bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promoters forChlamydiaType III Secretion Genes Show a Differential Response to DNA Supercoiling That Correlates with Temporal Expression Pattern
Authors: Case Elizabeth Di Russo , Peterson Ellena M. , Tan Ming 
Published: March 2010

ABSTRACTType III secretion (T3S) is important for the establishment and maintenance of a chlamydial infection. The genes encoding T3S components inChlamydiaare transcribed as separate temporal classes, but the mechanisms that regulate the timing of their expression are not understood. In this study, we demonstrate that promoters for 10 predicted T3S transcriptional units are each transcribedin vitroby the major form of chlamydial RNA polymerase but not by an alternative form of RNA polymerase containing σ28. Since changes in DNA supercoiling during chlamydial development have been proposed as a mechanism for temporal gene regulation, we examined thein vitroresponse of T3S promoters to altered superhelical density. Promoters for three T3S genes that are upregulated at mid times were activated in response to increased DNA supercoiling. In contrast, promoters for three late T3S genes were not sensitive to changes in superhelical density. This differential response to changes in DNA topology is similar to the pattern that has been reported for representative mid and late chlamydial genes that are unrelated to the T3S system. Based on these results, we propose that the temporal expression of T3S genes inChlamydiais controlled by general mechanisms that regulate σ66-dependent gene expression during the developmental cycle. Our results are consistent with a model in which T3S genes that are upregulated in mid cycle are activated together with other mid genes in response to increased DNA supercoiling.
Quorum-Sensing Regulation of a Copper Toxicity System in
Pseudomonas aeruginosa
Authors: Thaden Joshua T. , Lory Stephen , Gardner Timothy S. 
Published: March 2010

ABSTRACT

The LasR/LasI quorum-sensing system in
Pseudomonas aeruginosa
influences global gene expression and mediates pathogenesis. In this study, we show that the quorum-sensing system activates, via the transcriptional regulator
PA4778
, a copper resistance system composed of 11 genes. The quorum-sensing global regulator LasR was recently shown to directly activate transcription of
PA4778
, a
cueR
homolog and a MerR-type transcriptional regulator. Using molecular genetic methods and bioinformatics, we verify the interaction of LasR with the
PA4778
promoter and further demonstrate the LasR binding site. We also identify a putative PA4778 binding motif and show that the protein directly binds to and activates five promoters controlling the expression of 11 genes—
PA3519
to -
15
,
PA3520
,
mexPQ-opmE
,
PA3574.1
, and
cueA
, a virulence factor in a murine model. Using gene disruptions, we show that
PA4778
, along with 7 of 11 gene targets of PA4778, increases the sensitivity of
P. aeruginosa
to elevated copper concentrations. This work identifies a cellular function for
PA4778
and four other previously unannotated genes (
PA3515
,
PA3516
,
PA3517
, and
PA3518
) and suggests a potential role for copper in the quorum response. We propose to name
PA4778 cueR
.
Interactions of the RNA-Binding Protein Hfq withcspAmRNA, Encoding the Major Cold Shock Protein
Authors: Hankins J. S. , Denroche H. , Mackie G. A. 
Published: March 2010

ABSTRACTCspA, a small protein that is highly induced by cold shock, is encoded by a monocistronic mRNA of 428 nucleotides (nt) whose half-life and abundance are greatly increased following cold shock. We show here thatin vitro cspAmRNA can bind multiple copies of Hfq, a hexameric Sm-like protein which promotes a variety of RNA-RNA interactions. Binding of the first Hfq hexamer occurs with an apparentKd(dissociation constant) of <40 nM; up to seven additional hexamers can bind sequentially at higher concentrations. Known ligands of Hfq, including the small regulatory RNA, RyhB, compete withcspAmRNA. Several experiments suggest that the first binding site to be occupied by Hfq is located at or near the 3′ end ofcspAmRNA. The consequences of limited Hfq bindingin vitroinclude nearly total inhibition of RNase E cleavage at a site ∼35 nt from the 3′ end of the mRNA, stimulation of polyadenylation by poly(A) polymerase 1, and subsequent exonucleolytic degradation by polynucleotide phosphorylase. We propose that Hfq may play a facilitating role in the metabolism ofcspAmRNA.
Exopolysaccharides Produced by
Streptococcus mutans
Glucosyltransferases Modulate the Establishment of Microcolonies within Multispecies Biofilms
Authors: Koo H. , Xiao J. , Klein M. I. , Jeon J. G. 
Published: March 2010

