bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving Sensitivity of Direct Microscopy for Detection of Acid-Fast Bacilli in Sputum: Use of Chitin in Mucus Digestion
Authors: Farnia P. , Mohammadi F. , Zarifi Z. , Tabatabee D. J. , Ganavi J. , Ghazisaeedi K. , Farnia P. K. , Gheydi M. , Bahadori M. , Masjedi M. R. , Velayati A. A. 
Published: July 2002

ABSTRACT

In order to try to improve the results of direct smear microscopy, we used the mucus-digesting quality of chitin in tuberculosis (TB) laboratories. For this purpose, a total of 430 sputum specimens were processed by the
N
-acetyl-
l
-cysteine concentration, sodium hypochlorite (NaOCl) liquefaction, chitin sedimentation, and direct microscopy methods. Then, the smear sensitivity for acid-fast bacillus detection by chitin-treated sputum was compared with the sensitivity of smears prepared by other methods. Our results showed that the chitin solution took less time to completely homogenize the mucoid sputum than did the
N
-acetyl-
l
-cysteine and NaOCl methods. The
N
-acetyl-
l
-cysteine concentration method demonstrated sensitivity and specificity levels of 83 and 97%, respectively. In comparison, the sensitivity of chitin sedimentation was 80%, with a specificity of 96.7%. The NaOCl liquefaction method showed a sensitivity of 78%, with a specificity of 96%. Finally, the sensitivity of direct microscopy was lower than those of the other tested methods and was only 46%, with a specificity of 90%. The chitin and NaOCl liquefaction methods are both easy to perform, and they do not require additional equipment (centrifuges). Also, our results demonstrated that the chitin method is less time-consuming than the NaOCl method, since only 30 min of incubation is required to bring complete sedimentation of bacilli in chitin-treated sputum whereas the NaOCl method needs 10 to 12 h to give the same results in the same sputum specimens. Therefore, the chitin liquefaction and sedimentation method may provide better results in TB laboratories of developing countries than the
N
-acetyl-
l
-cysteine concentration, NaOCl overnight sedimentation, and direct smear microscopy methods.
Specific Identification of
Listeria welshimeri
and
Listeria monocytogenes
by PCR Assays Targeting a Gene Encoding a Fibronectin-Binding Protein
Authors: Gilot Philippe , Content Jean 
Published: July 2002

ABSTRACT

We have cloned and sequenced a
Listeria welshimeri
DNA fragment homologous to the previously described fibronectin-binding protein-encoding gene (
fbp
) of
Listeria monocytogenes
(P. Gilot, Y. Jossin, and J. Content, J. Med. Microbiol., 49:887-896, 2000). This
L. welshimeri
DNA fragment expresses a 24.8-kDa protein that binds to human fibronectin. Based on the
fbp
sequences, we developed novel PCR assays for the identification of
L. welshimeri
and
L. monocytogenes
.
Periodontal Bacteria in Rabbit Mandibular and Maxillary Abscesses
Authors: Tyrrell Kerin L. , Citron Diane M. , Jenkins Jeffrey R. , Goldstein Ellie J. C. 
Published: July 2002

ABSTRACT

Despite the high incidence of odontogenic abscesses in pet rabbits, published data on the bacteriology of these infections are lacking, and clinical cultures are often ambiguous, making antibiotic choices difficult. In order to define the bacteriology of these infections, 12 rabbit mandibular and maxillary abscesses were cultured aerobically and anaerobically. All specimens yielded pathogenic bacteria, including
Fusobacterium nucleatum
,
Prevotella heparinolytica
,
Prevotella
spp.,
Peptostreptococcus micros
,
Streptococcus milleri
group,
Actinomyces israelii
, and
Arcanobacterium haemolyticum
. These organisms are consistent with the characterized bacteriology of periodontal disease in human and other mammalian studies. The isolates were tested against 10 antimicrobial agents commonly used to treat rabbits; 100% of the strains tested were susceptible to clindamycin, 96% were susceptible to penicillin and ceftriaxone, 54% were susceptible to ciprofloxacin, and only 7% were susceptible to trimethoprim-sulfamethoxazole.
Molecular Typing of Selected
Enterococcus faecalis
Isolates: Pilot Study Using Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis
Authors: Nallapareddy Sreedhar R. , Duh Ruay-Wang , Singh Kavindra V. , Murray Barbara E. 
Published: July 2002

