bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quinolone-Resistant Escherichia coli O127a:K63 Serotype with an Extended-Spectrum-Beta-Lactamase Phenotype from a Food Poisoning Outbreak in China
Authors: Hao Rongzhang , Qiu Shaofu , Wang Yong , Yang Guang , Su Wenli , Song Lixue , Zhang Jia , Chen Jiaxu , Jia Leili , Wang Ligui , Song Hongbin 
Published: May 2012

ABSTRACT

We report an atypical enteropathogenic
Escherichia coli
O127a:K63 strain with resistance to quinolones and extended-spectrum cephalosporins isolated from a 2010 food poisoning outbreak involving 112 adults in China. Two resistance genes [
bla
CTX-M-15
,
aac
(
6′
)
-Ib-c
] and five mutations (two in
gyrA
, two in
parC
, one in
parE
) coexisted in this enteropathogenic
E. coli
strain.
Rapid Spoligotyping of Mycobacterium tuberculosis Complex Bacteria by Use of a Microarray System with Automatic Data Processing and Assignment
Authors: Ruettger Anke , Nieter Johanna , Skrypnyk Artem , Engelmann Ines , Ziegler Albrecht , Moser Irmgard , Monecke Stefan , Ehricht Ralf , Sachse Konrad 
Published: May 2012

ABSTRACT
Membrane-based spoligotyping has been converted to DNA microarray format to qualify it for high-throughput testing. We have shown the assay's validity and suitability for direct typing from tissue and detecting new spoligotypes. Advantages of the microarray methodology include rapidity, ease of operation, automatic data processing, and affordability.
Detection of NDM-1, VIM-1, KPC, OXA-48, and OXA-162 Carbapenemases by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Hrabák Jaroslav , Študentová Vendula , Walková Radka , Žemličková Helena , Jakubů Vladislav , Chudáčková Eva , Gniadkowski Marek , Pfeifer Yvonne , Perry John D. , Wilkinson Kathryn , Bergerová Tamara 
Published: May 2012

ABSTRACT

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a potentially useful tool for the detection of antimicrobial resistance, especially that conferred by β-lactamases. Here we describe a modification of a previously reported MALDI-TOF MS meropenem hydrolysis assay. The modified method was validated on 108 carbapenemase-producing members of the
Enterobacteriaceae
, two NDM-1-producing
Acinetobacter baumannii
isolates, and 35 carbapenem-resistant enterobacteria producing no carbapenemase. The detection of carbapenemases by MALDI-TOF MS seems to be a powerful, quick, and cost-effective method for microbiological laboratories.
Molecular Characterization of Multidrug- and Extensively Drug-Resistant Mycobacterium tuberculosis Strains in Jiangxi, China
Authors: Yuan Xiaoliang , Zhang Tiantuo , Kawakami Kazuyoshi , Zhu Jiaxin , Li Hongtao , Lei Jianping , Tu Shaohua 
Published: May 2012

ABSTRACT

In this study, a total of 77 multidrug-resistant and extensively drug-resistant (MDR and XDR, respectively) isolates of
Mycobacterium tuberculosis
were characterized among samples from patients living in Jiangxi province, China. The following two approaches were used: (i) genotyping all drug-resistant isolates by the 15-locus MIRU-VNTR (mycobacterial interspersed repetitive-unit–variable-number tandem-repeat) method and identifying the Beijing family genotype using the RD105 deletion targeted multiplex PCR and (ii) determining the mutation profiles associated with the resistance to the first-line antituberculous drugs rifampin (RIF) and isoniazid (INH) and the second-line drugs ofloxacin (OFX), kanamycin (KAN), amikacin (AMK), and capreomycin (CAP) with DNA sequencing. Six loci were examined:
rpoB
(for resistance to RIF),
katG
and
mabA-inhA
(INH),
gyrA
and
gyrB
(OFX), and
rrs
(KAN, AMK, and CAP). It is shown that the Beijing genotype was predominant (80.5%) among these strains and that the selected drug-resistant strains were genetically diverse, suggesting that they probably had independently acquired drug resistance. In comparison to the phenotypic data, the sensitivities for the detection of RIF, INH, OFX, and KAN/AMK/CAP resistance by DNA sequencing were 94.8, 80.5, 84.6, and 78.9%, respectively. The most prevalent mutations involved in RIF, INH, OFX, and KAN/AMK/CAP resistance were Ser531Leu in
rpoB
(44.2%), Ser315Thr in
katG
(55.8%) and C-15T in
mabA-inhA
(11.7%), Asp94Gly in
gyrA
(48.7%), and A1401G in
rrs
(73.7%), respectively. Five novel
katG
mutants (Trp191Stop, Thr271Pro, Trp328Phe, Leu546Pro, and Asp695Gly) and six new alleles (Ile569Val, Ile572Met, Phe584Ser, Val615Met, Asp626Glu, and Lys972Thr) in the
rpoB
gene were identified.
Evidence for a Genetic and Physical Interaction between Nonstructural Proteins NS1 and NS4B That Modulates Replication of West Nile Virus
Authors: Youn Soonjeon , Li Tuo , McCune Broc T. , Edeling Melissa A. , Fremont Daved H. , Cristea Ileana M. , Diamond Michael S. 
Published: May 2012