ABSTRACT

Streptococcus mutans
is a key contributor to the formation of the extracellular polysaccharide (EPS) matrix in dental biofilms. The exopolysaccharides, which are mostly glucans synthesized by streptococcal glucosyltransferases (Gtfs), provide binding sites that promote accumulation of microorganisms on the tooth surface and further establishment of pathogenic biofilms. This study explored (i) the role of
S. mutans
Gtfs in the development of the EPS matrix and microcolonies in biofilms, (ii) the influence of exopolysaccharides on formation of microcolonies, and (iii) establishment of
S. mutans
in a multispecies biofilm
in vitro
using a novel fluorescence labeling technique. Our data show that the ability of
S. mutans
strains defective in the
gtfB
gene or the
gtfB
and
gtfC
genes to form microcolonies on saliva-coated hydroxyapatite surfaces was markedly disrupted. However, deletion of both
gtfB
(associated with insoluble glucan synthesis) and
gtfC
(associated with insoluble and soluble glucan synthesis) is required for the maximum reduction in EPS matrix and biofilm formation.
S. mutans
grown with sucrose in the presence of
Streptococcus oralis
and
Actinomyces naeslundii
steadily formed exopolysaccharides, which allowed the initial clustering of bacterial cells and further development into highly structured microcolonies. Concomitantly,
S. mutans
became the major species in the mature biofilm. Neither the EPS matrix nor microcolonies were formed in the presence of glucose in the multispecies biofilm. Our data show that GtfB and GtfC are essential for establishment of the EPS matrix, but GtfB appears to be responsible for formation of microcolonies by
S. mutans
; these Gtf-mediated processes may enhance the competitiveness of
S. mutans
in the multispecies environment in biofilms on tooth surfaces.
[18F]FDG PET/CT imaging of colorectal cancer: a pictorial review
Authors: Chowdhury Fahmid U , Shah Nehal , Scarsbrook Andrew F , Bradley Kevin M 
Published: March 2010

Abstract
Integrated positron emission tomography/CT (PET/CT) with 2-[18F]fluoro-2-deoxy-d-glucose (FDG) is a hybrid imaging modality which has recently become established in the staging, restaging and therapy response assessment of oncology patients. FDG PET/CT has several recognised applications in colorectal cancer (CRC) imaging including preoperative evaluation of apparently limited metastatic disease, detection of disease recurrence, clarification of equivocal lesions at initial staging, investigation of unexplained rising tumour markers, and incidental detection of occult primary colonic tumours. With a constantly advancing body of evidence and increasing availability, applications of PET/CT in CRC are likely to emerge in therapy response assessment, radiotherapy planning, use of novel tracers and ‘one-stop’ imaging techniques such as iodinated contrast-enhanced PET/CT. With the use of illustrative clinical examples, this article reviews the utility of FDG PET/CT in the management of CRC, discussing its role and limitations in the multimodality imaging of these patients.
Design of shear reinforcement for thick plates using a strut-and-tie model
Authors: Marzouk H. , Rizk E. , Tiller R. 
Published: March 2010

The strut-and-tie method is a rational approach to structural concrete design that results in a uniform and consistent design philosophy. A strut-and-tie model has been developed to model the punching-shear behaviour of thick concrete plates. This model provides a quick and simple approach to check the punching-shear behaviour. Thick concrete slabs (250–500 mm) without shear reinforcement can exhibit brittle shear failure under a central force and an unbalanced moment. Shear reinforcement has proven to be very effective in preventing such failures. The developed strut-and-tie model has also been used to evaluate the minimum shear reinforcement required to prevent brittle shear failure of two-way slabs in the vicinity of concentrated loads. The strut-and-tie model for symmetric punching consists of a “bottle-shaped” compressive zone in the upper section of the slab depth, leading to a “rectangular-stress” compressive zone in the lower section of the slab depth. Inclined shear cracking develops in the bottle-shaped zone prior to failure in the lower zone. Cracking in the bottle-shaped zone is related to the splitting tensile strength of concrete.
Influence of phosphorus, potassium, and copper on methane biofiltration performanceA paper submitted to the Journal of Environmental Engineering and Science.
Authors: Nikiema Josiane , Brzezinski Ryszard , Heitz Michèle 
Published: March 2010

