bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence Analysis of the 144-Kilobase Accessory Plasmid pSmeSM11a, Isolated from a DominantSinorhizobium melilotiStrain Identified during a Long-Term Field Release Experiment
Authors: Stiens M. , Schneiker S. , Keller M. , Kuhn S. , Pühler A. , Schlüter A. 
Published: May 2006

ABSTRACTThe genome ofSinorhizobium melilotitype strain Rm1021 consists of three replicons: the chromosome and two megaplasmids, pSymA and pSymB. Additionally, many indigenousS. melilotistrains possess one or more smaller plasmids, which represent the accessory genome of this species. Here we describe the complete nucleotide sequence of an accessory plasmid, designated pSmeSM11a, that was isolated from a dominant indigenousS. melilotisubpopulation in the context of a long-term field release experiment with genetically modifiedS. melilotistrains. Sequence analysis of plasmid pSmeSM11a revealed that it is 144,170 bp long and has a mean G+C content of 59.5 mol%. Annotation of the sequence resulted in a total of 160 coding sequences. Functional predictions could be made for 43% of the genes, whereas 57% of the genes encode hypothetical or unknown gene products. Two plasmid replication modules, one belonging to therepABCreplicon family and the other belonging to the plasmid type A replicator region family, were identified. Plasmid pSmeSM11a contains a mobilization (mob) module composed of the type IV secretion system-related genestraGandtraAand a putativemobCgene. A large continuous region that is about 42 kb long is very similar to a corresponding region located onS. melilotiRm1021 megaplasmid pSymA. Single-base-pair deletions in the homologous regions are responsible for frameshifts that result in nonparalogous coding sequences. Plasmid pSmeSM11a carries additional copies of the nodulation genesnodPandnodQthat are responsible for Nod factor sulfation. Furthermore, atauDgene encoding a putative taurine dioxygenase was identified on pSmeSM11a. AnacdSgene located on pSmeSM11a is the first example of such a gene inS. meliloti. The deducedacdSgene product is able to deaminate 1-aminocyclopropane-1-carboxylate and is proposed to be involved in reducing the phytohormone ethylene, thus influencing nodulation events. The presence of numerous insertion sequences suggests that these elements mediated acquisition of accessory plasmid modules.
Use of Fluorescence Resonance Energy Transfer for Rapid Detection of Enteroviral Infection In Vivo
Authors: Hwang Yu-Chen , Chen Wilfred , Yates Marylynn V. 
Published: May 2006

ABSTRACTEnteroviruses can be easily transmitted through the fecal-oral route and cause a diverse array of clinical manifestations. Recent outbreaks associated with enteroviral contamination in aquatic environments have called for the development of a more efficient and accurate virus monitoring system. To develop a simple, rapid, and direct method for identifying enteroviral infections, we generated a fluorescent reporter system in which genetically engineered cells express a hybrid fluorescent indicator composed of a linker peptide, which is exclusively cleaved by the 2A protease (2Apro), flanked with a cyan fluorescent protein (CFP) and a yellow fluorescent protein undergoing fluorescence resonance energy transfer. The covalent linkage between two fluorophores is disrupted due to 2Aproactivity upon viral infection, which results in an increase in CFP intensity. This allows the rapid (within 7.5 h) detection of very low numbers (10 PFU or fewer) of infectious enteroviruses.
Single-Nucleotide-Polymorphism-Specific PCR for Quantification and Discrimination of
Chlamydia pneumoniae
Genotypes by Use of a “Locked” Nucleic Acid
Authors: Rupp Jan , Solbach Werner , Gieffers Jens 
Published: May 2006

ABSTRACT
Single-nucleotide polymorphisms (SNPs) are targets to discriminate intraspecies diversity of bacteria and to correlate a genotype with a potential pathotype. Quantification of polygenotypic populations supports this task for in vitro and in vivo applications. We present a novel assay capable of quantifying mixtures of two genotypes differing by only one SNP.
Incidence of
Helicobacter felis
and the Effect of Coinfection with
Helicobacter pylori
on the Gastric Mucosa in the African Population
Authors: Fritz E. Lekunze , Slavik Tomas , Delport Wayne , Olivier Brenda , van der Merwe Schalk W. 
Published: May 2006

