent sugar phosphotransferase system. Phospho-α-glucosidase and EIIA are encoded by genes at the LSEI_0369 (simA) and LSEI_0374 (simF) loci, respectively, in a block of seven genes comprising thesucroseisomermetabolism (sim) operon. Northern blot analyses provided evidence that three mRNA transcripts were up-regulated during logarithmic growth ofL. caseiATCC 334 on sucrose isomers. InternalsimAandsimFgene probes hybridized to ∼1.5- and ∼1.3-kb transcripts, respectively. A 6.8-kb mRNA transcript was detected by both probes, which was indicative of cotranscription of the entiresimoperon.
Human RNA “Rumor” Viruses: the Search for Novel Human Retroviruses in Chronic Disease
Authors: Voisset Cécile , Weiss Robin A. , Griffiths David J. 
Published: March 2008

SUMMARYRetroviruses are an important group of pathogens that cause a variety of diseases in humans and animals. Four human retroviruses are currently known, including human immunodeficiency virus type 1, which causes AIDS, and human T-lymphotropic virus type 1, which causes cancer and inflammatory disease. For many years, there have been sporadic reports of additional human retroviral infections, particularly in cancer and other chronic diseases. Unfortunately, many of these putative viruses remain unproven and controversial, and some retrovirologists have dismissed them as merely “human rumor viruses.” Work in this field was last reviewed in depth in 1984, and since then, the molecular techniques available for identifying and characterizing retroviruses have improved enormously in sensitivity. The advent of PCR in particular has dramatically enhanced our ability to detect novel viral sequences in human tissues. However, DNA amplification techniques have also increased the potential for false-positive detection due to contamination. In addition, the presence of many families of human endogenous retroviruses (HERVs) within our DNA can obstruct attempts to identify and validate novel human retroviruses. Here, we aim to bring together the data on “novel” retroviral infections in humans by critically examining the evidence for those putative viruses that have been linked with disease and the likelihood that they represent genuine human infections. We provide a background to the field and a discussion of potential confounding factors along with some technical guidelines. In addition, some of the difficulties associated with obtaining formal proof of causation for common or ubiquitous agents such as HERVs are discussed.
Inhibition of Urinary Bladder Carcinogenesis by Broccoli Sprouts
Authors: Munday Rex , Mhawech-Fauceglia Paulette , Munday Christine M. , Paonessa Joseph D. , Tang Li , Munday John S. , Lister Carolyn , Wilson Paula , Fahey Jed W. , Davis Warren , Zhang Yuesheng 
Published: March 2008

Abstract
Isothiocyanates are a well-known class of cancer chemopreventive agents, and broccoli sprouts are a rich source of several isothiocyanates. We report herein that dietary administration to rats of a freeze-dried aqueous extract of broccoli sprouts significantly and dose-dependently inhibited bladder cancer development induced by N-butyl-N-(4-hydroxybutyl) nitrosamine. The incidence, multiplicity, size, and progression of bladder cancer were all inhibited by the extract, while the extract itself caused no histologic changes in the bladder. Moreover, inhibition of bladder carcinogenesis by the extract was associated with significant induction of glutathione S-transferase and NAD(P)H:quinone oxidoreductase 1 in the bladder, enzymes that are important protectants against oxidants and carcinogens. Isothiocyanates are metabolized to dithiocarbamates in vivo, but dithiocarbamates readily dissociate to isothiocyanates. We found that &gt;70% of the isothiocyanates present in the extract were excreted in the urine as isothiocyanate equivalents (isothiocyanates + dithiocarbamates) in 12 h after a single p.o. dose, indicating high bioavailability and rapid urinary excretion. In addition, the concentrations of isothiocyanate equivalents in the urine of extract-treated rats were 2 to 3 orders of magnitude higher than those in plasma, indicating that the bladder epithelium, the major site of bladder cancer development, is most exposed to p.o. dosed isothiocyanate. Indeed, tissue levels of isothiocyanate equivalents in the bladder were significantly higher than in the liver. In conclusion, broccoli sprout extract is a highly promising substance for bladder cancer prevention and the isothiocyanates in the extract are selectively delivered to the bladder epithelium through urinary excretion. [Cancer Res 2008;68(5):1593–600]
Small Molecular Weight Variants of p53 Are Expressed in Human Melanoma Cells and Are Induced by the DNA-Damaging Agent Cisplatin
Authors: Avery-Kiejda Kelly A. , Zhang Xu Dong , Adams Luke J. , Scott Rodney J. , Vojtesek Borivoj , Lane David P. , Hersey Peter 
Published: March 2008

