bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Putative Response Regulator BaeR Stimulates Multidrug Resistance of
Escherichia coli
via a Novel Multidrug Exporter System, MdtABC
Authors: Nagakubo Satoshi , Nishino Kunihiko , Hirata Takahiro , Yamaguchi Akihito 
Published: July 2002

ABSTRACT

Overproduction of the response regulator BaeR confers resistance to novobiocin and bile salts in a Δ
acrAB
mutant by stimulating drug exporter gene expression. The
mdtABC
(multidrug transporter ABC, formerly known as
yegMNO
) genes, which encode a resistance-nodulation-cell division (RND) drug efflux system, are responsible for resistance. The MdtABC system comprises the transmembrane MdtB/MdtC heteromultimer and MdtA membrane fusion protein. MdtAC also confers bile salt, but not novobiocin, resistance. This indicates that the evolution from an MdtC homomultimer to an MdtBC heteromultimer contributed to extend the drug resistance spectrum. A BLAST search suggested that such a heteromultimer-type RND exporter constitutes a unique family among gram-negative organisms.
Structural and Genetic Analysis of the BldB Protein of
Streptomyces coelicolor
Authors: Eccleston Marcus , Ali Reem Ahmed , Seyler Richard , Westpheling Janet , Nodwell Justin 
Published: July 2002

ABSTRACT

We have demonstrated that the
bldB
gene of
Streptomyces coelicolor
is required for the formation of aerial hyphae and the synthesis of antibiotics. We also found that BldB forms a higher-order complex (most likely a dimer) and that amino acid residues 20 to 78 are important for this interaction. This region is conserved in the BldB family, suggesting that dimer formation may be a common feature of these proteins.
Transcriptome and Proteome Analysis ofBacillus subtilisGene Expression Modulated by Amino Acid Availability
Authors: Mäder Ulrike , Homuth Georg , Scharf Christian , Büttner Knut , Bode Rüdiger , Hecker Michael 
Published: July 2002

ABSTRACTA comprehensive study ofBacillus subtilisgene expression patterns in response to amino acid availability was performed by means of proteomics and transcriptomics. The methods of two-dimensional protein gel electrophoresis and DNA macroarray technology were combined to analyze cells exponentially grown in minimal medium with and without 0.2% Casamino Acids (CAA). This approach revealed about 120 genes predominantly involved in amino acid biosynthesis, sporulation, and competence, which were downregulated in CAA-containing medium. Determination of sporulation frequencies confirmed the physiological relevance of the expression data.
Clinical Evaluation of the ZstatFlu-II Test: a Chemiluminescent Rapid Diagnostic Test for Influenza Virus
Authors: Hamilton Marilyn S. , Abel David M. , Ballam Yolanda J. , Otto Mary K. , Nickell Angela F. , Pence Lisa M. , Appleman James R. , Shimasaki Craig D. , Achyuthan Komandoor E. 
Published: July 2002

ABSTRACT

Exploiting the high sensitivity of the chemiluminescence phenomenon, an accurate and sensitive point-of-care test, called the ZstatFlu-II test (ZymeTx, Inc., Oklahoma City, Okla.), was developed to detect influenza virus infections. The ZstatFlu-II test takes 20 min and requires approximately 2 min of “hands-on” time for operational steps. The ZstatFlu-II test does not distinguish between infections with influenza virus types A and B. ZstatFlu-II test results are printed on Polaroid High-Speed Detector Film, allowing test results to be archived. A prototype version of the ZstatFlu-II test was evaluated during the 2000-to-2001 flu season with 300 nasal aspirate specimens from children at a pediatric hospital. Compared to culture, the ZstatFlu-II test had 88% sensitivity and 92% specificity. The Directigen test had a sensitivity of 75% and a specificity of 93%. The sensitivity of the ZstatFlu-II test was significantly higher than that of the Directigen test (
P
< 0.0574).
Comparison of an Industry-Derived LCx
Chlamydia pneumoniae
PCR Research Kit to In-House Assays Performed in Five Laboratories
Authors: Chernesky Max , Smieja Marek , Schachter Julius , Summersgill James , Schindler Laura , Solomon Natalie , Campbell Karen , Campbell LeeAnn , Cappuccio Alison , Gaydos Charlotte , Chong Sylvia , Moncada Jeanne , Phillips Jack , Jang Dan , Wood Billie Jo , Petrich Astrid , Hammerschlag Margaret , Cerney Mike , Mahony James 
Published: July 2002