ABSTRACT

Helicobacter pylori
and
Helicobacter felis
are two of the
Helicobacter
spp. that infect humans.
H. pylori
has been linked to significant gastric pathology. Coinfection with
Helicobacter
spp. may influence infectious burden, pathogenesis, and antibiotic resistance; however, this has not been studied. The aims of this study were to identify the incidence of
H. felis
and to analyze the effects of coinfection with both organisms on gastric pathology in a well-characterized South African population. Biopsy samples from the gastric corpora and antra of volunteers (
n
= 90) were subjected to histological examination and PCR for the identification of
H. pylori
and
H. felis
. We further investigated the effect of global strain type on the occurrence of precursor lesions by assigning nucleotide sequences derived from PCR amplification of three genes to global groupings (ancestral Africa1, ancestral Africa2, ancestral Europe, ancestral Asia, and mixed).
H. pylori
was detected in 75 (83.3%),
H. felis
in 23 (25.6%), and coinfection in 21 (23.3%) of the volunteers by PCR.
H. felis
was randomly distributed among adults and children but clustered within families, suggesting intrafamilial transmission. Analysis of histopathology scores revealed no differences in atrophy, activity, and helicobacter density between
H. felis
-positive and
H. felis
-negative volunteers.
H. pylori
substrains common to southern Africa showed no differences in inflammation or atrophy scores. The incidences of
H. felis
and coinfection with
H. pylori
in the African population are high.
H. felis
infection, however, does not influence specific gastric pathology in this population.
Sensitivity of the Multispot HIV-1/HIV-2 Rapid Test Using Samples from Human Immunodeficiency Virus Type 1-Positive Individuals with Various Levels of Exposure to Highly Active Antiretroviral Therapy
Authors: O'Connell Robert J. , Agan Brian K. , Anderson Stephanie A. , Malia Jennifer A. , Michael Nelson L. 
Published: May 2006

ABSTRACT
The Multispot HIV-1/HIV-2 rapid test detects human immunodeficiency virus type 1 (HIV-1) gp41 antibodies, which can wane over time in some HIV-1-infected populations, resulting in false-negative screening results. Multispot sensitivity was 100% using 248 sera from one such population, and it correctly identified serostatus in individuals who previously tested false negative with rapid testing.
Presence of a Novel DNA Methylation Enzyme in Methicillin-Resistant
Staphylococcus aureus
Isolates Associated with Pig Farming Leads to Uninterpretable Results in Standard Pulsed-Field Gel Electrophoresis Analysis
Authors: Bens Corina C. P. M. , Voss Andreas , Klaassen Corné H. W. 
Published: May 2006

ABSTRACT

Genomic DNA from methicillin-resistant
Staphylococcus aureus
isolates recovered from pigs and their caretakers proved resistant to SmaI digestion, leading to uninterpretable results in standard pulsed-field gel electrophoresis. This is the result of a yet unknown restriction/methylation system in the genus
Staphylococcus
with the recognition sequence CCNGG.
Splicing Factor Tra2-β1 Is Specifically Induced in Breast Cancer and Regulates Alternative Splicing of theCD44Gene
Authors: Watermann Dirk O. , Tang Yesheng , zur Hausen Axel , Jäger Markus , Stamm Stefan , Stickeler Elmar 
Published: May 2006

AbstractThe human CD44 gene undergoes extensive alternative splicing of multiple variable exons positioned in a cassette in the middle of the gene. Expression of alternative exons is often restricted to certain tissues and could be associated with tumor progression and metastasis of several human malignancies, including breast cancer. Exon v4 contains multiple copies of a C/A-rich exon enhancer sequence required for optimal inclusion of the exon and binding to the nucleic acid–binding proteins YB-1 and human Tra2-β1. Here, we show that hTra2-β1, a member of the extended family of serine/arginine-rich (SR) splicing factors, enhances the in vivo inclusion of CD44 exons v4 and v5. It increased inclusion of exons v4 and v5 and acted synergistically with YB-1. Activation required the C/A-rich enhancer within exon v4. Several other SR proteins had none or only a slight effect on CD44 exon inclusion. In contrast, SC35 inhibited exon usage and antagonized the effects of Tra2 or YB-1. In a matched pair analysis of human breast cancers and their corresponding nonpathologic tissue controls, we found a significant induction of Tra2-β1 in invasive breast cancer, both on the RNA and protein levels. Together with our functional data, these results suggest an important role for Tra2-β1 in breast cancer. Induction of this splicing factor might be responsible for splicing of CD44 isoforms associated with tumor progression and metastasis. (Cancer Res 2006; 66(9): 4774-80)
Epigenetic Inactivation of Betaig-h3 Gene in Human Cancer Cells
Authors: Shao Genze , Berenguer Jessica , Borczuk Alain C. , Powell Charles A. , Hei Tom K. , Zhao Yongliang 
Published: May 2006