ABSTRACT
Flavivirus NS1 is a nonstructural glycoprotein that is expressed on the cell surface and secreted into the extracellular space. Despite its transit through the secretory pathway, NS1 is an essential gene linked to early viral RNA replication. How this occurs has remained a mystery given the disparate localization of NS1 and the viral RNA replication complex, as the latter is present on the cytosolic face of the endoplasmic reticulum (ER). We recently identified an N-terminal di-amino acid motif in NS1 that modulates protein targeting and affected viral replication. Exchange of two amino acids at positions 10 and 11 from dengue virus (DENV) into West Nile virus (WNV) NS1 (RQ10NK) changed its relative surface expression and secretion and attenuated infectivity. However, the phenotype of WNV containing NS1 RQ10NK was unstable, as within two passages heterogeneous plaque variants were observed. Here, using a mutant WNV encoding the NS1 RQ10NK mutation, we identified a suppressor mutation (F86C) in NS4B, a virally encoded transmembrane protein with loops on both the luminal and cytoplasmic sides of the ER membrane. Introduction of NS4B F86C specifically rescued RNA replication of mutant WNV but did not affect the wild-type virus. Mass spectrometry and coimmunoprecipitation studies established a novel physical interaction between NS1 and NS4B, suggesting a mechanism for how luminal NS1 conveys signals to the cytoplasm to regulate RNA replication.
Therapeutic Blockade of Transforming Growth Factor Beta Fails To Promote Clearance of a Persistent Viral Infection
Authors: Garidou Lucile , Heydari Sara , Gossa Selamawit , McGavern Dorian B. 
Published: May 2012

ABSTRACTPersistent viral infections often overburden the immune system and are a major cause of disease in humans. During many persistent infections, antiviral T cells are maintained in a state of immune exhaustion characterized by diminished effector and helper functions. In mammalian systems, an extensive immune regulatory network exists to limit unwanted, potentially fatal immunopathology by inducing T cell exhaustion. However, this regulatory network at times overprotects the host and fosters viral persistence by severely dampening adaptive immune responsiveness. Importantly, recent studies have shown that T cell exhaustion is mediated in part by host immunoregulatory pathways (e.g., programmed death 1 [PD-1], interleukin 10 [IL-10]) and that therapeutic blockade of these pathways either before or during persistent infection can promote viral clearance. Transforming growth factor beta (TGF-β) is another immunosuppressive cytokine known to impede both self- and tumor-specific T cells, but its role in regulating antiviral immunity is not entirely understood. In this study, we inhibited TGF-β with three potent antagonists to determine whether neutralization of this regulatory molecule is a viable approach to control a persistent viral infection. Our results revealed that these inhibitors modestly elevate the number of antiviral T cells following infection with a persistent variant of lymphocytic choriomeningitis virus (LCMV) but have no impact on viral clearance. These data suggest that therapeutic neutralization of TGF-β is not an efficacious means to promote clearance of a persistent viral infection.
An In-Frame Deletion in the NS Protein-Coding Sequence of Parvovirus H-1PV Efficiently Stimulates Export and Infectivity of Progeny Virions
Authors: Weiss Nadine , Stroh-Dege Alexandra , Rommelaere Jean , Dinsart Christiane , Salomé Nathalie 
Published: May 2012

