bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assembly of the MexAB-OprM Multidrug Pump of
Pseudomonas aeruginosa
: Component Interactions Defined by the Study of Pump Mutant Suppressors
Authors: Nehme Dominic , Poole Keith 
Published: June 2007

ABSTRACT

In an effort to identify key domains of the Pseudo
monas aeruginosa
MexAB-OprM drug efflux system involved in component interactions, extragenic suppressors of various inactivating mutations in individual pump constituents were isolated and studied. The multidrug hypersusceptibility of
P. aeruginosa
expressing MexB with a mutation in a region of the protein implicated in oligomerization (G220S) was suppressed by mutations in the α/β domain of MexA. MexB(G220S) showed a reduced ability to bind MexA in vivo while representative MexA suppressors (V66M and V259F) restored the MexA-MexB interaction. Interestingly, these suppressors also restored resistance in
P. aeruginosa
expressing OprM proteins with mutations at the proximal (periplasmic) tip of OprM that is predicted to interact with MexB, suggesting that these suppressors generally overcame defects in MexA-MexB and MexB-OprM interaction. The multidrug hypersusceptibility arising from a mutation in the helical hairpin of MexA implicated in OprM interaction (V129M) was suppressed by mutations (T198I and F439I) in the periplasmic α-helical barrel of OprM. Again, the MexA mutation compromised an in vivo interaction with OprM that was restored by the T198I and F439I substitutions in OprM, consistent with the hairpin domain mediating MexA binding to this region of OprM. Interestingly, these OprM suppressor mutations restored multidrug resistance in
P. aeruginosa
expressing MexB(G220S). Finally, the
oprM
(
T198I
) suppressor mutation enhanced the yields of all three constituents of a MexA-MexB-OprM(T198I) pump as detected in whole-cell extracts. These data highlight the importance of MexA and interactions with this adapter in promoting MexAB-OprM pump assembly and in stabilizing the pump complex.
ClpP Modulates the Activity of theBacillus subtilisStress Response Transcription Factor, σB
Authors: Reeves Adam , Gerth Ulf , Völker Uwe , Haldenwang W. G. 
Published: June 2007

ABSTRACTThe general stress regulon ofBacillus subtilisis controlled by the activity state of σB, a transcription factor that is switched on following exposure to either physical or nutritional stress. ClpP is the proteolytic component of an ATP-dependent protease that is essential for the proper regulation of multiple adaptive responses inB. subtilis. Among the proteins whose abundance increases in ClpP−B. subtilisare several known to depend on σBfor their expression. In the current work we examine the relationship of ClpP to the activity of σB. The data reveal that the loss of ClpP in otherwise wild-typeB. subtilisresults in a small increase in σBactivity during growth and a marked enhancement of σBactivity following its induction by either physical or nutritional stress. It appears to be the persistence of σB's activity rather than its induction that is principally affected by the loss of ClpP. σB-dependent reporter gene activity rose in parallel in ClpP+and ClpP−B. subtilisstrains but failed to display its normal transience in the ClpP−strain. The putative ClpP targets are likely to be stress generated and novel. Enhanced σBactivity in ClpP−B. subtiliswas triggered by physical stress but not by the induced synthesis of the physical stress pathway's positive regulator (RsbT). In addition, Western blot analyses failed to detect differences in the levels of the principal known σBregulators in ClpP+and ClpP−B. subtilisstrains. The data suggest a model in which ClpP facilitates the turnover of stress-generated factors, which persist in ClpP's absence to stimulate ongoing σBactivity.
Spore Coat Architecture of
Clostridium novyi
NT Spores
Authors: Plomp Marco , McCaffery J. Michael , Cheong Ian , Huang Xin , Bettegowda Chetan , Kinzler Kenneth W. , Zhou Shibin , Vogelstein Bert , Malkin Alexander J. 
Published: June 2007

