bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Human Anti-Flavivirus Antibodies with a West Nile Virus Recombinant Antigen Microsphere Immunoassay
Authors: Wong Susan J. , Demarest Valerie L. , Boyle Rebekah H. , Wang Tian , Ledizet Michel , Kar Kalipada , Kramer Laura D. , Fikrig Erol , Koski Raymond A. 
Published: January 2004

ABSTRACTWe report a new, suspended-microsphere diagnostic test to detect antibodies to West Nile (WN) virus in human serum and cerebrospinal fluid (CSF). The microsphere immunofluorescence assay can be performed in less than 3 h on specimens of ≤30 μl. A recombinant WN virus envelope (E) protein antigen is covalently coupled to fluorescent polystyrene microspheres. After incubation with diluted serum or CSF, antibodies bound to the E protein antigen are detected with fluorescently labeled anti-human immunoglobulin antibody and flow analysis in a dual-laser Luminex 100 instrument. Retrospective testing of 833 sera from New York patients with suspected viral encephalitis demonstrated concordance with results obtained with the traditional enzyme-linked immunosorbent assay for immunoglobulin G (IgG) antibodies to WN virus (kappa = 0.85). One hundred eighty-eight (22.4%) of the samples, which were collected from June to November 2002, tested positive for antibodies to WN virus in the microsphere assay. Specimens depleted of IgG with anti-IgG antibody were reassayed to measure anti-E protein IgM antibodies and to provide an indication of current or recent WN virus infection. The assay also detects antibodies to E proteins from related flaviviruses, including St. Louis encephalitis, Japanese encephalitis, and dengue viruses. The new microsphere immunoassay provides a sensitive and rapid alternative to traditional enzyme-linked immunosorbent assays that detect antibodies to flavivirus E proteins. This assay can aid physicians and public health workers in the management of outbreaks of WN virus and related flaviviruses.
Identification and Susceptibility Testing of
Enterobacteriaceae
and
Pseudomonas aeruginosa
by Direct Inoculation from Positive BACTEC Blood Culture Bottles into Vitek 2
Authors: Bruins Marjan J. , Bloembergen Peter , Ruijs Gijs J. H. M. , Wolfhagen Maurice J. H. M. 
Published: January 2004

ABSTRACT

Inoculation of an automated system for rapid identification (ID) and antimicrobial susceptibility testing (AST) directly from positive blood culture bottles will reduce the turnaround time of laboratory diagnosis of septicemic patients, which benefits clinical outcome and decreases patient costs. Direct test results, however, must always be confirmed by testing a pure overnight culture, which is the “gold standard.” We studied the accuracy of direct testing versus repeat testing in order to investigate the possibility of refraining from repeat testing. We also assessed the clinical risk of reporting results based on direct testing only. We inoculated Vitek 2 (bioMérieux) directly from 410 positive BACTEC 9240 (BD) blood culture bottles containing gram-negative rods and studied the ID and AST results. In a comparison of direct inoculation with the standard method, a total of 344 isolates of
Enterobacteriaceae
and
Pseudomonas aeruginosa
were tested, and 93.0% were correctly identified. Of the 39 (10.2%) samples that contained bacilli not identifiable by Vitek 2, only 1 gave a conclusive, correct result. The overall MIC agreement among 312 isolates was 99.2%, with 0.8% very major and 0.02% major error rates. Of only three (polymicrobial) samples, the direct susceptibility pattern would be reported to the clinician as too sensitive. Vitek 2 results obtained from direct inoculation of blood culture bottles containing gram-negative bacilli are safe enough for immediate reporting, provided that ID and AST are consistent. Repeat testing is not necessary, unless Gram stain or overnight subculture results raise doubt about the purity of the culture.
Adaptive Resistance to Biocides inSalmonella entericaandEscherichia coliO157 and Cross-Resistance to Antimicrobial Agents
Authors: Braoudaki M. , Hilton A. C. 
Published: January 2004

