bluuebunny/crossref_metadata_2025_split huggingface dataset:
NasT-Mediated Antitermination Plays an Essential Role in the Regulation of the Assimilatory Nitrate Reductase Operon in Azotobacter vinelandii
Authors: Wang Baomin , Pierson Leland S. , Rensing Christopher , Gunatilaka Malkanthi K. , Kennedy Christina 
Published: July 2012

ABSTRACT

Azotobacter vinelandii
is a well-studied model system for nitrogen fixation in bacteria. Regulation of nitrogen fixation in
A. vinelandii
is independent of NtrB/NtrC, a conserved nitrogen regulatory system in proteobacteria. Previous work showed that an
ntrC
mutation in
A. vinelandii
resulted in a loss of induction of assimilatory nitrate and nitrite reductases encoded by the
nasAB
operon. In addition to NtrC, several other proteins, including NasT, a protein containing a potential RNA-binding domain ANTAR (
A
miR and
N
asR
t
ranscription
a
ntitermination
r
egulators), have been implicated in
nasAB
regulation. In this work, we characterize the sequence upstream of
nasA
and identify several DNA sequence elements, including two potential NtrC binding sites and a putative intrinsic transcriptional terminator upstream of
nasA
that are potentially involved in
nasAB
regulation. Our analyses confirm that the
nasAB
promoter,
P
nasA
, is under NtrC control. However, unlike NtrC-regulated promoters in enteric bacteria,
P
nasA
shows high activity in the presence of ammonium; in addition, the
P
nasA
activity is altered in the
nifA
gene mutation background. We discuss the implication of these results on NtrC-mediated regulation in
A. vinelandii
. Our study provides direct evidence that induction of
nasAB
is regulated by NasT-mediated antitermination, which occurs within the leader region of the operon. The results also support the hypothesis that NasT binds the promoter proximal hairpin of
nasAB
for its regulatory function, which contributes to the understanding of the regulatory mechanism of ANTAR-containing antiterminators.
Multiple Transcription-Activating Sequences Regulate the RsmZ Regulatory Small RNA of Pseudomonas brassicacearum
Authors: Lalaouna D. , Fochesato S. , Barakat M. , Ortet P. , Achouak W. 
Published: July 2012

ABSTRACTThemutS-rpoSregion is known to be a highly polymorphic segment of the chromosome owing to horizontal gene transfer and evolutionary processes. InPseudomonas,mutS-fdxA-rsmZ-rpoSorganization is highly conserved, as well as the promoter region of the RsmZ small RNA (sRNA)-encoding gene. One exception to this conservation is inPseudomonas brassicacearum, where a 308-nucleotide (nt) sequence, predicted to form a hairpin structure in single-stranded DNA (ssDNA), is inserted between therpoSandrsmZgenes. Using MEME software, we identified nine consensus motifs in thersmZpromoter region of 16 sequencedPseudomonasgenomes. We observed that an upstream activation sequence (UAS) and an M1 motif (located between the −10 promoter element and the UAS) are shared among examinedPseudomonasgenomes. A third motif, the M2 motif, is localized within the coding sequence of therpoSgene. Constructs fusing the different identified motifs to thelacZreporter were produced. Ourin vivoanalysis of thersmZ-activating elements indicates that the palindromic UAS located 180 bp upstream of thersmZtranscriptional start inP. brassicacearumNFM 421 is essential, but not sufficient, for fullrsmZexpression. Here, we demonstrate a role for the three motifs in the activation of thersmZgene, and we hypothesize the role of additional transcriptional factors, along with the DNA structuring role of the hairpin in the complex network controlling the expression ofrsmZ.
CbrA Is a Flavin Adenine Dinucleotide Protein That Modifies the Escherichia coli Outer Membrane and Confers Specific Resistance to Colicin M
Authors: Helbig Stephanie , Hantke Klaus , Ammelburg Moritz , Braun Volkmar 
Published: July 2012