ABSTRACTAn in-frame, 114-nucleotide-long deletion that affects the NS-coding sequence was created in the infectious molecular clone of the standard parvovirus H-1PV, thereby generating Del H-1PV. The plasmid was transfected and further propagated in permissive human cell lines in order to analyze the effects of the deletion on virus fitness. Our results show key benefits of this deletion, as Del H-1PV proved to exhibit (i) higher infectivity (lower particle-to-infectivity ratio)in vitroand (ii) enhanced tumor growth suppressionin vivocompared to wild-type H-1PV. This increased infectivity correlated with an accelerated egress of Del H-1PV progeny virions in producer cells and with an overall stimulation of the viral life cycle in subsequently infected cells. Indeed, virus adsorption and internalization were significantly improved with Del H-1PV, which may account for the earlier appearance of viral DNA replicative forms that was observed with Del H-1PV than wild-type H-1PV. We hypothesize that the internal deletion within the NS2 and/or NS1 protein expressed by Del H-1PV results in the stimulation of some step(s) of the viral life cycle, in particular, a maturation step(s), leading to more efficient nuclear export of infectious viral particles and increased fitness of the virus produced.
Neutralization Resistance of Virological Synapse-Mediated HIV-1 Infection Is Regulated by the gp41 Cytoplasmic Tail
Authors: Durham Natasha D. , Yewdall Alice W. , Chen Ping , Lee Rebecca , Zony Chati , Robinson James E. , Chen Benjamin K. 
Published: May 2012

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) infection can spread efficiently from infected to uninfected T cells through adhesive contacts called virological synapses (VSs). In this process, cell-surface envelope glycoprotein (Env) initiates adhesion and viral transfer into an uninfected recipient cell. Previous studies have found some HIV-1-neutralizing patient sera to be less effective at blocking VS-mediated infection than infection with cell-free virus. Here we employ sensitive flow cytometry-based infection assays to measure the inhibitory potency of HIV-1-neutralizing monoclonal antibodies (MAb) and HIV-1-neutralizing patient sera against cell-free and VS-mediated infection. To various degrees, anti-Env MAbs exhibited significantly higher 50% inhibitory concentration (IC50s) against VS-mediated infection than cell-free infection. Notably, the MAb 17b, which binds a CD4-induced (CD4i) epitope on gp120, displayed a 72-fold reduced efficacy against VS-mediated inocula compared to cell-free inocula. A mutant with truncation mutation in the gp41 cytoplasmic tail (CT) which is unable to modulate Env fusogenicity in response to virus particle maturation but which can still engage in cell-to-cell infection was tested for the ability to resist neutralizing antibodies. The ΔCT mutation increased cell surface staining by neutralizing antibodies, significantly enhanced neutralization of VS-mediated infection, and had reduced or no effect on cell-free infection, depending upon the antibody. Our results suggest that the gp41 CT regulates the exposure of key neutralizing epitopes during cell-to-cell infection and plays an important role in immune evasion. Vaccine strategies should consider immunogens that reflect Env conformations exposed on the infected cell surface to enhance protection against VS-mediated HIV-1 spread.
Substitutions at Amino Acid Positions 143, 148, and 155 of HIV-1 Integrase Define Distinct Genetic Barriers to Raltegravir Resistance
In Vivo
Authors: Fransen Signe , Gupta Soumi , Frantzell Arne , Petropoulos Christos J. , Huang Wei 
Published: May 2012

ABSTRACT
Mutations at amino acids 143, 148, and 155 in HIV-1 integrase (IN) define primary resistance pathways in subjects failing raltegravir (RAL)-containing treatments. Although each pathway appears to be genetically distinct, shifts in the predominant resistant virus population have been reported under continued drug pressure. To better understand this dynamic, we characterized the RAL susceptibility of 200 resistant viruses, and we performed sequential clonal analysis for selected cases. Patient viruses containing Y143R, Q148R, or Q148H mutations consistently exhibited larger reductions in RAL susceptibility than patient viruses containing N155H mutations. Sequential analyses of virus populations from three subjects revealed temporal shifts in subpopulations representing N155H, Y143R, or Q148H escape pathways. Evaluation of molecular clones isolated from different time points demonstrated that Y143R and Q148H variants exhibited larger reductions in RAL susceptibility and higher IN-mediated replication capacity (RC) than N155H variants within the same subject. Furthermore, shifts from the N155H pathway to either the Q148R or H pathway or the Y143R pathway were dependent on the amino acid substitution at position 148 and the secondary mutations in Y143R- or Q148R- or H-containing variants and correlated with reductions in RAL susceptibility and restorations in RC. Our observations in patient viruses were confirmed by analyzing site-directed mutations. In summary, viruses that acquire mutations defining the 143 or 148 escape pathways are less susceptible to RAL and exhibit greater RC than viruses containing 155 pathway mutations. These selective pressures result in the displacement of N155H variants by 143 or 148 variants under continued drug exposure.
HIV-1 Virus-Like Particles Produced by Stably Transfected Drosophila S2 Cells: a Desirable Vaccine Component
Authors: Yang Lifei , Song Yufeng , Li Xiaomin , Huang Xiaoxing , Liu Jingjing , Ding Heng , Zhu Ping , Zhou Paul 
Published: May 2012