ABSTRACTThe mechanisms by which bacteria resist killing by antibiotics and biocides are still poorly defined, although repeated exposure to sublethal concentrations of antibacterial agents undoubtedly contributes to their development. This study aimed both to investigate the potential ofSalmonella entericaandEscherichia coliO157 for adaptive resistance to commonly used biocides and to determine any cross-resistance to antibiotics. Strains were repeatedly passaged in media containing increasing concentrations of a biocide or antibiotic until adaptive resistance was obtained. A wide panel of antimicrobial agents was then screened by using the adapted strain to determine cross-resistance, if any. Adaptive resistance was readily achieved for bothS. entericaandE. coliO157. Cross-resistance in adaptively resistantS. entericavaried with the serotype;Salmonella entericaserovar Enteritidis expressed cross-resistance to chloramphenicol, whereasSalmonella entericaserovar Typhimurium expressed cross-resistance to chlorhexidine. Benzalkonium chloride-resistantSalmonella entericaserovar Virchow showed elevated resistance to chlorhexidine; however, chlorhexidine-resistantSalmonellaserovar Virchow did not demonstrate reciprocal cross-resistance to benzalkonium chloride, suggesting specific rather than generic resistance mechanisms.E. coliO157 strains acquired high levels of resistance to triclosan after only two sublethal exposures and, when adapted, repeatedly demonstrated decreased susceptibilities to various antimicrobial agents, including chloramphenicol, erythromycin, imipenem, tetracycline, and trimethoprim, as well as to a number of biocides. These observations raise concern over the indiscriminate and often inappropriate use of biocides, especially triclosan, in situations where they are unnecessary, whereby they may contribute to the development of microbial resistance mechanisms.
Sensitivity of Respiratory Virus Culture When Screening with R-Mix Fresh Cells
Authors: Dunn James J. , Woolstenhulme R. Dean , Langer Janine , Carroll Karen C. 
Published: January 2004

ABSTRACT
Use of R-Mix Fresh Cells has been shown to be a rapid and sensitive method for the detection and identification of respiratory viruses. We prospectively evaluated the impact of incorporation of R-Mix shell vials on the sensitivity and time to detection of seven respiratory viruses recovered in a comprehensive culture during the course of an entire respiratory season in a high-volume clinical laboratory. In this study, R-Mix shell vials were used as part of the culture of 3,803 respiratory specimens. A total of 428 respiratory viruses were recovered. Staining of R-Mix vials after overnight incubation allowed initial detection of 274 of 279 influenza viruses, 33 of 38 parainfluenza viruses, 35 of 51 adenoviruses, and 52 of 60 respiratory syncytial viruses (RSVs). The time to reporting of all positive cultures after in-lab specimen receipt was 2.9 days on average and those initially detected in R-Mix cells were reported in 2.3 days on average. A combination of direct fluorescent-antibody (DFA) staining and virus culture was performed on a subset of 711 respiratory specimens. Of 152 viruses identified, 57 were observed only with DFA testing (55 RSV and 2 influenza A viruses) and 31 were recovered only in cell culture. After overnight incubation, R-Mix cells detected 87.1% of respiratory viruses not observed by DFA testing and 96.9% of viruses positive by both methods. The sensitivities of DFA testing and R-Mix cells for identification of influenza viruses were 70.5% and 96.7%, respectively. The R-Mix method detected influenza virus in 18 samples that were negative by DFA testing.
Dynamics of
Streptococcus agalactiae
Colonization in Women during and after Pregnancy and in Their Infants
Authors: Hansen Søren Mose , Uldbjerg Niels , Kilian Mogens , Sørensen Uffe B. Skov 
Published: January 2004

ABSTRACT

The population dynamics of
Streptococcus agalactiae
(group B streptococci [GBS]) colonization of the vagina and anorectal area was investigated in a cohort of 77 Danish women during and after their pregnancy by a new sensitive method. The mean carriage rate among individual observations was 36%, and the cumulative carriage rate over the entire observation period was 54%. Examination of more than 1,500 GBS isolates by pulsed-field gel electrophoresis demonstrated that the GBS population was remarkably homogeneous and stable in each carrier. Virtually all carriers were colonized by a single GBS clone on all occasions spanning up to 2 years. Repeated detection of the same clone even in women who were recorded as intermittent carriers suggests that the actual carrier rate exceeds 50% but that fluctuations in the GBS proportions of the flora occasionally preclude their detection. Newborns and young infants usually carried the same GBS clone as their mothers. However, only twice were identical clones of GBS detected in different women in contrast to the observed clonal relationships of clinical isolates. These observations strongly suggest differences in the properties and epidemiology of virulent GBS clones compared to clones commonly carried by healthy individuals.
RickettsiaSpecies InfectingAmblyomma cooperiTicks from an Area in the State of São Paulo, Brazil, Where Brazilian Spotted Fever Is Endemic
Authors: Labruna Marcelo B. , Whitworth Ted , Horta Maurício C. , Bouyer Donald H. , McBride Jere W. , Pinter Adriano , Popov Vsevolod , Gennari Solange M. , Walker David H. 
Published: January 2004