ABSTRACT

The present study compared the recently developed multilocus sequence typing (MLST) approach with a well-established molecular typing technique, pulsed-field gel electrophoresis (PFGE), for subspecies differentiation of
Enterococcus faecalis
isolates. We sequenced intragenic regions of three
E. faecalis
antigen-encoding genes (
ace
, encoding a collagen and laminin adhesin;
efaA
, encoding an endocarditis antigen; and
salA
, encoding a cell wall associated antigen) and one housekeeping gene (
pyrC
) of 22
E. faecalis
isolates chosen largely for their temporal and geographical diversity, but also including some outbreak isolates. MLST analysis of polymorphic regions of these four genes identified 13 distinct sequence types (STs) with different allelic profiles; the composite sequences generated from the four sequenced gene fragments of individual isolates showed 98.3 to 100% identity among the 22 isolates. We also found that the allelic profiles from two sequences,
ace
and
salA
, were sufficient to distinguish all 13 STs of this study. The 13 STs corresponded to 12 different PFGE types, with one previously designated PFGE clone (a widespread U.S. clone of β-lactamase-producing isolates) being classified into two highly related STs which differed at 2 of 2,894 bases, both in the same allele. MLST also confirmed the clonal relationships among the isolates of two other PFGE clonal groups, including vancomycin resistant isolates. Thus, this pilot study with representative
E. faecalis
isolates suggests that, similar to PFGE, the sequence-based typing method may be useful for differentiating isolates of
E. faecalis
to the subspecies level in addition to identifying outbreak isolates.
Identification, Characterization, and Distribution of a Shiga Toxin 1 Gene Variant (
stx
1c
) in
Escherichia coli
Strains Isolated from Humans
Authors: Zhang Wenlan , Bielaszewska Martina , Kuczius Thorsten , Karch Helge 
Published: July 2002

ABSTRACT

By using sequence analysis of Shiga toxin 1 (Stx 1) genes from human and ovine Stx-producing
Escherichia coli
(STEC) strains, we identified an Stx1 variant in STEC of human origin that was identical to the Stx1 variant from ovine STEC, but demonstrated only 97.1 and 96.6% amino acid sequence identity in its A and B subunits, respectively, to the Stx1 encoded by bacteriophage 933J. We designated this variant “Stx1c” and developed
stxB
1
restriction fragment length polymorphism and
stx
1c
-specific PCR strategies to determine the frequency and distribution of
stx
1c
among 212 STEC strains isolated from humans.
stx
1c
was identified in 36 (17.0%) of 212 STEC strains, 19 of which originated from asymptomatic subjects and 16 of which were from patients with uncomplicated diarrhea.
stx
1c
was most frequently (in 23 STEC strains [63.9%]) associated with
stx
2d
, but 12 (33.3%) of the 36 STEC strains possessed
stx
1c
only. A single STEC strain possessed
stx
1c
together with
stx
2
and was isolated from a patient with hemolytic-uremic syndrome. All 36
stx
1c
-positive STEC strains were
eae
negative and belonged to 10 different serogroups, none of which was O157, O26, O103, O111, or O145. Stx1c was produced by all
stx
1c
-containing STEC strains, but reacted weakly with a commercial immunoassay. We conclude that STEC strains harboring the
stx
1c
variant account for a significant proportion of human STEC isolates. The procedures developed in this study now allow the determination of the frequency of STEC strains harboring
stx
1c
among clinical STEC isolates and their association with human disease in prospective studies.
Evaluation of an Automated Sample Preparation Protocol for Quantitative Detection of Hepatitis C Virus RNA
Authors: Stelzl Evelyn , Kormann-Klement Andrea , Haas Josef , Daghofer Elisabeth , Santner Brigitte I. , Marth Egon , Kessler Harald H. 
Published: July 2002

ABSTRACT
The COBAS AMPLIPREP instrument for automated sample preparation has recently been introduced. In this study, the COBAS AMPLIPREP/COBAS AMPLICOR HCV MONITOR test, which includes this new molecular device, was evaluated and compared to the COBAS AMPLICOR HCV MONITOR test, which includes a manual extraction protocol. Interassay and intra-assay variation, precision, and linearity were determined, and a total of 130 clinical specimens were investigated. For determination of interassay variation, coefficients of variation were found to be between 9 and 59% for the COBAS AMPLIPREP/COBAS AMPLICOR HCV MONITOR test and between 13 and 69% for the COBAS AMPLICOR HCV MONITOR test. For determination of intra-assay variation, coefficients of variation were found to be between 7 and 13% for the COBAS AMPLIPREP/COBAS AMPLICOR HCV MONITOR test and between 8 and 16% for the COBAS AMPLICOR HCV MONITOR test. When precision of the COBAS AMPLIPREP/COBAS AMPLICOR HCV MONITOR test was tested, all results were found to be within ±0.5 log of the expected results. Determination of linearity resulted in a quasilinear curve over 3 logs. When clinical samples were tested with the COBAS AMPLIPREP/COBAS AMPLICOR HCV MONITOR test and compared with the COBAS AMPLICOR HCV MONITOR test, all results were found within ±0.5 log. In conclusion, the assay, which included the new molecular device, proved to be suitable for the routine molecular laboratory. It was found to be laborsaving and easy to handle.
Suppression of Acute Viremia by Short-Term Postexposure Prophylaxis of Simian/Human Immunodeficiency Virus SHIV-RT-Infected Monkeys with a Novel Reverse Transcriptase Inhibitor (GW420867) Allows for Development of Potent Antiviral Immune Responses Resulting in Efficient Containment of Infection
Authors: Mori Kazuyasu , Yasutomi Yasuhiro , Sawada Shuzo , Villinger Francois , Sugama Kazushige , Rosenwith Brigitte , Heeney Jonathan L. , Überla Klaus , Yamazaki Shudo , Ansari Aftab A. , Rübsamen-Waigmann Helga 
Published: July 2002