In addition to a carbon source, bacteria require for growth a variety of nutrients such as phosphorus, potassium, and several other micronutrients including copper. The study described in this paper was conducted with the aim of determining the influence of phosphorus, potassium, and copper on methane elimination in a biofilter. The study revealed that the particular phosphorus concentration leading to the greatest methane elimination capacity, which was 44.7 g m–3 h–1at a methane inlet load of 75 g m–3 h–1, was 3.1 g/L. The influence of the phosphorus concentration on the methane elimination capacities was also investigated for methane inlet loads of between 8 and 95 g m–3 h–1. The optimum range of the nitrogen–phosphorus mass ratios, determined during this study ranged from 0.5 to 2.5. It was established that, in comparison with phosphorus, potassium does not seem to be a determining element for the biological removal efficiency and does not significantly affect the microorganisms’ behaviour. However, a concentration of 0.076 g/L of potassium is recommended in the irrigation nutrient solution for an inlet load of 75 g m–3 h–1. The influence of the copper concentration was also studied by varying its concentration between the values of 0 and 0.006 g/L. The results have also shown that copper has a minor impact on the biofiltration of methane. This paper is the first report describing the influence of several nutrients in a biofilter. The knowledge provided by this study is necessary for the achievement of a biofilter indebted to methane control.
Investigation of bond between lap-spliced steel bar and self-compacting concrete: The role of silica fume
Authors: Karatas Mehmet , Turk Kazim , Ulucan Zulfu C. 
Published: March 2010

In this study, normal concrete (NC) and four types of self-compacting concrete (SCC), in which cement was partially replaced by 5%, 10%, 15%, and 20% of silica fume (SF), were used to evaluate the effect of SF content on the bond strength of tension lap-spliced bars embedded in NC and SCC specimens. Therefore, 15 full-scale beam specimens (2000 × 300 × 200 mm3) were tested and 20 mm reinforcing bars were used with a 300-mm splice length as tension reinforcement. Each beam was designed with bars spliced in a constant moment region at midspan. It was found that the bond strength of the reinforcement embedded in SCC beams was higher than that of the reinforcement in NC beams, whilst the bond strength increased with increase in the replacement of cement by SF from 5% to 10%. Moreover, the beam specimens produced from SCC containing 5% SF had the highest normalized bond strength of 1.07 followed by SCC beams with 10% SF, 15% SF, NC beams, and 20% SF.
A halogenated pseudopterane diterpene from the Bahamian octocoral Pseudopterogorgia acerosa
Authors: Kate Abhijeet S. , Richard Kelly , Ramanathan Balaji , Kerr Russell G. 
Published: March 2010

Two new pseudopteranoid diterpenes have been isolated from the gorgonian coral Pseudopterogorgia acerosa and have been characterized by NMR and mass spectrometry. These include 15-chlorodeoxypseudopterolide (1), the first halogenated pseudopterane diterpene, and 11-epi-pseudopteranol (2), an epimer of the previously described 11-pseudopteranol. In addition, six known diterpenes were also isolated from this collection including deoxypseudopterolide (3), pseudopteradiene (4), acerosolide (5), pseudopterolide-methanol adduct (6), 11-pseudopteranol (7), and isogorgiacerodiol (8). The cytotoxicity of these eight compounds towards three cancer cell lines (HeLa, PC-3, and HCT116) was assessed and the chlorinated pseudopteranoid 1 was found to have modest but selective activity against HCT116 (IC50 2.7 µmol/L), whereas its nonchlorinated derivative 3 was inactive. This indicates that the halo functionality can modify the cytotoxic activity of pseudopteranoids and potentially other classes of deterpenes.
Theoretical study of H bonds of HArF and HF with isoelectronic systems N2, CO, and BF
Authors: Li An Yong , Cao Li Juan , Ji Hong Bo 
Published: March 2010