ABSTRACT

Spores of the anaerobic bacterium
Clostridium novyi
NT are able to germinate in and destroy hypoxic regions of tumors in experimental animals. Future progress in this area will benefit from a better understanding of the germination and outgrowth processes that are essential for the tumorilytic properties of these spores. Toward this end, we have used both transmission electron microscopy and atomic force microscopy to determine the structure of both dormant and germinating spores. We found that the spores are surrounded by an amorphous layer intertwined with honeycomb parasporal layers. Moreover, the spore coat layers had apparently self-assembled, and this assembly was likely to be governed by crystal growth principles. During germination and outgrowth, the honeycomb layers, as well as the underlying spore coat and undercoat layers, sequentially dissolved until the vegetative cell was released. In addition to their implications for understanding the biology of
C. novyi
NT, these studies document the presence of proteinaceous growth spirals in a biological organism.
The
Bordetella
Bps Polysaccharide Is Critical for Biofilm Development in the Mouse Respiratory Tract
Authors: Sloan Gina Parise , Love Cheraton F. , Sukumar Neelima , Mishra Meenu , Deora Rajendar 
Published: June 2007

ABSTRACT

Bordetellae are respiratory pathogens that infect both humans and animals.
Bordetella bronchiseptica
establishes asymptomatic and long-term to life-long infections of animal nasopharynges. While the human pathogen
Bordetella pertussis
is the etiological agent of the acute disease whooping cough in infants and young children, it is now being increasingly isolated from the nasopharynges of vaccinated adolescents and adults who sometimes show milder symptoms, such as prolonged cough illness. Although it has been shown that
Bordetella
can form biofilms in vitro, nothing is known about its biofilm mode of existence in mammalian hosts. Using indirect immunofluorescence and scanning electron microscopy, we examined nasal tissues from mice infected with
B. bronchiseptica
. Our results demonstrate that a wild-type strain formed robust biofilms that were adherent to the nasal epithelium and displayed architectural attributes characteristic of a number of bacterial biofilms formed on inert surfaces. We have previously shown that the
Bordetella
Bps polysaccharide encoded by the
bpsABCD
locus is critical for the stability and maintenance of three-dimensional structures of biofilms. We show here that Bps is essential for the formation of efficient nasal biofilms and is required for the colonization of the nose. Our results document a biofilm lifestyle for
Bordetella
in mammalian respiratory tracts and highlight the essential role of the Bps polysaccharide in this process and in persistence of the nares.
Impact of Hepatitis C Virus (HCV) Genotypes on Quantification of HCV RNA in Serum by COBAS AmpliPrep/COBAS TaqMan HCV Test, Abbott Antiretroviral Therapy HCV RealTime Assay, and VERSANT HCV RNA Assay
Authors: Tuaillon Edouard , Mondain Anne-Marie , Ottomani Laure , Roudière Laurent , Perney Pascal , Picot Marie-Christine , Séguret Fabienne , Blanc François , Larrey Dominique , Van de Perre Philippe , Ducos Jacques 
Published: June 2007

ABSTRACT

The VERSANT HCV RNA 3.0 (bDNA), COBAS AmpliPrep/COBAS TaqMan HCV, and Abbott ART HCV RealTime assays were compared for hepatitis C virus RNA quantification in 158 clinical specimens (genotypes 1 to 5). RNA values differed significantly between methods (
P
< 0.0001), and mean titer differences ranged from 0.01 to 0.50 log
10
IU/ml depending on the genotypes.
Response Prediction and Treatment Tailoring for Chronic Hepatitis C Virus Genotype 1 Infection
Authors: Lindh Magnus , Alestig Erik , Arnholm Birgitta , Eilard Anders , Hellstrand Kristoffer , Lagging Martin , Wahlberg Thomas , Wejstål Rune , Westin Johan , Norkrans Gunnar 
Published: June 2007