Abstract
Purpose: Metastatic melanoma is largely unresponsive to DNA-damaging chemotherapy agents, although WTp53 is frequently detected. Several isoforms of p53 have been discovered, some of which inhibit p53 function. We therefore examined whether p53 isoforms were present in melanoma and whether they may contribute to aberrant p53 function in melanoma.
Experimental Design: We studied the expression and subcellular localization of p53 and its isoforms in a panel of human melanoma cell lines using Western blot, two-dimensional electrophoresis, and reverse transcription-PCR. We also characterized the relationship between the expression of p53, p53 isoforms, and p53 target genes following treatment with the DNA-damaging agent cisplatin.
Results: We report that p53β and Δ40p53 were expressed in the majority of melanoma cell lines at the mRNA level, but were absent or expressed at low levels in fibroblasts and melanocytes, suggesting that their expression may play a role in melanoma development. Analysis by two-dimensional gel electrophoresis revealed that p53β was expressed at the protein level in melanoma cells. Both p53 and the small molecular weight forms of p53 were aberrantly expressed between the nuclear and cytosolic fractions of melanoma cell lines, compared with normal fibroblasts. Treatment with cisplatin had differential effects on WTp53 and the small molecular weight form of p53 that were cell line dependent. Δ40p53 was shown to inhibit, whereas p53β was shown to enhance, p53-dependent transcription of p21 and PUMA.
Conclusions: p53β and Δ40p53 are expressed in melanoma and this may have important implications for understanding resistance of melanoma to DNA-damaging chemotherapy.
Molecular, Pathologic, and Clinical Features of Early-Onset Endometrial Cancer: Identifying Presumptive Lynch Syndrome Patients
Authors: Walsh Michael D. , Cummings Margaret C. , Buchanan Daniel D. , Dambacher Wendy M. , Arnold Sven , McKeone Diane , Byrnes Rebecca , Barker Melissa A. , Leggett Barbara A. , Gattas Michael , Jass Jeremy R. , Spurdle Amanda B. , Young Joanne , Obermair Andreas 
Published: March 2008

Abstract
Purpose: A woman with early-onset endometrial cancer (EC) may represent the “sentinel” cancer event in a Lynch syndrome kindred. The aim of this study was to determine the incidence of Lynch syndrome in a series of young-onset EC, and to identify molecular, clinical, and pathologic features that may alert clinicians to the presence of this disorder.
Experimental Design: Patients with EC, ages ≤50 years, were identified from the Queensland Centre for Gynaecological Cancer. Tumor sections underwent histopathology review and were immunostained for mismatch repair proteins. Tumor DNA was tested for microsatellite instability and methylation of MLH1. Patients were conservatively classified as presumptive Lynch syndrome if their tumors showed loss of at least one mismatch repair protein and were negative for methylation of MLH1. Personal and family history of cancer was reviewed where available.
Results: Presumptive Lynch syndrome was seen in 26 of 146 (18%) tumors. These tumors were more likely to be poorly differentiated, International Federation of Gynecology and Obstetrics stage II and above, have tumor-infiltrating lymphocytes, have higher mitotic rate, and have deeper myometrial invasion (P &lt; 0.05). Lynch syndrome cases were more likely to be associated with a positive family history when analyzed for Amsterdam criteria II, diagnosis of a Lynch syndrome spectrum cancer in at least one first-degree relative, and family history of any cancer (P &lt; 0.05).
Conclusion: Presumptive Lynch syndrome was identified in 18% of early-onset EC. A risk of this magnitude would argue for routine immunohistochemical testing of tumors in patients diagnosed with EC at or before the age of 50 years.
Sorafenib, but not sunitinib, affects function of dendritic cells and induction of primary immune responses
Authors: Hipp Madeleine M. , Hilf Norbert , Walter Steffen , Werth Daniela , Brauer Katharina M. , Radsak Markus P. , Weinschenk Toni , Singh-Jasuja Harpreet , Brossart Peter 
Published: March 2008