ABSTRACTColicin M (Cma) is a protein toxin produced byEscherichia colithat kills sensitiveE. colicells by inhibiting murein biosynthesis in the periplasm. Recombinant plasmids carryingcbrA(formerlyyidS) strongly increased resistance of cells to Cma, whereas deletion ofcbrAincreased Cma sensitivity. Transcription ofcbrAis positively controlled by the two-component CreBC system. A ΔcreBmutant was highly Cma sensitive because little CbrA was synthesized. Treatment of CbrA-overproducing cells by osmotic shock failed to render cells Cma sensitive because the cells were resistant to osmotic shock. In a natural environment with a growth-limiting nutrient supply, cells producing CbrA defend themselves against colicin M synthesized by competing cells. Isolated CbrA is a protein with noncovalently bound flavin adenine dinucleotide. Sequence comparison and structure prediction assign the closest relative of CbrA with a known crystal structure as digeranylgeranyl-glycerophospholipid reductase ofThermoplasma acidophilum. CbrA is found inEscherichia coli,Citrobacter, andSalmonella bongoribut not in other enterobacteria. The next homologs with the highest identity (over 50%) are found in the anaerobicClostridium botulinumgroup 1 and a few otherFirmicutes.
TolC-Dependent Secretion of an Ankyrin Repeat-Containing Protein of Rickettsia typhi
Authors: Kaur Simran J. , Rahman M. Sayeedur , Ammerman Nicole C. , Beier-Sexton Magda , Ceraul Shane M. , Gillespie Joseph J. , Azad Abdu F. 
Published: July 2012

ABSTRACTRickettsia typhi, the causative agent of murine (endemic) typhus, is an obligate intracellular pathogen with a life cycle involving both vertebrate and invertebrate hosts. In this study, we characterized a gene (RT0218) encoding a C-terminal ankyrin repeat domain-containing protein, namedRickettsiaankyrinrepeatprotein 1 (RARP-1), and identified it as a secreted effector protein ofR. typhi.RT0218showed differential transcript abundance at various phases ofR. typhiintracellular growth. RARP-1 was secreted byR. typhiinto the host cytoplasm duringin vitroinfection of mammalian cells. Transcriptional analysis revealed thatRT0218was cotranscribed with adjacent genesRT0217(hypothetical protein) andRT0216(TolC) as a single polycistronic mRNA. Given one of its functions as a facilitator of extracellular protein secretion in some Gram-negative bacterial pathogens, we tested the possible role of TolC in the secretion of RARP-1. UsingEscherichia coliC600 and an isogenictolCinsertion mutant as surrogate hosts, our data demonstrate that RARP-1 is secreted in a TolC-dependent manner. Deletion of either the N-terminal signal peptide or the C-terminal ankyrin repeats abolished RARP-1 secretion by wild-typeE. coli. Importantly, expression ofR. typhitolCin theE. colitolCmutant restored the secretion of RARP-1, suggesting that TolC has a role in RARP-1 translocation across the outer membrane. This work implies that the TolC component of the putative type 1 secretion system ofR. typhiis involved in the secretion process of RARP-1.
Functional Analysis of Bacillus subtilis Genes Involved in the Biosynthesis of 4-Thiouridine in tRNA
Authors: Rajakovich Lauren J. , Tomlinson John , Dos Santos Patricia C. 
Published: July 2012

ABSTRACTThiI has been identified as an essential enzyme involved in the biosynthesis of thiamine and the tRNA thionucleoside modification, 4-thiouridine. InEscherichia coliandSalmonella enterica, ThiI acts as a sulfurtransferase, receiving the sulfur donated from the cysteine desulfurase IscS and transferring it to the target molecule or additional sulfur carrier proteins. However, inBacillus subtilisand most species from theFirmicutesphylum, ThiI lacks the rhodanese domain that contains the site responsible for the sulfurtransferase activity. The lack of the gene encoding for a canonical IscS cysteine desulfurase and the presence of a short sequence of ThiI in these bacteria pointed to mechanistic differences involving sulfur trafficking reactions in both biosynthetic pathways. Here, we have carried out functional analysis ofB. subtilisthiIand the adjacent gene,nifZ, encoding for a cysteine desulfurase. Gene inactivation experiments inB. subtilisindicate the requirement of ThiI and NifZ for the biosynthesis of 4-thiouridine, but not thiamine.In vitrosynthesis of 4-thiouridine by ThiI and NifZ, along with labeling experiments, suggests the occurrence of an alternate transient site for sulfur transfer, thus obviating the need for a rhodanese domain.In vivocomplementation studies inE. coliIscS- or ThiI-deficient strains provide further support for specific interactions between NifZ and ThiI. These results are compatible with the proposal thatB. subtilisNifZ and ThiI utilize mechanistically distinct and mutually specific sulfur transfer reactions.
Variation in safety culture dimensions within and between US and Swiss Hospital Units: an exploratory study
Authors: Schwendimann René , Zimmermann Natalie , Küng Kaspar , Ausserhofer Dietmar , Sexton Bryan 
Published: July 2012