ABSTRACTWe monitored early viral response during the treatment of hepatitis C virus (HCV) infection with the aim of identifying predictors of treatment outcome. We studied 53 patients with genotype 1 infection who received 180 μg/week pegylated interferon alfa-2a and 1,000 or 1,200 mg/day ribavirin depending on body weight and serially assessed HCV RNA in serum, using the Cobas TaqMan assay. Thirty-one patients (58%) achieved sustained viral response (SVR). SVR was obtained in 100% (10/10) of patients with pretreatment viremia concentrations below 400,000 IU/ml, in 100% (14/14) of patients with more than 1.5 log reduction of HCV RNA after 4 days of treatment, and in 95% (22/23) of patients with a rate of decline in viremia higher than 0.70 log units/week during the second phase. Non-SVR was seen in all patients with a second-phase decline rate lower than 0.35 log units/week. Patients with slopes between 0.50 and 0.80 log units/week achieved SVR (4/4) unless the treatment dose was modified (3/3). We conclude that the second-phase slope appears to be an accurate and useful predictor of treatment response. On the basis of these findings, we propose a model of tailored treatment which takes into account the second-phase slope and the amount of HCV RNA after 21 days of treatment.
Quality Control of Direct Molecular Diagnostics for Methicillin-Resistant
Staphylococcus aureus
Authors: van Belkum Alex , Niesters Hubert G. M. , MacKay William G. , van Leeuwen Willem B. 
Published: June 2007

ABSTRACT

Ten samples containing various amounts of methicillin-resistant
Staphylococcus aureus
(MRSA), methicillin-susceptible
S. aureus
, methicillin-resistant
Staphylococcus epidermidis
(MRSE), and combinations thereof were distributed to 51 laboratories for molecular diagnostics testing. Samples containing 10
2
to 10
3
MRSA cells were frequently reported to be negative. MRSE samples were scored as negative by all commercial tests but by only two out of three in-house tests.
Molecular Typing of
Aspergillus terreus
Isolates Collected in Houston, Texas, and Innsbruck, Austria: Evidence of Great Genetic Diversity
Authors: Lass-Flörl Cornelia , Grif Katharina , Kontoyiannis Dimitrios P. 
Published: June 2007

ABSTRACT

Aspergillus terreus
isolates collected from patients at The M. D. Anderson Cancer Center in Houston, TX, and at The University Hospital of Innsbruck, Austria, were analyzed using random amplification of polymorphic DNA-PCR with three different primers. No strain similarity in either institution was detected, indicating great genetic diversity of
A. terreus
.
Shedding and Reversion of Oral Polio Vaccine Type 3 in Mexican Vaccinees: Comparison of Mutant Analysis by PCR and Enzyme Cleavage to a Real-Time PCR Assay
Authors: Gnanashanmugam Devasena , Falkovitz-Halpern Meira S. , Dodge Anthony , Fang Melanie , Wong Lisa J. , Esparza Melissa , Hammon Rebecca , Rivas-Merelles Enrique E. , Santos Jose I. , Maldonado Yvonne 
Published: June 2007