ABSTRACT
A nonnucleoside reverse transcriptase (RT) inhibitor, GW420867, was tested for postexposure prophylaxis (PEP) in rhesus macaques experimentally infected with 100 50% tissue culture infective doses of a chimeric simian/human immunodeficiency virus (SHIV) containing the RT gene of HIV-1 (SHIV-RT). Animals were either mock treated, or treated for 4 weeks starting at 8 or 24 h postinfection (p.i.) with GW420867. While such therapy led to undetectable plasma viremia in three of six monkeys, a transient plasma viremia was noted in the other three treated animals at 2 to 4 weeks following cessation of therapy. Following this transient viremia all drug-treated animals showed low or undetectable levels of plasma viremia up to the last sample examined at 90 weeks p.i. Despite low and/or undetectable viremia, virus-specific cytotoxic T lymphocyte and viral Env-specific proliferative responses were seen in the peripheral blood mononuclear cells of both mock- and drug-treated animals as early as 3 weeks p.i. Such virus-specific cellular responses, however, were better maintained in the drug-treated animals than the mock-treated animals. In contrast to the virus-specific cellular response, the magnitude and kinetics of virus specific humoral responses appeared to correlate with the detection of viremia. These data support the view that a short-term PEP with GW420867 permits the generation and maintenance of long-lasting virus-specific cell-mediated immune responses while markedly reducing viral loads to undetectable levels for a prolonged period of time (90 weeks) and leads to long-term disease protection. This model provides a unique means to define mechanisms and correlates of disease protection.
Depletion of Lymphocytes and Diminished Cytokine Production in Mice Infected with a Highly Virulent Influenza A (H5N1) Virus Isolated from Humans
Authors: Tumpey Terrence M. , Lu Xiuhua , Morken Timothy , Zaki Sherif R. , Katz Jacqueline M. 
Published: July 2002

ABSTRACTPreviously, we observed that several virulent influenza A (H5N1) viruses which caused severe or fatal disease in humans were also lethal in BALB/c mice following dissemination of the virus to solid organs, including the brain. In contrast, one particular human H5N1 virus was nonlethal in mice and showed no evidence of systemic spread. To compare H5N1 viruses of varying pathogenicity for their ability to alter the mammalian immune system, mice were infected with either influenza A/Hong Kong/483/97 (HK/483) (lethal) or A/Hong Kong/486/97 (HK/486) (nonlethal) virus and monitored for lymphocyte depletion in the blood, lungs, and lymphoid tissue. Intranasal infection with HK/483 resulted in a significant decrease in the total number of circulating leukocytes evident as early as day 2 postinfection. Differential blood counts demonstrated up to an 80% drop in lymphocytes by day 4 postinfection. In contrast, nonlethal HK/486-infected mice displayed only a transient drop of lymphocytes during the infectious period. Analysis of lung and lymphoid tissue from HK/483-infected mice demonstrated a reduction in the number of CD4+and CD8+T cells and reduced synthesis of the cytokines interleukin-1β and gamma interferon and the chemokine macrophage inflammatory protein compared with HK/486-infected mice. In contrast, the cytokine and chemokine levels were increased in the brains of mice infected with HK/483 but not HK/486. Evidence of apoptosis in the spleen and lung of HK/483-infected mice was detected in situ, suggesting a mechanism for lymphocyte destruction. These results suggest that destructive effects on the immune system may be one factor that contributes to the pathogenesis of H5N1 viruses in mammalian hosts.
High-Efficiency Utilization of the Bovine Integrin α
v
β
3
as a Receptor for Foot-and-Mouth Disease Virus Is Dependent on the Bovine β
3
Subunit
Authors: Neff Sherry , Mason Peter W. , Baxt Barry 
Published: July 2002