BackgroundThe purpose of this study was to explore the variability in safety culture dimensions within and between Swiss and US clinical areas.MethodsCross-sectional design. The 30-item Safety Attitudes Questionnaire (SAQ) was distributed in 2009 to clinicians involved in direct patient care in medical and surgical units of two Swiss and 10 US hospitals. At the unit level, results were calculated as the percentage of respondents within a unit who reported positive perceptions. MANOVA and ANOVA were used to test for differences between and within US and Swiss hospital units.ResultsIn total, 1370 clinicians from 54 hospital units responded (response rate 84%), including 1273 nurses and 97 physicians. In Swiss hospital units, three SAQ dimensions were lower (safety climate, p=0.024; stress recognition, p<0.001; and perceptions of management, p<0.001) compared with US hospital units.There was significant variability in four out of six SAQ dimensions (teamwork climate, safety climate, job satisfaction and perceptions of unit management) (p<0.001). Moreover, intraclass correlations indicate that these four dimensions vary more at the unit level than hospital level, whereas stress recognition and working conditions vary more at the hospital level.ConclusionsThe authors found differences in SAQ dimensions at the country, hospital and unit levels. The general emphases placed on teamwork and safety climate in quality and safety efforts appear to be highlighting dimensions that vary more at the unit than hospital level. They suggest that patient safety improvement interventions target unit level changes, and they support the emphasis being placed on teamwork and safety climate, as these vary significantly at the unit level across countries.
The importance of low-risk HPV infection for the risk of abnormal cervical cytology/histology in more than 40 000 Danish women
Authors: Nielsen Ann , Iftner Thomas , Nørgaard Mia , Munk Christian , Junge Jette , Kjaer Susanne Krüger 
Published: July 2012

ObjectivesTo estimate the age and type-specific distribution of low-risk (LR) human papillomavirus (HPV) types in cervical samples from women in the general population and to assess the distribution of LR-HPV without the coexistence of high-risk HPV types in different cytology and histology categories.MethodsIn a cross-sectional study, liquid-based cytology samples (SurePath) were collected over a 3-year period. The samples were HPV tested by Hybrid Capture II (HC2; Digene) and genotyped using a PCR-based assay (INNO-LiPAv2; Innogenetics Inc.). A total of 40 382 women (14–95 years of age) were included in the study. By linkage with the nationwide Pathology Data Bank, the HPV test results were directly linked to cytological diagnoses made from the same samples and to subsequent histology results.ResultsOverall, 2790 women (6.9%) tested positive for LR-HPV types, with HPV6 and HPV70 being the most frequent types detected, whereas HPV11 was uncommon. The highest prevalence was observed in the youngest age group (≤19 years). The LR-HPV prevalence was 6.3% in women with normal cytology, 33.1% in atypical squamous cells of undetermined significance (ASCUS), 19.6% in low-grade squamous intraepithelial lesion and 12.7% in those with high-grade squamous intraepithelial lesion. When considering women with LR-HPV alone, the prevalence was 2.0% (normal cytology), 11.3% (ASCUS), 2.6% (low-grade squamous intraepithelial lesion) and 0.7% in women with high-grade squamous intraepithelial lesion, respectively. A similar pattern was observed in relation to the histological diagnoses with the majority of LR-HPV infections detected in CIN1 lesions (24.7%).ConclusionsLR-HPV types alone are relatively common in ASCUS, whereas LR-HPV types without coexisting high-risk HPV types are virtually never detected in severe cervical lesions.
Exploring staff attitudes to routine HIV testing in non-traditional settings: a qualitative study in four healthcare facilities
Authors: Thornton Alicia Claire , Rayment Michael , Elam Gillian , Atkins Mark , Jones Rachel , Nardone Anthony , Roberts Patrick , Tenant-Flowers Melinda , Anderson Jane , Sullivan Ann Kathleen ,   on behalf of the HINTS Study Group
Published: July 2012

ObjectivesTo explore staff attitudes towards and experiences of the implementation of routine HIV testing in four healthcare settings in areas of high diagnosed HIV prevalence.MethodsAs part of the HINTS (HIV Testing in Non-traditional Settings) Study, routine offer of an HIV test to all 16–65-year-old patients was conducted for 3 months in an emergency department, an acute admissions unit, a dermatology outpatients department and a primary care practice. The authors conducted focus groups with staff at these sites before and after the implementation of testing. Transcriptions of focus groups were subject to thematic analysis.ResultsFour major themes were identified: the stigma of HIV and exceptionalisation of HIV testing as a condition; the use of routine testing compared with a targeted strategy as a means of improving the acceptability of testing; the need for an additional skill set to conduct HIV testing; and the existence within these particular settings of operational barriers to the implementation of HIV testing. Specifically, the time taken to conduct testing and management of results were seen by staff as barriers. There was a clear change in staff perception before and after implementation of testing as staff became aware of the high level of patient acceptability.ConclusionsThe routine offer of HIV testing in general medical services is feasible, but implementation requires training and support for staff, which may be best provided by the local sexual health service.
Concomitant Targeting of Tumor Cells and Induction of T-cell Response Synergizes to Effectively Inhibit Trastuzumab-Resistant Breast Cancer
Authors: Wang Qingfei , Li Shau-Hsuan , Wang Hai , Xiao Yi , Sahin Ozgur , Brady Samuel W. , Li Ping , Ge Hailiang , Jaffee Elizabeth M. , Muller William J. , Hortobagyi Gabriel N. , Yu Dihua 
Published: July 2012