ABSTRACT

In a multicenter comparison of PCR assays utilizing 120 quantitated samples of 16
Chlamydia pneumoniae
isolates, an LCx research-use-only (RUO) PCR developed by Abbott Laboratories demonstrated 100% sensitivity on 48 samples with >1 copy of DNA per μl of specimen. The sensitivities of five in-house PCR assays ranged from 54 to 94% for the same samples. All six assays showed decreased sensitivities as the DNA copy numbers of the samples decreased. Overall, sensitivities ranged from 68% for the LCx PCR assay to 29% for one of the in-house tests. The LCx RUO PCR and three of the five in-house PCR tests reported no false positives with the 24 negative samples. Increasing the number of replicates tested increased the sensitivities of all of the assays, including the LCx PCR. The LCx RUO assay showed high reproducibility for a single technologist and between technologists, with a kappa agreement of 0.77. The within-center agreements of the five in-house PCR tests varied from 0.19 to 0.74 on two challenges of 60 specimens 1 month apart. The LCx
C. pneumoniae
RUO PCR shows excellent potential for use in clinical studies, which could enable standardization of results in the field.
Evaluation of the C6 Peptide Enzyme-Linked Immunosorbent Assay for Individuals Vaccinated with the Recombinant OspA Vaccine
Authors: Marques Adriana R. , Martin Dale S. , Philipp Mario T. 
Published: July 2002

ABSTRACTThe C6 enzyme-linked immunosorbent assay (ELISA), based on a peptide (C6) that reproduces the sequence of invariable region 6 of VlsE, the antigenic variation protein ofBorrelia burgdorferi, has been shown to be a sensitive and specific test for the serologic diagnosis of Lyme disease. We now report that none of 29 uninfected individuals vaccinated with the recombinant OspA vaccine had an antibody response to the C6 peptide. The C6 peptide ELISA can be used to diagnose Lyme disease in patients who have received the OspA vaccine.
Three Cases of Infection with Hepatitis C Virus Genotype 5 among Brazilian Hepatitis Patients
Authors: Levi José Eduardo , Takaoka Deise Tihe , Garrini Regina Helena , Fachini Roberta Maria , Focaccia Roberto , de Bortholi Santos Edgar , Mitre Heloisa Pedrosa , de Mendonça João Silva , de Paula Cavalheiro Norma , Barone Antonio Alci , Wendel Silvano 
Published: July 2002

ABSTRACT
During the course of routine genotyping of hepatitis C virus isolates by 5′ noncoding region sequencing, three samples were found to bear genotype 5-specific nucleotides. A serotyping method was subsequently applied and confirmed the finding. This is the first report of the occurrence of genotype 5 in Brazil.
Nationwide Survey of In Vitro Activities of Itraconazole and Voriconazole against Clinical
Aspergillus fumigatus
Isolates Cultured between 1945 and 1998
Authors: Verweij Paul E. , Te Dorsthorst Debbie T. A. , Rijs Anthonius J. M. M. , De Vries-Hospers Hilly G. , Meis Jacques F. G. M. ,   the Dutch Interuniversity Working Party for Invasive Mycoses
Published: July 2002