The H bonds of HArF and HF with N2, CO, and BF were studied at the MP2(full)/6-311++G(2d, 2p) level. The results show that only the complexes WY···HArF (WY = N2, OC) and WY···HF (WY = N2, OC, FB) are stable, the H-bonding WY···HArF leads to contraction of the HAr bond with a concomitant frequency blue shift, but the H-bonding WY···HF causes the HF bond to elongate with a frequency red shift. A quantity P is defined to measure polarization of the HX bond; the H bonding causes the P value of the HX bond (X = Ar, F) to increase. The HX bond length change and frequency shift in the H-bonding WY···HArF and WY···HF are mainly caused by intermolecular hyperconjugation, n(Y) → σ*(HX) (X = Ar, F), where electrostatic interaction has only a small contribution. In HArF, the strong intramolecular hyperconjugation, n(F) → σ*(HAr), can adjust electron density on σ*(HAr); upon formation of H bonding, the HAr stretching frequency blue shift is caused by a decrease of intramolecular hyperconjugation and an increase of the s character of the Ar hybrid in the HAr bond, induced by the intermolecular hyperconjugation. In the H bonds of HF without intramolecular hyperconjugation, the intermolecular hyperconjugation, n(Y) → σ*(HF), leads to a red shift of the HF bond, although there is also large rehybridization.
Characterization and expression of a novel holotype insecticidal crystal protein gene from nativeBacillus thuringiensisBM59-2
Authors: Zheng Aiping , Zhu Jun , Wang Lingxia , Li Shuangcheng , Deng Qiming , Wang Shiquan , Tan Furong , Yu Xiumei , Guan Peng , Liang Hongxia , Li Ping 
Published: March 2010

We characterized a novel holotype cry gene (cry52Ba1) harbored in a Bacillus thuringiensis isolate BM59-2 native to China that expresses a spherical crystal protein of about 80 kDa. In this study, the full length of the cry52Ba1 gene was cloned from this strain. Sequence analysis of the gene was also performed. Furthermore, cry52Ba1 was expressed in Escherichia coli BL21(DE)pLysS, and the resulting insecticidal activity showed that the Cry52Ba1 protein exhibited high larvicidal activity against Aedes aegypti (Diptera), with a lethal concentration 50 of 1.526 µg/mL (95% confidence: 0.740–3.499 µg/mL).
Spatial distribution and habitat selection of Barrow’s and Common goldeneyes wintering in the St. Lawrence marine system
Authors: Ouellet Jean-François , Guillemette M. , Robert M. 
Published: March 2010

Our study addresses winter spatial distribution of Barrow’s Goldeneyes ( Bucephala islandica (Gmelin, 1789)) and Common Goldeneyes ( Bucephala clangula (L., 1758)) at the scale of the St. Lawrence marine system (estuary and northwestern gulf), eastern Canada. Our objectives were (i) to identify and compare the physical factors that control their distributions, (ii) to quantify the level of sympatry between the two species, and (iii) to compare their distribution patterns. We analyzed large-scale synoptic views of winter distribution of both goldeneye species obtained through helicopter-borne surveys. Habitat description was obtained through spatial analyses and remote sensing. Both species showed strong preference for the tidal zone and river mouths. A multiscale analysis showed a decreasing level of sympatry as spatial resolution was refined. The distribution of the Barrow’s Goldeneye was more clustered compared with that of the Common Goldeneye, and Barrow’s Goldeneye was repeatedly observed in the same few areas. A use-availability analysis identified the northern coast of the St. Lawrence estuary as the main wintering ground for Barrow’s Goldeneye in eastern North America.
Forkhead Box F1 Regulates Tumor-Promoting Properties of Cancer-Associated Fibroblasts in Lung Cancer
Authors: Saito Roy-Akira , Micke Patrick , Paulsson Janna , Augsten Martin , Peña Cristina , Jönsson Per , Botling Johan , Edlund Karolina , Johansson Leif , Carlsson Peter , Jirström Karin , Miyazono Kohei , Östman Arne 
Published: March 2010

Abstract
Cancer-associated fibroblasts (CAF) attract increasing attention as potential cancer drug targets due to their ability to stimulate, for example, tumor growth, invasion, angiogenesis, and metastasis. However, the molecular mechanisms causing the tumor-promoting properties of CAFs remain poorly understood. Forkhead box F1 (FoxF1) is a mesenchymal target of hedgehog signaling, known to regulate mesenchymal-epithelial interactions during lung development. Studies with FoxF1 gain- and loss-of-function fibroblasts revealed that FoxF1 regulates the contractility of fibroblasts, their production of hepatocyte growth factor and fibroblast growth factor-2, and their stimulation of lung cancer cell migration. FoxF1 status of fibroblasts was also shown to control the ability of fibroblasts to stimulate xenografted tumor growth. FoxF1 was expressed in CAFs of human lung cancer and associated with activation of hedgehog signaling. These observations suggest that hedgehog-dependent FoxF1 is a clinically relevant lung CAF-inducing factor, and support experimentally the general concept that CAF properties can be induced by activation of developmentally important transcription factors. Cancer Res; 70(7); 2644–54
Serial Transcriptome Analysis and Cross-Species Integration Identifies Centromere-Associated Protein E as a Novel Neuroblastoma Target
Authors: Balamuth Naomi J. , Wood Andrew , Wang Qun , Jagannathan Jayanti , Mayes Patrick , Zhang Zhe , Chen Zhongxue , Rappaport Eric , Courtright Joshua , Pawel Bruce , Weber Barbara , Wooster Richard , Sekyere Eric O. , Marshall Glenn M. , Maris John M. 
Published: March 2010