Abstract
Trastuzumab is an iconic rationally designed targeted therapy for HER2-positive breast cancers. However, the low response rate and development of resistance call for novel approaches for the treatment of patients. Here, we report that concurrent targeting of tumor cells and activation of T cells in the tumor microenvironment results in a synergistic inhibitory effect on tumor growth and overcomes resistance in two distinct PTEN loss–mediated trastuzumab-resistant mammary tumor mouse models. In vivo combination treatment with HER2/Neu antibody and Akt inhibitor triciribine effectively inhibited tumor growth in both models via inhibiting PI3K/AKT and mitogen-activated protein kinase signaling accompanied by increased T-cell infiltration in the tumor microenvironment. We showed that both CD8+ and CD4+ T cells were essential to the optimal antitumor effect of this combination treatment in an IFN-γ–dependent manner. Importantly, the antitumor activities of HER2/Neu antibody and triciribine combination treatment were further improved when coinhibitory receptor cytotoxic T-lymphocyte–associated antigen 4 was blocked to enhance the T-cell response. Our data indicate that multitargeted combinatorial therapies targeting tumor cells and concomitantly enhancing T-cell response in the tumor microenvironment could cooperate to exert maximal therapeutic activity, suggesting a promising clinical strategy for treating trastuzumab-resistant breast cancers and other advanced malignancies. Cancer Res; 72(17); 4417–28. ©2012 AACR.
Glutamine Deprivation Enhances Antitumor Activity of 3-Bromopyruvate through the Stabilization of Monocarboxylate Transporter-1
Authors: Cardaci Simone , Rizza Salvatore , Filomeni Giuseppe , Bernardini Roberta , Bertocchi Fabio , Mattei Maurizio , Paci Maurizio , Rotilio Giuseppe , Ciriolo Maria Rosa 
Published: July 2012

Abstract
Anticancer drug efficacy might be leveraged by strategies to target certain biochemical adaptations of tumors. Here we show how depriving cancer cells of glutamine can enhance the anticancer properties of 3-bromopyruvate, a halogenated analog of pyruvic acid. Glutamine deprival potentiated 3-bromopyruvate chemotherapy by increasing the stability of the monocarboxylate transporter-1, an effect that sensitized cells to metabolic oxidative stress and autophagic cell death. We further elucidated mechanisms through which resistance to chemopotentiation by glutamine deprival could be circumvented. Overall, our findings offer a preclinical proof-of-concept for how to employ 3-bromopyruvate or other monocarboxylic-based drugs to sensitize tumors to chemotherapy. Cancer Res; 72(17); 4526–36. ©2012 AACR.
Molecular Pathways: Context-Dependent Approaches to Notch Targeting as Cancer Therapy
Authors: Egloff Ann Marie , Grandis Jennifer R. 
Published: July 2012

Abstract
Recent high-throughput genomic sequencing studies of solid tumors, including head and neck squamous cell carcinoma (SCC), ovarian cancer, lung adenocarcinoma, glioblastoma, breast cancer, and lung SCC, have highlighted DNA mutation as a mechanism for aberrant Notch signaling. A primary challenge of targeting Notch for treatment of solid malignancies is determining whether Notch signaling is cancer promoting or tumor suppressing for a specific cancer. We compiled reported Notch receptor and ligand missense and nonsense mutations to glean insights into aberrant Notch signaling. Frequencies of coding mutations differed for the 4 NOTCH genes. A total of 4.7% of tumors harbored NOTCH1 missense or nonsense mutations. NOTCH2, and NOTCH3 had similar overall mutation rates of 1.5% and 1.3%, respectively, whereas NOTCH4 mutations were rarer. Notch ligand genes were rarely mutated. The combined mutation frequency and position spectra of the 4 Notch paralogs across the different cancers provide an opportunity to begin to illuminate the different contributions of each Notch paralog to each tumor type and to identify opportunities for therapeutic targeting. Notch signaling pathway activators and inhibitors are currently in early clinical development for treatment of solid malignancies. Defining the status and consequences of altered Notch signaling will be important for selection of appropriate treatment. Clin Cancer Res; 18(19); 5188–95. ©2012 AACR.
A Role for Homologous Recombination and Abnormal Cell-Cycle Progression in Radioresistance of Glioma-Initiating Cells
Authors: Lim Yi Chieh , Roberts Tara L. , Day Bryan W. , Harding Angus , Kozlov Sergei , Kijas Amanda W. , Ensbey Kathleen S. , Walker David G. , Lavin Martin F. 
Published: July 2012