ABSTRACT

The isolates in a collection of 170
Aspergillus fumigatus
isolates recovered from 114 patients and 21 different medical centers in The Netherlands over a period of 53 years were tested for the presence of resistance to itraconazole and voriconazole according to the guidelines of NCCLS document M38-P and by the E-test. Three isolates were highly resistant to itraconazole, and voriconazole MICs were low for all isolates.
Rapid Identification of
Staphylococcus aureus
and the
mecA
Gene from BacT/ALERT Blood Culture Bottles by Using the LightCycler System
Authors: Shrestha Nabin K. , Tuohy Marion J. , Hall Gerri S. , Isada Carlos M. , Procop Gary W. 
Published: July 2002

ABSTRACT

One hundred BacT/ALERT blood culture bottles growing gram-positive cocci in clusters were cultured and studied by LightCycler PCR for the
sa442
and
mecA
genes. PCR was 100% sensitive and specific for detecting
Staphylococcus aureus
and methicillin resistance in
S. aureus
but was less accurate for methicillin resistance in coagulase-negative staphylococci.
PCR for Detection of
cdt-III
and the Relative Frequencies of Cytolethal Distending Toxin Variant-Producing
Escherichia coli
Isolates from Humans and Cattle
Authors: Clark Clifford G. , Johnson Shelley T. , Easy Russell H. , Campbell Jennifer L. , Rodgers Frank G. 
Published: July 2002

ABSTRACT

A PCR assay that uses primers whose sequences were obtained from the published sequence of the
cdt-III
gene was developed to determine the frequencies of the
cdt-I
,
cdt-II
, and
cdt-III
genes in
Escherichia coli
isolates from humans and animals.
E. coli
isolates producing cytolethal distending toxin (CDT) were infrequently detected. The
cdt-I
gene was preferentially detected in strains with the
cnf1
gene, while the
cdt-III
gene was found in strains carrying the
cnf2
gene. The
cdt-III
genotype was more prevalent in animal isolates, while the
cdt-I
and
cdt-II
genotypes were more evident in human isolates. The presence of further
cdt
gene variants was indicated by the presence of toxin activity in cell culture in the absence of PCR amplification of the
cdt-I
,
cdt-II
, or
cdt-III
gene.
Characterization of Low- and Very-Low-Density Hepatitis C Virus RNA-Containing Particles
Authors: André P. , Komurian-Pradel F. , Deforges S. , Perret M. , Berland J. L. , Sodoyer M. , Pol S. , Bréchot C. , Paranhos-Baccalà G. , Lotteau V. 
Published: July 2002

ABSTRACT
The presence of hepatitis C virus (HCV) RNA-containing particles in the low-density fractions of plasma has been associated with high infectivity. However, the nature of circulating HCV particles and their association with immunoglobulins or lipoproteins as well as the characterization of cell entry have all been subject to conflicting reports. For a better analysis of HCV RNA-containing particles, we quantified HCV RNA in the low-density fractions of plasma corresponding to the very-low-density lipoprotein (VLDL), intermediate-density lipoprotein, and low-density lipoprotein (LDL) fractions from untreated chronically HCV-infected patients. HCV RNA was always found in at least one of these fractions and represented 8 to 95% of the total plasma HCV RNA. Surprisingly, immunoglobulins G and M were also found in the low-density fractions and could be used to purify the HCV RNA-containing particles (lipo-viro-particles [LVP]). Purified LVP were rich in triglycerides; contained at least apolipoprotein B, HCV RNA, and core protein; and appeared as large spherical particles with a diameter of more than 100 nm and with internal structures. Delipidation of these particles resulted in capsid-like structures recognized by anti-HCV core protein antibody. Purified LVP efficiently bind and enter hepatocyte cell lines, while serum or whole-density fractions do not. Binding of these particles was competed out by VLDL and LDL from noninfected donors and was blocked by anti-apolipoprotein B and E antibodies, whereas upregulation of the LDL receptor increased their internalization. These results suggest that the infectivity of LVP is mediated by endogenous proteins rather than by viral components providing a mechanism of escape from the humoral immune response.
Correlation of Major Histocompatibility Complex Class I Downregulation with Resistance of Human T-Cell Leukemia Virus Type 1-Infected T Cells to Cytotoxic T-Lymphocyte Killing in a Rat Model
Authors: Ohashi Takashi , Hanabuchi Shino , Suzuki Reiko , Kato Hirotomo , Masuda Takao , Kannagi Mari 
Published: July 2002