ABSTRACTThe development of a successful vaccine against human immunodeficiency virus type 1 (HIV-1) likely requires immunogens that elicit both broadly neutralizing antibodies against envelope spikes and T cell responses that recognize multiple viral proteins. HIV-1 virus-like particles (VLP), because they display authentic envelope spikes on the particle surface, may be developed into such immunogens. However, in one way or the other current systems for HIV-1 VLP production have many limitations. To overcome these, in the present study we developed a novel strategy to produce HIV-1 VLP using stably transfectedDrosophilaS2 cells. We cotransfected S2 cells with plasmids encoding HIV-1 envelope, Gag, and Rev proteins and a selection marker. After stably transfected S2 clones were established, HIV-1 VLP and their immunogenicity in mice were carefully evaluated. Here, we report that HIV-1 envelope proteins are properly cleaved, glycosylated, and incorporated into VLP with Gag. The amount of VLP released into culture supernatants is comparable to those produced by insect cells infected with recombinant baculoviruses. Moreover, cryo-electron microscopy tomography revealed average 17 spikes per purified VLP, and antigenic epitopes on the spikes were recognized by the broadly neutralizing antibodies 2G12, b12, VRC01, and 4E10 but not by PG16. Finally, mice primed with DNA and boosted with VLP in the presence of CpG exhibited anti-envelope antibody responses, including ELISA-binding, neutralizing, antibody-dependent cell-mediated cytotoxicity and antibody-dependent cell-mediated viral inhibition, as well as envelope and Gag-specific CD8 T cell responses. Thus, we conclude that HIV-1 VLP produced by the S2 expression system has many desirable features to be developed into a vaccine component against HIV-1.
Seismic investigations of buried tunnel valleys on- and offshore Denmark
Authors: Andersen Theis Raaschou , Huuse Mads , Jørgensen Flemming , Christensen Steen 
Published: May 2012

Abstract

Tunnel valleys on- and offshore Denmark have been investigated based on a database of 1000 km two-dimensional (2D) onshore seismic data, 5600 km 2D offshore seismic data and 1200 km
2
three-dimensional (3D) offshore seismic data. From the 2D data we identified 216 onshore and 674 offshore seismic tunnel valley intersections, and 55 individual valleys were identified from three 3D surveys. The majority of the valleys have depths ranging from 50 to 200 m and widths between 500 and 1500 m. Up to seven generations of tunnel valleys were identified, indicating repeated erosion and deposition within the study area. The valleys were most likely formed by subglacial meltwater erosion during the last three glaciations. Statistical analyses conducted on the data show that there are no significant differences between the onshore and offshore valleys with respect to their depth and shape; they share morphological and structural characteristics. The onshore seismic data have been analysed in conjunction with lithological information from boreholes. The analyses show that tunnel valley bottoms terminate equally commonly in substrates dominated by clay and sand, and that the valley shapes are similar for the two substrates.
Ordovician proglacial sediments in Algeria: insights into the controls on hydrocarbon reservoirs in the In Amenas field, Illizi Basin
Authors: Hirst J. Philip P. 
Published: May 2012

Abstract
Ordovician proglacial deposits form gas reservoirs in the In Amenas field, Illizi Basin, Algeria. Depositional models were developed to understand the context and disposition of the main reservoirs through an evaluation of core and analogous outcrops from the Tassili N'Ajjer.
Tunnel valleys initially accumulated sandstones with tractional structures. Subsequent failures of subaqueous grounding line sediment deposited proglacial debrites comprising poorly sorted argillaceous sandstone with granules. These were interbedded with high-density turbidity sandstones; their fine grain size indicates they were dynamically disconnected from the lithologically varied debrites. A lobate geometry has been defined for one subsurface composite turbidite.
Periodic catastrophic outflows, possibly evacuating subglacial lakes, incised the network of subglacial tunnels and in the process delivered sand to the turbidite outwashes. Bedforms indicate high-energy, transcritical to supercritical outflows that were stable for extended periods. During ice retreat, a period of ice margin stability may have occurred due to grounding over the In Amenas granitic palaeohighs. Outwash fan apices were located along this grounding line with feeder channels developing where the substrate was more easily eroded such as between the palaeohighs. Following further ice retreat, deposition evolved to variably sinuous channels and thence to pelagic fines with dropstones.
Phosphoinositide Signaling
Authors: Boss Wendy F. , Im Yang Ju 
Published: May 2012