AbstractThe tyrosine kinase inhibitors sorafenib and sunitinib are approved for the treatment of patients with malignant diseases. To analyze the possible use of these compounds in combination with immunotherapeutic approaches, we analyzed the effects of both inhibitors on the immunostimulatory capacity of human dendritic cells (DCs) and the induction of primary immune responses in vivo. Sorafenib, but not sunitinib, inhibits function of DCs, characterized by reduced secretion of cytokines and expression of CD1a, major histocompatibility complex, and costimulatory molecules in response to TLR ligands as well as by their impaired ability to migrate and stimulate T-cell responses. These inhibitory effects are mediated by inhibition of PI3 and MAP kinases and NFκB signaling. In contrast, sorafenib had no influence on the phenotype and proliferation of T cells. To analyze the effects of both TKIs on cytotoxic T-cell induction in vivo, C57BL/6 mice were pretreated with sorafenib or sunitinib and immunized with OVA257-264 peptide. Sorafenib, but not sunitinib, application significantly reduced the induction of antigen-specific T cells. Numbers of regulatory T cells were reduced in peripheral blood mononuclear cells from mice treated with sunitinib. These results indicate that sunitinib, but not sorafenib, is suitable for combination with immunotherapeutic approaches for treatment of cancer patients.
Inhibition of endogenous TGF-β signaling enhances lymphangiogenesis
Authors: Oka Masako , Iwata Caname , Suzuki Hiroshi I. , Kiyono Kunihiko , Morishita Yasuyuki , Watabe Tetsuro , Komuro Akiyoshi , Kano Mitsunobu R. , Miyazono Kohei 
Published: March 2008

AbstractLymphangiogenesis is induced by various growth factors, including VEGF-C. Although TGF-β plays crucial roles in angiogenesis, the roles of TGF-β signaling in lymphangiogenesis are unknown. We show here that TGF-β transduced signals in human dermal lymphatic microvascular endothelial cells (HDLECs) and inhibited the proliferation, cord formation, and migration toward VEGF-C of HDLECs. Expression of lymphatic endothelial cell (LEC) markers, including LYVE-1 and Prox1 in HDLECs, as well as early lymph vessel development in mouse embryonic stem cells in the presence of VEGF-A and C, were repressed by TGF-β but were induced by TGF-β type I receptor (TβR-I) inhibitor. Moreover, inhibition of endogenous TGF-β signaling by TβR-I inhibitor accelerated lymphangiogenesis in a mouse model of chronic peritonitis. Lymphangiogenesis was also induced by TβR-I inhibitor in the presence of VEGF-C in pancreatic adenocarcinoma xenograft models inoculated in nude mice. These findings suggest that TGF-β transduces signals in LECs and plays an important role in the regulation of lymphangiogenesis in vivo.
Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions
Authors: Murakami Katsuhiko , Imanishi Tadashi , Gojobori Takashi , Nakai Kenta 
Published: March 2008

AbstractBackgroundIt is essential in modern biology to understand how transcriptional regulatory regions are composed ofcis-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and their positional distribution.ResultsWe predicted the positions of 228 known binding motifs for transcription factors in phylogenetically conserved regions within -2000 and +1000 bp of transcriptional start sites (TSSs) of human genes and visualized their correlated non-overlapping occurrences. In the 8,454 significantly correlated motif pairs, two major classes were observed: 248 pairs in Class 1 were mainly found around TSSs, whereas 4,020 Class 2 pairs appear at rather arbitrary distances from TSSs. These classes are distinct in a number of aspects. First, the positional distribution of the Class 1 constituent motifs shows a single peak near the TSSs, whereas Class 2 motifs show a relatively broad distribution. Second, genes that harbor the Class 1 pairs are more likely to be CpG-rich and to be expressed ubiquitously than those that harbor Class 2 pairs. Third, the 'hub' motifs, which are used in many different motif pairs, are different between the two classes. In addition, many of the transcription factors that correspond to the Class 2 hub motifs contain domains rich in specific amino acids; these domains may form disordered regions important for protein-protein interaction.ConclusionThere exist at least two classes of motif pairs with respect to TSSs in human promoters, possibly reflecting compositional differences between promoters and enhancers. We anticipate that our visualization method may be useful for the further characterisation of promoters.