Abstract
Gene silencing by CpG island methylation in the promoter region is one of the mechanisms by which tumor suppressor genes are inactivated in human cancers. It has been shown previously that Betaig-h3 gene, which encodes an extracellular matrix protein involved in cell adhesion and tumorigenesis, is down-regulated or silenced in a variety of human cancer cell lines. To unravel the underlying molecular mechanism(s) for this phenomenon, DNA methylation patterns of Betaig-h3 CpG island were examined in normal, immortalized, and cancer cell lines derived from lung, prostate, mammary, and kidney. A good correlation was observed between promoter hypermethylation and lost expression of Betaig-h3 gene, which was supported by the data that demethylation of promoter by 5-aza-2′-deoxycytidine reactivated Betaig-h3 and restored its expression in Betaig-h3-silenced tumor cell lines. This result was further substantiated by a luciferase reporter assay, showing the restoration of promoter activities and increased response to transforming growth factor-β treatment in Betaig-h3-negative 293T cells when transfected with unmethylated Betaig-h3 promoter. In contrast, activity of Betaig-h3 promoter was completely inactivated by in vitro methylation. Furthermore, CpG methylation of Betaig-h3 promoter was also shown in primary lung tumors that expressed decreased level of Betaig-h3 protein. These results suggest that promoter methylation plays a critical role in promoter silencing of the Betaig-h3 gene in human tumor cells. (Cancer Res 2006; 66(9): 4566-73)
Collagen Type I Induces Disruption of E-Cadherin–Mediated Cell-Cell Contacts and Promotes Proliferation of Pancreatic Carcinoma Cells
Authors: Koenig Alexander , Mueller Claudia , Hasel Cornelia , Adler Guido , Menke Andre 
Published: May 2006

Abstract
Pancreatic cancer is characterized by its invasiveness, early metastasis, and the production of large amounts of extracellular matrix (ECM). We analyzed the influence of type I collagen and fibronectin on the regulation of cellular adhesion in pancreatic cancer cell lines to characterize the role of ECM proteins in the development of pancreatic cancer. We show that collagen type I is able to initiate a disruption of the E-cadherin adhesion complex in pancreatic carcinoma cells. This is due to the increased tyrosine phosphorylation of the complex protein β-catenin, which correlates with collagen type I–dependent activation of the focal adhesion kinase and its association with the E-cadherin complex. The activation and recruitment of focal adhesion kinase to the E-cadherin complex depends on the interaction of type I collagen with β1-containing integrins and an integrin-mediated activation of the cellular kinase Src. The disassembly of the E-cadherin adhesion complex correlates with the nuclear translocation of β-catenin, which leads to an increasing expression of the β-catenin-Lef/Tcf target genes, cyclin D1 and c-myc. In addition to that, cells grown on collagen type I show enhanced cell proliferation. We show that components of the ECM, produced by the tumor, contribute to invasiveness and metastasis by reducing E-cadherin–mediated cell-cell adhesion and enhance proliferation in pancreatic tumor cells. (Cancer Res 2006; 66(9): 4662-71)
Gefitinib Modulates the Function of Multiple ATP-Binding Cassette Transporters In vivo
Authors: Leggas Markos , Panetta John C. , Zhuang Yanli , Schuetz John D. , Johnston Brad , Bai Feng , Sorrentino Brian , Zhou Sheng , Houghton Peter J. , Stewart Clinton F. 
Published: May 2006