AbstractGlioblastoma multiforme (GBM) is the most common form of brain tumor with a poor prognosis and resistance to radiotherapy. Recent evidence suggests that glioma-initiating cells play a central role in radioresistance through DNA damage checkpoint activation and enhanced DNA repair. To investigate this in more detail, we compared the DNA damage response in nontumor forming neural progenitor cells (NPC) and glioma-initiating cells isolated from GBM patient specimens. As observed for GBM tumors, initial characterization showed that glioma-initiating cells have long-term self-renewal capacity. They express markers identical to NPCs and have the ability to form tumors in an animal model. In addition, these cells are radioresistant to varying degrees, which could not be explained by enhanced nonhomologous end joining (NHEJ). Indeed, NHEJ in glioma-initiating cells was equivalent, or in some cases reduced, as compared with NPCs. However, there was evidence for more efficient homologous recombination repair in glioma-initiating cells. We did not observe a prolonged cell cycle nor enhanced basal activation of checkpoint proteins as reported previously. Rather, cell-cycle defects in the G1–S and S-phase checkpoints were observed by determining entry into S-phase and radioresistant DNA synthesis following irradiation. These data suggest that homologous recombination and cell-cycle checkpoint abnormalities may contribute to the radioresistance of glioma-initiating cells and that both processes may be suitable targets for therapy. Mol Cancer Ther; 11(9); 1863–72. ©2012 AACR.
Human ATP–Binding Cassette G1 Controls Macrophage Lipoprotein Lipase Bioavailability and Promotes Foam Cell Formation
Authors: Olivier Maryline , Tanck Michael W. , Out Ruud , Villard Elise F. , Lammers Bart , Bouchareychas Laura , Frisdal Eric , Superville Alexandre , Van Berkel Theo , Kastelein John J. , Eck Miranda Van , Jukema J. Wouter , Chapman M. John , Dallinga-Thie Geesje M. , Guerin Maryse , Goff Wilfried Le 
Published: July 2012

Objective—

The physiological function of the ATP–binding cassette G1 (ABCG1) transporter in humans is not yet elucidated, as no genetic disease caused by
ABCG1
mutations has been documented. The goal of our study was, therefore, to investigate the potential role(s) of ABCG1 in lipid metabolism in humans.

Methods and Results—

Here we report that among the 104 polymorphisms present in the
ABCG1
gene, the analysis of the frequent functional rs1893590 and rs1378577 single nucleotide polymorphisms located in the regulatory region of
ABCG1
in the Regression Growth Evaluation Statin Study population revealed that both
ABCG1
single nucleotide polymorphisms were significantly associated with plasma lipoprotein lipase (LPL) activity. Moreover, we observed that plasma LPL activity was modestly reduced in
Abcg1
−/−
mice as compared with control mice. Adipose tissue and skeletal muscle are the major tissues accounting for levels and activity of plasma LPL in the body. However, beyond its lipolytic action in the plasma compartment, LPL was also described to act locally at the cellular level. Thus, macrophage LPL was reported to promote foam cell formation and atherosclerosis in vivo. Analysis of the relationship between ABCG1 and LPL in macrophages revealed that the knockdown of ABCG1 expression (ABCG1 knockdown) in primary cultures of human monocyte–derived macrophages using small interfering RNAs led to a marked reduction of both the secretion and activity of LPL. Indeed, LPL was trapped at the cell surface of ABCG1 knockdown human monocyte–derived macrophages, likely in cholesterol-rich domains, thereby reducing the bioavailability and activity of LPL. As a consequence, LPL–mediated lipid accumulation in human macrophage foam cells in the presence of triglyceride-rich lipoproteins was abolished when ABCG1 expression was repressed.

Conclusion—
We presently report that ABCG1 controls LPL activity and promotes lipid accumulation in human macrophages in the presence of triglyceride-rich lipoproteins, thereby suggesting a potential deleterious role of macrophage ABCG1 in metabolic situations associated with high levels of circulating triglyceride-rich lipoproteins together with the presence of macrophages in the arterial wall.