All things flow and change…even in the stillest matter there is unseen flux and movement. Attributed to Heraclitus (530–470 BC) From The Story of Philosophy by Will Durant ( 28 ) Heraclitus, a Greek philosopher, was thinking on a much larger scale than molecular signaling; however, his visionary comments are an important reminder for those studying signaling today. Even in unstimulated cells, signaling pathways are in constant metabolic flux and provide basal signals that travel throughout the organism. In addition, negatively charged phospholipids, such as the polyphosphorylated inositol phospholipids, provide a circuit board of on/off switches for attracting or repelling proteins that define the membranes of the cell. This template of charged phospholipids is sensitive to discrete changes and metabolic fluxes—e.g., in pH and cations—which contribute to the oscillating signals in the cell. The inherent complexities of a constantly fluctuating system make understanding how plants integrate and process signals challenging. In this review we discuss one aspect of lipid signaling: the inositol family of negatively charged phospholipids and their functions as molecular sensors and regulators of metabolic flux in plants.
Cancer Cell Secretion of the DAMP Protein HMGB1 Supports Progression in Malignant Mesothelioma
Authors: Jube Sandro , Rivera Zeyana S. , Bianchi Marco E. , Powers Amy , Wang Ena , Pagano Ian , Pass Harvey I. , Gaudino Giovanni , Carbone Michele , Yang Haining 
Published: May 2012

Abstract
Human malignant mesothelioma is an aggressive and highly lethal cancer that is believed to be caused by chronic exposure to asbestos and erionite. Prognosis for this cancer is generally poor because of late-stage diagnosis and resistance to current conventional therapies. The damage-associated molecular pattern protein HMGB1 has been implicated previously in transformation of mesothelial cells. Here we show that HMGB1 establishes an autocrine circuit in malignant mesothelioma cells that influences their proliferation and survival. Malignant mesothelioma cells strongly expressed HMGB1 and secreted it at high levels in vitro. Accordingly, HMGB1 levels in malignant mesothelioma patient sera were higher than that found in healthy individuals. The motility, survival, and anchorage-independent growth of HMGB1-secreting malignant mesothelioma cells was inhibited in vitro by treatment with monoclonal antibodies directed against HMGB1 or against the receptor for advanced glycation end products, a putative HMGB1 receptor. HMGB1 inhibition in vivo reduced the growth of malignant mesothelioma xenografts in severe-combined immunodeficient mice and extended host survival. Taken together, our findings indicate that malignant mesothelioma cells rely on HMGB1, and they offer a preclinical proof-of-principle that antibody-mediated ablation of HMBG1 is sufficient to elicit therapeutic activity, suggesting a novel therapeutic approach for malignant mesothelioma treatment. Cancer Res; 72(13); 3290–301. ©2012 AACR.
Combined EGFR/MET or EGFR/HSP90 Inhibition Is Effective in the Treatment of Lung Cancers Codriven by Mutant EGFR Containing T790M and MET
Authors: Xu Lu , Kikuchi Eiki , Xu Chunxiao , Ebi Hiromichi , Ercan Dalia , Cheng Katherine A. , Padera Robert , Engelman Jeffrey A. , Jänne Pasi A. , Shapiro Geoffrey I. , Shimamura Takeshi , Wong Kwok-Kin 
Published: May 2012

Abstract
Tyrosine kinase inhibitors (TKI) that target the EGF receptor (EGFR) are effective in most non–small cell lung carcinoma (NSCLC) patients whose tumors harbor activating EGFR kinase domain mutations. Unfortunately, acquired resistance eventually emerges in these chronically treated cancers. Two of the most common mechanisms of acquired resistance to TKIs seen clinically are the acquisition of a secondary “gatekeeper” T790M EGFR mutation that increases the affinity of mutant EGFR for ATP and activation of MET to offset the loss of EGFR signaling. Although up to one-third of patient tumors resistant to reversible EGFR TKIs harbor concurrent T790M mutation and MET amplification, potential therapies for these tumors have not been modeled in vivo. In this study, we developed a preclinical platform to evaluate potential therapies by generating transgenic mouse lung cancer models expressing EGFR-mutant Del19-T790M or L858R-T790M, each with concurrent MET overexpression. We found that monotherapy targeting EGFR or MET alone did not produce significant tumor regression. In contrast, combination therapies targeting EGFR and MET simultaneously were highly efficacious against EGFR TKI–resistant tumors codriven by Del19-T790M or L858R-T790M and MET. Our findings therefore provide an in vivo model of intrinsic resistance to reversible TKIs and offer preclinical proof-of-principle that combination targeting of EGFR and MET may benefit patients with NSCLC. Cancer Res; 72(13); 3302–11. ©2012 AACR.