ABSTRACTOwing to the potential role of the tickAmblyomma cooperiin the enzootic cycle ofRickettsia rickettsii, the etiologic agent of Brazilian spotted fever (BSF), this study evaluated infection byRickettsiaspecies inA. cooperiticks collected from an area in Brazil where BSF is endemic. Among a total of 40A. cooperiadult ticks collected in an area of BSF endemicity in the state of São Paulo, PCR analysis detected DNA ofRickettsia belliiin 16 ticks (40%), and 3 other ticks (7.5%) were positive for a previously unidentified spotted-fever-group (SFG) rickettsia. Cultivation in Vero cell cultures by the shell vial technique with individualA. cooperiticks resulted in two isolates ofR. belliiand one isolate genotypically characterized as an SFG rickettsia. The twoR. belliiisolates were established in Vero cell cultures in the laboratory and were confirmed to beR. belliiby molecular analysis of thegltAand 17-kDa protein-encoding genes and by electron microscopic analysis. The SFG rickettsial isolate could not be stably passaged in cell culture in the laboratory, but molecular analysis of early passages suggested that it was closely related toRickettsia parkeri,Rickettsia africae, andRickettsia sibirica.These results do not support the role ofA. cooperiin the ecology ofR. rickettsiiin the area studied, but they add two more species of rickettsiae to the poorly developed list of species occurring in ticks in South America.
Infection with a Proposed New Subspecies ofBabesia canis,Babesia canissubsp.presentii, in Domestic Cats
Authors: Baneth Gad , Kenny Martin J. , Tasker Séverine , Anug Yigal , Shkap Varda , Levy Amos , Shaw Susan E. 
Published: January 2004

ABSTRACTParasitemia with a largeBabesiaspecies was identified in two domestic cats from Israel. One cat, also coinfected with feline immunodeficiency virus and “CandidatusMycoplasma haemominutum,” had profound icterus and anemia which resolved after therapy, whereas a second cat was an asymptomatic carrier. Amplification and sequencing of the 18S rRNA gene, followed by phylogenetic analyses, indicated that infection was caused byBabesia canis. However, the sequences of the internal transcribed and 5.8S rRNA regions of the ribosomal operon used for subspeciation ofB. caniswere markedly different from the recognized subspecies ofB. canis, which includeB. canis vogeli,B. canis canis, andB. canis rossi. Based on phylogenetic comparisons of the 18S rRNA gene, 5.8S, and internal transcribed spacer sequences of the isolates from the cats and on the smaller sizes of the merozoite and trophozoite stages of this parasite, which distinguish it from the subspecies ofB. canispresent in dogs, we propose to identify the novel feline genotype ofB. canisdescribed in the present study as a new subspecies,B. canissubsp.presentii.
A Nonproliferating Parvovirus Vaccine Vector Elicits Sustained, Protective Humoral Immunity following a Single Intravenous or Intranasal Inoculation
Authors: Palmer Gene A. , Brogdon Jennifer L. , Constant Stephanie L. , Tattersall Peter 
Published: January 2004

ABSTRACTAn ideal vaccine delivery system would elicit persistent protection following a single administration, preferably by a noninvasive route, and be safe even in the face of immunosuppression, either inherited or acquired, of the recipient. We have exploited the unique life cycle of the autonomous parvoviruses to develop a nonproliferating vaccine platform that appears to both induce priming and continually boost a protective immune response following a single inoculation. A crippled parvovirus vector was constructed, based on a chimera between minute virus of mice (MVM) and LuIII, which expressesBorrelia burgdorferiouter surface protein A (OspA) instead of its coat protein. The vector was packaged into an MVM lymphotropic capsid and inoculated into naive C3H/HeNcr mice. Vaccination with a single vector dose, either intravenously or intranasally, elicited high-titer anti-OspA-specific antibody that provided protection from live spirochete challenge and was sustained over the lifetime of the animal. Both humoral and cell-mediated Th1immunity was induced, as shown by anti-OspA immunoglobulin G2a antibody and preferential gamma interferon production by OspA-specific CD4+T cells.
Downregulation of Major Histocompatibility Complex Class I by Human Ubiquitin Ligases Related to Viral Immune Evasion Proteins
Authors: Bartee Eric , Mansouri Mandana , Hovey Nerenberg Bianca T. , Gouveia Kristine , Früh Klaus 
Published: January 2004