ABSTRACT
A uracil-to-cytosine mutation at nucleotide position 472 of oral poliovirus vaccine type 3 (OPV3) contributes to the development of vaccine-associated paralytic poliomyelitis (VAPP). To analyze OPV3 shedding patterns, we previously used the multistep method of mutant analysis by PCR and enzyme cleavage (MAPREC). This involves conventional reverse transcription-PCR to detect OPV3, followed by a restriction digest to quantify position 472 reversion. Real-time PCR detects and quantifies nucleic acid as PCR occurs and avoids postreaction processing. The goal of this study was to compare a real-time PCR method to MAPREC. Seventy-three stool samples from Mexican OPV recipients underwent the reverse transcription-PCR step of MAPREC and real-time PCR. Real-time PCR identified 23% more OPV3-positive samples than conventional reverse transcription-PCR. When reversion was compared, the revertant proportion (RP), defined as the percentage of revertants in a sample, differed by ≤10% in 21/25 (84%) samples. The four samples differing by >10% were obtained within 5 days of OPV administration. The real-time PCR assay identified samples with an RP of ≥85% with 94% sensitivity and 86% specificity compared to MAPREC. The mean difference in RP between the two methods was 3.6% (95% confidence interval, −0.3 to 7.5%). Real-time PCR methods reliably detect OPV3, and reversion estimates correlate more consistently with MAPREC when OPV3 reversion rates are high. Detecting VAPP-related mutations by real-time PCR is rapid and efficient and can be useful in monitoring ongoing global polio eradication efforts.
Role of Human Immunodeficiency Virus (HIV)-Specific T-Cell Immunity in Control of Dual HIV-1 and HIV-2 Infection
Authors: Zheng Natalie N. , McElrath M. Juliana , Sow Papa-Salif , Hawes Stephen E. , Diallo-Agne Habibatou , Stern Joshua E. , Li Fusheng , Mesher Andrew L. , Robinson Akeliah D. , Gottlieb Geoffrey S. , Huang Yunda , Kiviat Nancy B. 
Published: June 2007

ABSTRACTProgressive immune dysfunction and AIDS develop in most cases of human immunodeficiency virus type 1 (HIV-1) infection but in only 25 to 30% of persons with HIV-2 infection. However, the natural history and immunologic responses of individuals with dual HIV-1 and HIV-2 infection are largely undefined. Based on our previous findings, we hypothesized that among patients with dual infection the control of HIV-1 is associated with the ability to respond to HIV-2 Gag epitopes and to maintain HIV-specific CD4+T-cell responses. To test this, we compared the HIV-specific ex vivo IFN-γ enzyme-linked immunospot (ELISPOT) assay responses of 19 dually infected individuals to those of persons infected with HIV-1 or HIV-2 only. Further, we assessed the functional profile of HIV Gag-specific CD4+and CD8+T cells from nine HIV dually infected patients by using a multicolor intracellular cytokine staining assay. As determined by ELISPOT assay, the magnitude and frequency of IFN-γ-secreting T-cell responses to gene products of HIV-1 were higher than those to gene products of HIV-2 (2.64 versus 1.53 log10IFN-γ spot-forming cells/106cells [90% versus 63%, respectively].) Further, HIV-1 Env-, Gag-, and Nef- and HIV-2 Gag-specific responses were common; HIV-2 Nef-specific responses were rare. HIV-specific CD4+T helper responses were detected in nine of nine dually infected subjects, with the majority of these T cells producing gamma interferon (IFN-γ) and tumor necrosis factor alpha (TNF-α) and, to a lesser extent, interleukin-2. The HIV-1 plasma viral load was inversely correlated with HIV-2 Gag-specific IFN-γ-/TNF-α-secreting CD4+and HIV-2 Gag-specific IFN-γ-secreting CD8+T cells. In conclusion, the T-cell memory responses associated with containment of single HIV-1 and HIV-2 infection play a similar significant role in the immune control of dual HIV-1 and HIV-2 infection.
A New E6/P63 Pathway, Together with a Strong E7/E2F Mitotic Pathway, Modulates the Transcriptome in Cervical Cancer Cells
Authors: Teissier Sébastien , Ben Khalifa Youcef , Mori Marcella , Pautier Patricia , Desaintes Christian , Thierry Françoise 
Published: June 2007