ABSTRACTHuman T-cell leukemia virus type 1 (HTLV-1) causes adult T-cell leukemia (ATL) in infected individuals after a long incubation period. Despite the apparent transforming ability of HTLV-1 under experimental conditions, most HTLV-1 carriers are asymptomatic. These facts suggest that HTLV-1 is controlled by host immunity in most carriers. To understand the interplay between host immunity and HTLV-1-infected cells, in this study, we isolated several HTLV-1 Tax-specific cytotoxic T-lymphocyte (CTL) lines from rats inoculated with Tax-coding DNA and investigated the long-term effects of the CTL on syngeneic HTLV-1-infected T cells. Our results demonstrated that long-term mixed culture of these CTL and the virus-infected T cells led to the emergence of CTL-resistant HTLV-1-infected cells. Although the Tax expression level in these resistant cells was equivalent to that in the parental cells, expression of surface major histocompatibility complex class I (MHC-I) was significantly downregulated in the resistant cells. Downregulation of MHC-I was more apparent in RT1.Al, which presents a Tax epitope recognized by the CTL established in this study. Moreover, peptide pulsing resulted in killing of the resistant cells by CTL, indicating that resistance was caused by a decreased epitope density on the infected cell surface. This may be one of the mechanisms for persistence of HTLV-1-infected cells that evade CTL lysis and potentially develop ATL.
Aura Virus Structure Suggests that the T=4 Organization Is a Fundamental Property of Viral Structural Proteins
Authors: Zhang Wei , Fisher Bonnie R. , Olson Norman H. , Strauss James H. , Kuhn Richard J. , Baker Timothy S. 
Published: July 2002

ABSTRACT
Aura and Sindbis viruses are closely related alphaviruses. Unlike other alphaviruses, Aura virus efficiently encapsidates both genomic RNA (11.8 kb) and subgenomic RNA (4.2 kb) to form virus particles. Previous studies on negatively stained Aura virus particles predicted that there were two major size classes with potential T=3 and T=4 capsid structures. We have used cryoelectron microscopy and three-dimensional image reconstruction techniques to examine the native morphology of different classes of Aura virus particles produced in BHK cells. Purified particles separated into two components in a sucrose gradient. Reconstructions of particles in the top and bottom components were computed to resolutions of 17 and 21 Å, respectively, and compared with reconstructions of Sindbis virus and Ross River virus particles. Aura virus particles of both top and bottom components have similar, T=4 structures that resemble those of other alphaviruses. The morphology of Aura virus glycoprotein spikes closely resembles that of Sindbis virus spikes and is detectably different from that of Ross River virus spikes. Thus, some aspects of the surface structure of members of the Sindbis virus lineage have been conserved, but other aspects have diverged from the Semliki Forest/Ross River virus lineage.
Sequence Requirements for Viral RNA Replication and VPg Uridylylation Directed by the Internal
cis
-Acting Replication Element (
cre
) of Human Rhinovirus Type 14
Authors: Yang Yan , Rijnbrand Rene , McKnight Kevin L. , Wimmer Eckard , Paul Aniko , Martin Annette , Lemon Stanley M. 
Published: July 2002