ABSTRACT
Poxviruses and gamma-2 herpesviruses share the K3 family of viral immune evasion proteins that inhibit the surface expression of glycoproteins such as major histocompatibility complex class I (MHC-I), B7.2, ICAM-1, and CD95(Fas). K3 family proteins contain an amino-terminal PHD/LAP or RING-CH domain followed by two transmembrane domains. To examine whether human homologues are functionally related to the viral immunoevasins, we studied seven membrane-associated RING-CH (MARCH) proteins. All MARCH proteins located to subcellular membranes, and several MARCH proteins reduced surface levels of known substrates of the viral K3 family. Two closely related proteins, MARCH-IV and MARCH-IX, reduced surface expression of MHC-I molecules. In the presence of MARCH-IV or MARCH-IX, MHC-I was ubiquitinated and rapidly internalized by endocytosis, whereas MHC-I molecules lacking lysines in their cytoplasmic tail were resistant to downregulation. The amino-terminal regions containing the RING-CH domain of several MARCH proteins examined catalyzed multiubiquitin formation in vitro, suggesting that MARCH proteins are ubiquitin ligases. The functional similarity of the MARCH family and the K3 family suggests that the viral immune evasion proteins were derived from MARCH proteins, a novel family of transmembrane ubiquitin ligases that seems to target glycoproteins for lysosomal destruction via ubiquitination of the cytoplasmic tail.
Template Sequence near the Initiation Nucleotide Can Modulate Brome Mosaic Virus RNA Accumulation in Plant Protoplasts
Authors: Hema M. , Kao C. Cheng 
Published: January 2004

ABSTRACT

Bromoviral templates for plus-strand RNA synthesis are rich in A or U nucleotides in comparison to templates for minus-strand RNA synthesis. Previous studies demonstrated that plus-strand RNA synthesis by the brome mosaic virus (BMV) RNA replicase is more efficient if the template contains an A/U-rich template sequence near the initiation site (K. Sivakumaran and C. C. Kao, J. Virol.
73:
6415-6423, 1999). These observations led us to examine the effects of nucleotide changes near the template's initiation site on the accumulation of BMV RNA3 genomic minus-strand, genomic plus-strand, and subgenomic RNAs in barley protoplasts transfected with wild-type and mutant BMV transcripts. Mutations in the template for minus-strand synthesis had only modest effects on BMV replication in barley protoplasts. Mutants with changes to the +3, +5, and +7 template nucleotides accumulated minus-strand RNA at levels similar to the the wild-type level. However, mutations at positions adjacent to the initiation cytidylate in the templates for genomic and subgenomic plus-strand RNA synthesis significantly decreased RNA accumulation. For example, changes at the third template nucleotide for plus-strand RNA3 synthesis resulted in RNA accumulation at between 18 and 24% of the wild-type level, and mutations in the third template nucleotide for subgenomic RNA4 resulted in accumulations at between 7 and 14% of the wild-type level. The effects of the mutations generally decreased as the mutations occurred further from the initiation nucleotide. These findings demonstrate that there are different requirements of the template sequence near the initiation nucleotide for BMV RNA accumulation in plant cells.
Identification of Host-Specificity Determinants in Betanodaviruses by Using Reassortants between Striped Jack Nervous Necrosis Virus and Sevenband Grouper Nervous Necrosis Virus
Authors: Iwamoto Tokinori , Okinaka Yasushi , Mise Kazuyuki , Mori Koh-Ichiro , Arimoto Misao , Okuno Tetsuro , Nakai Toshihiro 
Published: January 2004