Abstract
The 4-anilinoquinazoline (4-AQ) derivative gefitinib (Iressa) is an oral epidermal growth factor receptor tyrosine kinase inhibitor. Oral administration of 4-AQ molecules, such as gefitinib, inhibits ATP-binding cassette (ABC) transporter–mediated drug efflux and strongly increases the apparent bioavailability of coadministered drug molecules that are transporter substrates. Based on in vitro studies investigating 4-AQ interactions with several transporters, these effects have primarily been attributed to the inhibition of breast cancer resistance protein (BCRP; ABCG2). Although 4-AQ shows in vitro inhibition of P-glycoprotein [multidrug resistance protein (MDR1); ABCB1], the in vivo effect on this and other transporters is not known. In our studies, pretreatment of Abcg2−/− and Mdr1(a/b)−/− mice with gefitinib increased oral absorption and decreased systemic clearance of topotecan, a model substrate, indicating that additional transporters were inhibited. These results were extended to human orthologues using engineered cell lines to show that gefitinib inhibited the efflux of BCRP and MDR1 substrates and restored vincristine sensitivity in MDR1-expressing cells. Although gefitinib inhibited BCRP more potently than MDR1 (10-fold), the inhibition of both transporters occurred at clinically relevant concentrations (e.g., 1-5 μmol/L). These studies illustrate the broad implications for the therapeutic combination of gefitinib or other 4-AQ molecules with agents that are BCRP and MDR1 substrates. 4-AQ molecules may offer a means to increase the low and variable oral drug absorption of transporter substrates while decreasing interpatient variability and reversing tumor drug resistance. (Cancer Res 2006; 66(9): 4802-7)
Attenuation of Mitogen- and Stress-Activated Protein Kinase-1–Driven Nuclear Factor-κB Gene Expression by Soy Isoflavones Does Not Require Estrogenic Activity
Authors: Vanden Berghe Wim , Dijsselbloem Nathalie , Vermeulen Linda , Ndlovu 'Matladi N. , Boone Elke , Haegeman Guy 
Published: May 2006

Abstract
We have analyzed in molecular detail how soy isoflavones (genistein, daidzein, and biochanin A) suppress nuclear factor-κB (NF-κB)–driven interleukin-6 (IL6) expression. In addition to its physiologic immune function as an acute stress cytokine, sustained elevated expression levels of IL6 promote chronic inflammatory disorders, aging frailty, and tumorigenesis. Our results in estrogen-unresponsive fibroblasts, mitogen- and stress-activated protein kinase (MSK) knockout cells, and estrogen receptor (ER)–deficient breast tumor cells show that phytoestrogenic isoflavones can selectively block nuclear NF-κB transactivation of specific target genes (in particular IL6), independently of their estrogenic activity. This occurs via attenuation of mitogen-activated protein/extracellular signal-regulated kinase (ERK) kinase (MEK) and ERK activity, which further down-regulates MSK-dependent NF-κB p65 and histone H3 phosphorylation. As constitutive NF-κB and MSK activity are hallmarks of aggressive metastatic ER-deficient breast cancer, the MSK signaling pathway may become an attractive target for chemotherapy. (Cancer Res 2006; 66(9): 4852-62)
Ex vivoCulture with Interleukin (IL)-12 Improves CD8+ T-Cell Adoptive Immunotherapy for Murine Leukemia Independent of IL-18 or IFN-γ but Requires Perforin
Authors: MacGregor Jennifer N. , Li Qiao , Chang Alfred E. , Braun Thomas M. , Hughes Dennis P.M. , McDonagh Kevin T. 
Published: May 2006

AbstractIn animal models and clinical trials, adoptive transfer of activated, antigen-specific CD8+ T cells mediates tumor regression in a cell dose-dependent manner. The cytokine interleukin (IL)-12 promotes CD8+ T-cell cytotoxicity and, with IL-18, synergistically up-regulates IFN-γ release. We have shown that culturing CD8+ T cells ex vivo with IL-12 and IL-18 enhanced antitumor responses in vivo and in vitro using a model of C1498/ovalbumin, a murine acute myeloid leukemia cell line expressing the antigen ovalbumin. Activated ovalbumin-specific CD8+ T cells cultured with IL-12, IL-18, both, or neither were assayed for antigen-specific cytokine production and cytolytic activity and adoptively transferred to C57BL/6 mice with established tumors. Maximal IFN-γ release occurred after T-cell culture with IL-12 and IL-18. Tumor-specific in vitro cytotoxicity was enhanced by IL-12, unaffected by addition of IL-18, and abrogated in perforin-deficient T cells irrespective of cytokine exposure. T cells cultured with IL-12 more effectively eliminated tumors, and addition of IL-18 did not further augment responses. IFN-γ-deficient CD8+ T cells showed effective antitumor activity that was enhanced by IL-12 with or without IL-18. Perforin-deficient CD8+ T cells were poor mediators of antitumor activity, though, and showed no improvement after culture with IL-12 and/or IL-18. Thus, ex vivo culture with IL-12 was sufficient to augment antigen-specific in vitro cytotoxicity and antitumor activity in vivo in an IFN-γ-independent but perforin-dependent manner. Ex vivo culture with IL-12 may improve CD8+ T-cell immunotherapy of cancer in the absence of donor cell–derived IFN-γ via perforin-mediated cytolysis. (Cancer Res 2006; 66(9): 4913-21)
Disruption of the Y-Box Binding Protein-1 Results in Suppression of the Epidermal Growth Factor Receptor and HER-2
Authors: Wu Joyce , Lee Cathy , Yokom Daniel , Jiang Helen , Cheang Maggie C.U. , Yorida Erika , Turbin Dmitry , Berquin Isabelle M. , Mertens Peter R. , Iftner Thomas , Gilks C. Blake , Dunn Sandra E. 
Published: May 2006