ABSTRACT

Until recently, the
cis
-acting signals required for replication of picornaviral RNAs were believed to be restricted to the 5′ and 3′ noncoding regions of the genome. However, an RNA stem-loop in the VP1-coding sequence of human rhinovirus type 14 (HRV-14) is essential for viral minus-strand RNA synthesis (K. L. McKnight and S. M. Lemon, RNA
4:
1569-1584, 1998). The nucleotide sequence of the apical loop of this internal
cis
-acting replication element (
cre
) was critical for RNA synthesis, while secondary RNA structure, but not primary sequence, was shown to be important within the duplex stem. Similar
cre
s have since been identified in other picornaviral genomes. These RNA segments appear to serve as template for the uridylylation of the genome-linked protein, VPg, providing the VPg-pUpU primer required for viral RNA transcription (A. V. Paul et al., J. Virol.
74:
10359-10370, 2000). Here, we show that the minimal functional HRV-14
cre
resides within a 33-nucleotide (nt) RNA segment that is predicted to form a simple stem-loop with a 14-nt loop sequence. An extensive mutational analysis involving every possible base substitution at each position within the loop segment defined the sequence that is required within this loop for efficient replication of subgenomic HRV-14 replicon RNAs. These results indicate that three consecutive adenosine residues (nt 2367 to 2369) within the 5′ half of this loop are critically important for
cre
function and suggest that a common RNNNAARNNNNNNR loop motif exists among the
cre
sequences of enteroviruses and rhinoviruses. We found a direct, positive correlation between the capacity of mutated
cre
s to support RNA replication and their ability to function as template in an in vitro VPg uridylylation reaction, suggesting that these functions are intimately linked. These data thus define more precisely the sequence and structural requirements of the HRV-14
cre
and provide additional support for a model in which the role of the
cre
in RNA replication is to act as template for VPg uridylylation.
Transgenic Expression of Theiler's Murine Encephalomyelitis Virus Genes inH-2bMice Inhibits Resistance to Virus-Induced Demyelination
Authors: Lin Xiaoqi , Njenga M. Kariuki , Johnson Aaron J. , Pavelko Kevin D. , David Chella S. , Pease Larry R. , Rodriguez Moses 
Published: July 2002

ABSTRACTWe investigated the role of the immune system in protecting against virus-induced demyelination by generating lines of transgenic B10 (H-2b) congenic mice expressing three independent contiguous coding regions of the Theiler's murine encephalomyelitis virus (TMEV) under the control of a class I major histocompatibility complex (MHC) promoter. TMEV infection of normally resistant B10 mice results in virus clearance and development of inflammatory demyelination in the spinal cord. Transgenic expression of the viral capsid genes resulted in inactivation of virus-specific CD8+T lymphocytes (class I MHC immune function) directed against the relevant peptides, but it did not affect production of virus capsid-specific antibodies or lymphocyte proliferation to the virus antigen (class II MHC immune functions). Following intracerebral infection with TMEV, all three lines of mice survived the acute encephalitis but transgenic mice expressing VP1 (or the cluster of virus capsid proteins [VP4, VP2, and VP3] mapping to the left of VP1 in the TMEV genome) developed virus persistence and subsequent demyelination in spinal cord white matter. Transgenic mice expressing noncapsid proteins mapping to the right of VP1 (2A, 2B, 2C, 3A, 3B, 3C, and 3D) cleared the virus and did not develop demyelination. These results are consistent with the hypothesis that virus capsid gene products of TMEV stimulate class I-restricted CD8+T-cell immune responses, which are important for virus clearance and for protection against myelin destruction. Presented within the context of self-antigens, inactivation of these cells by ubiquitous expression of relevant virus capsid peptides partially inhibited resistance to virus-induced demyelination.
Identification of Rotavirus VP6 Residues Located at the Interface with VP2 That Are Essential for Capsid Assembly and Transcriptase Activity
Authors: Charpilienne Annie , Lepault Jean , Rey Felix , Cohen Jean 
Published: July 2002