ABSTRACT
Cervical carcinoma is associated with certain types of human papillomaviruses expressing the E6 and E7 oncogenes, which are involved in carcinogenesis through their interactions with the p53 and pRB pathways, respectively. A critical event on the path to malignant transformation is often manifested by the loss of expression of the viral E2 transcription factor due to the integration into the host genome of the viral DNA. Using microarrays, we have previously shown that reintroduction of a functional E2 in the HeLa cervical carcinoma cell line activates a cluster of p53 target genes while at the same time severely repressing a group of E2F target genes. In the present study, using new high-density microarrays containing more than 22,000 human cDNA sequences, we identified a novel p63 pathway among E2-activated genes and 38 new mitotic genes repressed by E2. We then sought to determine the pathways through which these genes were modulated and used an approach that relies on small interfering RNA to demonstrate that the p63 target genes were activated through silencing of the E6/E6AP pathway while the mitotic genes were mainly repressed through E7 silencing. Importantly, a subset of the mitotic genes was shown to be significantly induced in biopsies of stage IV cervical cancers, which points to a prominent E7 pathway in cervical carcinoma.
Arenavirus Z-Glycoprotein Association Requires Z Myristoylation but Not Functional RING or Late Domains
Authors: Capul Althea A. , Perez Mar , Burke Emily , Kunz Stefan , Buchmeier Michael J. , de la Torre Juan C. 
Published: June 2007

ABSTRACT
Generation of infectious arenavirus-like particles requires the virus RING finger Z protein and surface glycoprotein precursor (GPC) and the correct processing of GPC into GP1, GP2, and a stable signal peptide (SSP). Z is the driving force of arenavirus budding, whereas the GP complex (GPc), consisting of hetero-oligomers of SSP, GP1, and GP2, forms the viral envelope spikes that mediate receptor recognition and cell entry. Based on the roles played by Z and GP in the arenavirus life cycle, we hypothesized that Z and the GPc should interact in a manner required for virion formation. Here, using confocal microscopy and coimmunoprecipitation assays, we provide evidence for subcellular colocalization and biochemical interaction, respectively, of Z and the GPc. Our results from mutation-function analysis reveal that Z myristoylation, but not the Z late (L) or RING domain, is required for Z-GPc interaction. Moreover, Z interacted directly with SSP in the absence of other components of the GPc. We obtained similar results with Z and GPC from the prototypical arenavirus lymphocytic choriomeningitis virus and the hemorrhagic fever arenavirus Lassa fever virus.
Cytokine and Antibody Responses in Gnotobiotic Pigs after Infection with Human Norovirus Genogroup II.4 (HS66 Strain)
Authors: Souza M. , Cheetham S. M. , Azevedo M. S. P. , Costantini V. , Saif L. J. 
Published: June 2007

ABSTRACTA human norovirus genogroup II.4 strain HS66 (HuNoV-HS66) infects and causes mild diarrhea in gnotobiotic (Gn) pigs (S. Cheetham, M. Souza, T. Meulia, S. Grimes, M. G. Han, and L. J. Saif, J. Virol. 80:10372-10381, 2006). In this study we evaluated systemic and intestinal humoral and cellular immune responses to HuNoV-HS66 in orally inoculated pigs. Antibodies and type I interferon (IFN-I or IFN-α), proinflammatory interleukin-6 (IL-6), Th1 (IL-12 and IFN-γ), Th2 (IL-4), and Th2/regulatory T ([Treg] IL-10) cytokine profiles in serum and intestinal contents (IC) of the HuNoV-HS66-inoculated pigs and controls were assessed by enzyme-linked immunosorbent assay at selected postinoculation days (0 to 28). Using an enzyme-linked immunospot assay, we evaluated immunoglobulin M (IgM), IgA, and IgG antibody-secreting cells (ASC) and cytokine-secreting cells (CSC) in intestine, spleen, and blood. In the HuNoV-inoculated pigs, antibody titers in serum and IC were generally low, and 65% seroconverted. Pigs with higher diarrhea scores were more likely to seroconvert and developed higher intestinal IgA and IgG antibody titers. The numbers of IgA and IgG ASC were higher systemically than in the gut. In serum, HuNoV induced persistently higher Th1 (low transient IFN-γ and high IL-12) than the other cytokines, but also low Th2 (IL-4) and Th2/Treg(IL-10) levels; low, transient proinflammatory (IL-6) cytokines; and, notably, a delayed IFN-α response. In contrast, intestinal innate (IFN-α early and late) and Th1 (IL-12 late) cytokines were significantly elevated postinfection. HuNoV-HS66 also elicited higher numbers of Th1 (IL-12 and IFN-γ) CSC than Th2 (IL-4) and proinflammatory (IL-6) CSC, with the latter responses low in blood and intestine, reflecting low intestinal inflammation in the absence of gut lesions. These data provide insights into the kinetics of cytokine secretion in serum and IC of HuNoV-inoculated Gn pigs and new information on intestinal humoral and cellular immune responses to HuNoV that are difficult to assess in human volunteers.
Vaccinia Virus Entry, Exit, and Interaction with Differentiated Human Airway Epithelia
Authors: Vermeer Paola D. , McHugh Julia , Rokhlina Tatiana , Vermeer Daniel W. , Zabner Joseph , Welsh Michael J. 
Published: June 2007