ABSTRACT
Betanodaviruses, the causal agents of viral nervous necrosis in marine fish, have bipartite positive-sense RNAs as genomes. The larger genomic segment, RNA1 (3.1 kb), encodes an RNA-dependent RNA polymerase, and the smaller genomic segment, RNA2 (1.4 kb), codes for the coat protein. Betanodaviruses have marked host specificity, although the primary structures of the viral RNAs and encoded proteins are similar among betanodaviruses. However, no mechanism underlying the host specificity has yet been reported. To evaluate viral factors that control host specificity, we first constructed a cDNA-mediated infectious RNA transcription system for sevenband grouper nervous necrosis virus (SGNNV) in addition to that for striped jack nervous necrosis virus (SJNNV), which was previously established by us. We then tested two reassortants between SJNNV and SGNNV for infectivity in the host fish from which they originated. When striped jack and sevenband grouper larvae were bath challenged with the reassortant virus comprising SJNNV RNA1 and SGNNV RNA2, sevenband groupers were killed exclusively, similar to inoculation with SGNNV. Conversely, inoculations with the reassortant virus comprising SGNNV RNA1 and SJNNV RNA2 killed striped jacks but did not affect sevenband groupers. Immunofluorescence microscopic studies using anti-SJNNV polyclonal antibodies revealed that both of the reassortants multiplied in the brains, spinal cords, and retinas of infected fish, similar to infections with parental virus inoculations. These results indicate that viral RNA2 and/or encoded coat protein controls host specificity in SJNNV and SGNNV.
Impaired Processing and Presentation of Cytotoxic-T-Lymphocyte (CTL) Epitopes Are Major Escape Mechanisms from CTL Immune Pressure in Human Immunodeficiency Virus Type 1 Infection
Authors: Yokomaku Yoshiyuki , Miura Hideka , Tomiyama Hiroko , Kawana-Tachikawa Ai , Takiguchi Masafumi , Kojima Asato , Nagai Yoshiyuki , Iwamoto Aikichi , Matsuda Zene , Ariyoshi Koya 
Published: January 2004

ABSTRACT

Investigating escape mechanisms of human immunodeficiency virus type 1 (HIV-1) from cytotoxic T lymphocytes (CTLs) is essential for understanding the pathogenesis of HIV-1 infection and developing effective vaccines. To study the processing and presentation of known CTL epitopes, we prepared Epstein-Barr virus-transformed B cells that endogenously express the
gag
gene of six field isolates by adopting an
env/nef
-deletion HIV-1 vector pseudotyped with vesicular stomatitis virus G protein and then tested them for the recognition by Gag epitope-specific CTL lines or clones. We observed that two field variants, SL
F
NTVA
V
L and S
V
YNTVATL, of an A*0201-restricted Gag CTL epitope SLYNTVATL, and three field variants, KY
R
LKH
L
VW,
Q
YRLKHIVW, and
R
Y
R
LKH
L
VW, of an A24-restricted Gag CTL epitope KYKLKHIVW escaped from being killed by the CTL lines, despite the fact that they were recognized when the synthetic peptides corresponding to these variant sequences were exogenously loaded onto the target cells. Thus, their escape is likely due to the changes that occur during the processing and presentation of epitopes in the infected cells. Mutations responsible for this mode of escape were located within the epitope regions rather than the flanking regions, and such mutations did not influence the virus replication. The results suggest that the impaired antigen processing and presentation often occur in HIV-1 field isolates and thus are one of the major mechanisms that enable HIV-1 to escape from CTL recognition. We emphasize the importance of testing HIV-1 variants in an endogenous expression system.
An Acidic Cluster of Human Cytomegalovirus UL99 Tegument Protein Is Required for Trafficking and Function
Authors: Jones Thomas R. , Lee Shi-Wu 
Published: January 2004

ABSTRACT
The human cytomegalovirus (HCMV) virion is comprised of a linear double-stranded DNA genome, proteinaceous capsid and tegument, and a lipid envelope containing virus-encoded glycoproteins. Of these components, the tegument is the least well defined in terms of both protein content and function. Several of the major tegument proteins are phosphoproteins (pp), including pp150, pp71, pp65, and pp28. pp28, encoded by the UL99 open reading frame (ORF), traffics to vacuole-like cytoplasmic structures and was shown recently to be essential for envelopment. To elucidate the UL99 amino acid sequences necessary for its trafficking and function in the HCMV replication cycle, two types of viral mutants were analyzed. Using a series of recombinant viruses expressing various UL99-green fluorescent protein fusions, we demonstrate that myristoylation at glycine 2 and an acidic cluster (AC; amino acids 44 to 57) are required for the punctate perinuclear and cytoplasmic (vacuole-like) localization observed for wild-type pp28. A second approach involving the generation of several UL99 deletion mutants indicated that at least the C-terminal two-thirds of this ORF is nonessential for viral growth. Furthermore, the data suggest that an N-terminal region of UL99 containing the AC is required for viral growth. Regarding virion incorporation or UL99-encoded proteins, we provide evidence that suggests that a hypophosphorylated form of pp28 is incorporated, myristoylation is required, and sequences within the first 57 amino acids are sufficient.