Abstract
The overexpression of the epidermal growth factor receptor (EGFR) and HER-2 underpin the growth of aggressive breast cancer; still, it is unclear what governs the regulation of these receptors. Our laboratories recently determined that the Y-box binding protein-1 (YB-1), an oncogenic transcription/translation factor, induced breast tumor cell growth in monolayer and in soft agar. Importantly, mutating YB-1 at Ser102, which resides in the DNA-binding domain, prevented growth induction. We reasoned that the underlying cause for growth attenuation by YB-1(Ser102) is through the regulation of EGFR and/or HER-2. The initial link between YB-1 and these receptors was sought by screening primary tumor tissue microarrays. We determined that YB-1 (n = 389 cases) was positively associated with EGFR (P &lt; 0.001, r = 0.213), HER-2 (P = 0.008, r = 0.157), and Ki67 (P &lt; 0.0002, r = 0.219). It was inversely linked to the estrogen receptor (P &lt; 0.001, r = −0.291). Overexpression of YB-1 in a breast cancer cell line increased HER-2 and EGFR. Alternatively, mutation of YB-1 at Ser102 &gt; Ala102 prevented the induction of these receptors and rendered the cells less responsive to EGF. The mutant YB-1 protein was also unable to optimally bind to the EGFR and HER-2 promoters based on chromatin immunoprecipitation. Furthermore, knocking down YB-1 with small interfering RNA suppressed the expression of EGFR and HER-2. This was coupled with a decrease in tumor cell growth. In conclusion, YB-1(Ser102) is a point of molecular vulnerability for maintaining the expression of EGFR and HER-2. Targeting YB-1 or more specifically YB-1(Ser102) are novel approaches to inhibiting the expression of these receptors to ultimately suppress tumor cell growth. (Cancer Res 2006; 66(9): 4872-9)
Noninvasive Bioluminescence Imaging of Normal and Spontaneously Transformed Prostate Tissue in Mice
Authors: Lyons Scott K. , Lim Ed , Clermont Anne O. , Dusich Joan , Zhu Lingyun , Campbell Kenneth D. , Coffee Richard J. , Grass David S. , Hunter John , Purchio Tony , Jenkins Darlene 
Published: May 2006

Abstract
Several transgenic mouse models of prostate cancer have been developed recently that are able to recapitulate many key biological features of the human condition. It would, therefore, be desirable to employ these models to test the efficacy of new therapeutics before clinical trial; however, the variable onset and nonvisible nature of prostate tumor development limit their use for such applications. We now report the generation of a transgenic reporter mouse that should obviate these limitations by enabling noninvasive in vivo bioluminescence imaging of normal and spontaneously transformed prostate tissue in the mouse. We used an 11-kb fragment of the human prostate-specific antigen (PSA) promoter to achieve specific and robust expression of firefly luciferase in the prostate glands of transgenic mice. Ex vivo bioluminescence imaging and in situ hybridization analysis confirmed that luciferase expression was restricted to the epithelium in all four lobes of the prostate. We also show that PSA-Luc mice exhibit decreased but readily detectable levels of in vivo bioluminescence over extended time periods following androgen ablation. These results suggest that this reporter should enable in vivo imaging of both androgen-dependent and androgen-independent prostate tumor models. As proof-of-principle, we show that we could noninvasively image SV40 T antigen–induced prostate tumorigenesis in mice with PSA-Luc. Furthermore, we show that our noninvasive imaging strategy can be successfully used to image tumor response to androgen ablation in transgenic mice and, as a result, that we can rapidly identify individual animals capable of sustaining tumor growth in the absence of androgen. (Cancer Res 2006; 66(9): 4701-7)