ABSTRACT

Rotavirus
has a complex triple-layered icosahedral capsid. The external layer consists of VP7 and VP4, the intermediate layer consists of VP6 trimers, and the internal layer consists of VP2. Double-layered particles (DLP) derived from the virus by solubilization of VP4 and VP7 are transcriptionally competent and extrude capped mRNA from their vertices. Analysis of the pseudoatomic model of the VP6 layer, obtained by placing the atomic structure of VP6 into electron microscopy reconstructions of the DLP, has identified the regions of the protein involved in interactions with the internal layer. To study the role of VP6 both in the assembly of DLP and in transcription, 13 site-specific substitution mutations of VP6, targeting the contacts between the two inner layers, were constructed and expressed in the baculovirus system. The effects of these mutations on VP6 expression, trimerization, and formation of macromolecular assemblies were investigated. Using either in vitro reconstituted DLP derived from purified viral cores and recombinant VP6 or in vivo self-assembled virus-like particles resulting from the coexpression of VP2 and VP6 in the baculovirus-Sf9 system (VLP2/6), we have identified the amino acids essential for recovery of transcription or assembly. All VP6 mutants formed stable trimers which, like wild-type VP6, assembled into tubular structures. The ability of VP6 to interact with VP2 was examined by several assays, including electron microscopy, coimmunoprecipitation, purification of VLP2/6, and monitoring of the transcriptase activity of reconstituted DLP. Of the 13 VP6 mutants examined, 3 were unable to assemble with VP2 and 3 others partially assembled. These mutants either did not rescue the transcriptase activity of core particles or did so only marginally. Four mutants as well as the wild-type VP6 assembled and transcribed very well. Three mutants assembled well on cores but, surprisingly, did not rescue the transcriptase activity of reconstituted DLP. Our results indicate that hydrophobic interactions between VP6 and VP2 residues are responsible for the stability of the DLP. They also show that subtle electrostatic interactions between VP6 and the underlying transcriptase machinery can be essential for mRNA synthesis.
Resistance to Infection by Subgroups B, D, and E Avian Sarcoma and Leukosis Viruses Is Explained by a Premature Stop Codon within a Resistance Allele of the
tvb
Receptor Gene
Authors: Klucking Sara , Adkins Heather B. , Young John A. T. 
Published: July 2002

ABSTRACT

Here we present the first molecular characterization of the defect associated with an avian sarcoma and leukosis virus (ASLV) receptor resistance allele,
tvb
r
. We show that resistance to infection by subgroups B, D, and E ASLV is explained by the presence of a single base pair mutation that distinguishes this allele from
tvb
s1
, an allele which encodes a receptor for all three viral subgroups. This mutation generates an in-frame stop codon that is predicted to lead to the production of a severely truncated protein.
Genetic and Biochemical Analyses of Receptor and Cofactor Determinants for T-Cell-Tropic Feline Leukemia Virus Infection
Authors: Lauring Adam S. , Cheng Heather H. , Eiden Maribeth V. , Overbaugh Julie 
Published: July 2002

ABSTRACT

Entry by retroviruses is mediated through interactions between the viral envelope glycoprotein and the host cell receptor(s). We recently identified two host cell proteins, FeLIX and Pit1, that are necessary for infection by cytopathic, T-cell-tropic feline leukemia viruses (FeLV-T). Pit1 is a classic multiple transmembrane protein used as a receptor by several other simple retroviruses, including subgroup B FeLV (FeLV-B), and FeLIX is a secreted cellular protein expressed from endogenous FeLV-related sequences (enFeLV). FeLIX is nearly identical to FeLV-B
envelope
sequences that encode the N-terminal half of the viral surface unit (SU), because these FeLV-B sequences are acquired by recombination with enFeLV. FeLV-B SUs can functionally substitute for FeLIX in mediating FeLV-T infection. Both of these enFeLV-derived cofactors can efficiently facilitate FeLV-T infection only of cells expressing Pit1, not of cells expressing the related transport protein Pit2. We therefore have used chimeric Pit1/Pit2 receptors to map the determinants for cofactor binding and FeLV-T infection. Three distinct determinants appear to be required for cofactor-dependent infection by FeLV-T. We also found that Pit1 sequences within these same domains were required for binding by FeLIX to the Pit receptor. In contrast, these determinants were not all required for receptor binding by the FeLV-B SU cofactors used in this study. These data indicate that cofactor binding is not sufficient for FeLV-T infection and suggest that there may be a direct interaction between FeLV-T and the Pit1 receptor.