ABSTRACT
Variola virus, the causative agent of smallpox, enters and exits the host via the respiratory route. To better understand the pathogenesis of poxvirus infection and its interaction with respiratory epithelia, we used vaccinia virus and examined its interaction with primary cultures of well-differentiated human airway epithelia. We found that vaccinia virus preferentially infected the epithelia through the basolateral membrane and released viral progeny across the apical membrane. Despite infection and virus production, epithelia retained tight junctions, transepithelial electrical conductance, and a steep transepithelial concentration gradient of virus, indicating integrity of the epithelial barrier. In fact, during the first four days of infection, epithelial height and cell number increased. These morphological changes and maintenance of epithelial integrity required vaccinia virus growth factor, which was released basolaterally, where it activated epidermal growth factor 1 receptors. These data suggest a complex interaction between the virus and differentiated airway epithelia; the virus preferentially enters the cells basolaterally, exits apically, and maintains epithelial integrity by stimulating growth factor receptors.
Proteomics Analysis of
Helicoverpa armigera
Single Nucleocapsid Nucleopolyhedrovirus Identified Two New Occlusion-Derived Virus-Associated Proteins, HA44 and HA100
Authors: Deng Fei , Wang Ranran , Fang Minggang , Jiang Yue , Xu Xushi , Wang Hanzhong , Chen Xinwen , Arif Basil M. , Guo Lin , Wang Hualin , Hu Zhihong 
Published: June 2007

ABSTRACT

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry were used to analyze the structural proteins of the occlusion-derived virus (ODV) of
Helicoverpa armigera
single nucleocapsid nucleopolyhedrovirus (HearNPV), a group II NPV. Twenty-three structural proteins of HearNPV ODV were identified, 21 of which have been reported previously as structural proteins or ODV-associated proteins in other baculoviruses. These include polyhedrin, P78/83, P49, ODV-E18, ODV-EC27, ODV-E56, P74, LEF-3, HA66 (AC66), DNA polymerase, GP41, VP39, P33, ODV-E25, helicase, P6.9, ODV/BV-C42, VP80, ODV-EC43, ODV-E66, and PIF-1. Two proteins encoded by HearNPV ORF44 (
ha44
) and ORF100 (
ha100
) were discovered as ODV-associated proteins for the first time.
ha44
encodes a protein of 378 aa with a predicted mass of 42.8 kDa.
ha100
encodes a protein of 510 aa with a predicted mass of 58.1 kDa and is a homologue of the gene for poly(ADP-ribose) glycohydrolase (
parg
). Western blot analysis and immunoelectron microscopy confirmed that HA44 is associated with the nucleocapsid and HA100 is associated with both the nucleocapsid and the envelope of HearNPV ODV. HA44 is conserved in group II NPVs and granuloviruses but does not exist in group I NPVs, while HA100 is conserved only in group II NPVs.