Abstract
Cancer genomic studies that rely on analysis of biopsies from primary tumors may not fully identify the molecular events associated with tumor progression. We hypothesized that characterizing the transcriptome during tumor progression in the TH-MYCN transgenic model would identify oncogenic drivers that would be targetable therapeutically. We quantified expression of 32,381 murine genes in nine hyperplastic ganglia harvested at three time points and four tumor cohorts of progressively larger size in mice homozygous for the TH-MYCN transgene. We found 93 genes that showed a linearly increasing or decreasing pattern of expression from the preneoplastic ganglia to end stage tumors. Cross-species integration identified 24 genes that were highly expressed in human MYCN-amplified neuroblastomas. The genes prioritized were not exclusively driven by increasing Myc transactivation or proliferative rate. We prioritized three targets [centromere-associated protein E (Cenpe), Gpr49, and inosine monophosphate dehydrogenase type II] with previously determined roles in cancer. Using siRNA knockdown in human neuroblastoma cell lines, we further prioritized CENPE due to inhibition of cellular proliferation. Targeting CENPE with the small molecular inhibitor GSK923295 showed inhibition of in vitro proliferation of 19 neuroblastoma cell lines (median IC50, 41 nmol/L; range, 27–266 nmol/L) and delayed tumor growth in three xenograft models (P values ranged from P &lt; 0.0001 to P = 0.018). We provide preclinical validation that serial transcriptome analysis of a transgenic mouse model followed by cross-species integration is a useful method to identify therapeutic targets and identify CENPE as a novel therapeutic candidate in neuroblastoma. Cancer Res; 70(7); 2749–58
Glutamine Synthetase Immunostaining Correlates with Pathologic Features of Hepatocellular Carcinoma and Better Survival after Radiofrequency Thermal Ablation
Authors: Dal Bello Barbara , Rosa Laura , Campanini Nicoletta , Tinelli Carmine , Torello Viera Francesca , D'Ambrosio Gioacchino , Rossi Sandro , Silini Enrico M. 
Published: March 2010

Abstract
Purpose: Activation of the wnt pathway identifies a subgroup of hepatocellular carcinomas (HCC) with specific epidemiologic and genetic profiles. Wnt activation is predicted by mutation and/or nuclear translocation of β-catenin and by glutamine synthetase (GS) immunoreactivity. We investigated whether GS staining associates with specific pathologic features of HCC and with survival after radiofrequency thermal ablation.
Experimental Design: Monoistitutional retrospective-prospective study in a tertiary hospital setting. Two hundred and seven cirrhotics (mean age, 70 years; 63% males, 82.1% hepatitis C virus positive) with early HCC were consecutively treated with radiofrequency thermal ablation (RFTA). Mean tumor size was 2.7 cm; 20.3% of patients had multiple nodules; and median follow-up was 36 months with 54.6% overall mortality. Tumor samples were mainly obtained by biopsy (92,5%) and examined by H&E and immunostaining for β-catenin and GS. Main outcome measures were overall and tumor-specific mortality by Kaplan-Meier analysis and Cox proportional hazard models corrected for competing risks.
Results: Ninety-one patients (43.9%) had GS-positive HCCs by immunostaining. These tumors had larger size (P = 0.012) and characteristic histology (low grade, pseudoacini, hydropic changes, bile staining, lack of steatosis, and fibrosis). Other clinical or treatment variables were similar between groups. Variables correlating with tumor-specific and overall mortality by univariate analysis were tumor recurrence, advanced disease, posttreatment α-fetoprotein levels, and GS staining. Yearly, overall mortality rate was lower in GS-positive patients (12.4 versus 20% yearly; P = 0.006). By multivariate analysis, GS immunostaining correlated with reduced specific (hazard ratio, 0.58; 95% confidence interval, 0.34-0.97) and overall mortality (hazard ratio, 0.62; 95% confidence interval, 0.40-0.96).
Conclusions: Standard histology and GS status identify a HCC subset with distinct clinical and pathologic features. Clin Cancer Res; 16(7); 2157–66. ©2010 AACR.