ABSTRACT

We have previously reported that
Foot-and-mouth disease virus
(FMDV), which is virulent for cattle and swine, can utilize the integrin α
v
β
3
as a receptor on cultured cells. Since those studies were performed with the human integrin, we have molecularly cloned the bovine homolog of the integrin α
v
β
3
and have compared the two receptors for utilization by FMDV. Both the α
v
and β
3
subunits of the bovine integrin have high degrees of amino acid sequence similarity to their corresponding human subunits in the ectodomains (96%) and essentially identical transmembrane and cytoplasmic domains. Within the putative ligand-binding domains, the bovine and human α
v
subunits have a 98.8% amino acid sequence similarity while there is only a 93% similarity between the β
3
subunits of these two species. COS cell cultures, which are not susceptible to FMDV infection, become susceptible if cotransfected with α
v
and β
3
subunit cDNAs from a bovine or human source. Cultures cotransfected with the bovine α
v
β
3
subunit cDNAs and infected with FMDV synthesize greater amounts of viral proteins than do infected cultures cotransfected with the human integrin subunits. Cells cotransfected with a bovine α
v
subunit and a human β
3
subunit synthesize viral proteins at levels equivalent to those in cells expressing both human subunits. However, cells cotransfected with the human α
v
and the bovine β
3
subunits synthesize amounts of viral proteins equivalent to those in cells expressing both bovine subunits, indicating that the bovine β
3
subunit is responsible for the increased effectiveness of this receptor. By engineering chimeric bovine-human β
3
subunits, we have shown that this increase in receptor efficiency is due to sequences encoding the C-terminal one-third of the subunit ectodomain, which contains a highly structured cysteine-rich repeat region. We postulate that amino acid sequence differences within this region may be responsible for structural differences between the human and bovine β
3
subunit, leading to more efficient utilization of the bovine receptor by this bovine pathogen.
Complex Formation between Potyvirus VPg and Translation Eukaryotic Initiation Factor 4E Correlates with Virus Infectivity
Authors: Léonard Simon , Plante Daniel , Wittmann Sylvie , Daigneault Nicole , Fortin Marc G. , Laliberté Jean-François 
Published: July 2002

ABSTRACT

The interaction between the viral protein linked to the genome (VPg) of turnip mosaic potyvirus (TuMV) and the translation eukaryotic initiation factor eIF(iso)4E of
Arabidopsis thaliana
has previously been reported. eIF(iso)4E binds the cap structure (m
7
GpppN, where N is any nucleotide) of mRNAs and has an important role in the regulation in the initiation of translation. In the present study, it was shown that not only did VPg bind eIF(iso)4E but it also interacted with the eIF4E isomer of
A. thaliana
as well as with eIF(iso)4E of
Triticum aestivum
(wheat). The interaction domain on VPg was mapped to a stretch of 35 amino acids, and substitution of an aspartic acid residue found within this region completely abolished the interaction. The cap analogue m
7
GTP, but not GTP, inhibited VPg-eIF(iso)4E complex formation, suggesting that VPg and cellular mRNAs compete for eIF(iso)4E binding. The biological significance of this interaction was investigated.
Brassica perviridis
plants were infected with a TuMV infectious cDNA (p35Tunos) and p35TuD77N, a mutant which contained the aspartic acid substitution in the VPg domain that abolished the interaction with eIF(iso)4E. After 20 days, plants bombarded with p35Tunos showed viral symptoms, while plants bombarded with p35TuD77N remained symptomless. These results suggest that VPg-eIF(iso)4E interaction is a critical element for virus production.
Coxsackievirus Expression of the Murine Secretory Protein Interleukin-4 Induces Increased Synthesis of Immunoglobulin G1 in Mice
Authors: Chapman Nora M. , Kim Kyung-Soo , Tracy Steven , Jackson John , Höfling Katja , Leser J. Smith , Malone James , Kolbeck Peter 
Published: July 2002

ABSTRACTWe cloned the sequence encoding murine interleukin-4 (mIL-4), including the secretory signal, into the genome of CVB3/0, an artificially attenuated strain of coxsackievirus B3, at the junction of the capsid protein 1D and the viral protease 2Apro. Two strains of chimeric CVB3 were constructed using, in one case, identical sequences to encode 2Apro cleavage sites (CVB3/0-mIL4/47) on either side of the inserted coding sequence and, in the other case, nonidentical sequences that varied at the nucleotide level without changing the amino acid sequences (CVB3-PL2-mIL4/46). Transfection of HeLa cells yielded progeny viruses that replicated with rates similar to that of the parental CVB3/0 strain, although yields of mIL-4-expressing strains were approximately 10-fold lower than those of the parental virus. Western blot analysis of viral proteins isolated from HeLa cells inoculated with either strain of chimeric virus demonstrated that the chimeric viruses synthesized capsid protein 1D at approximately twofold-higher levels than the parental virus. mIL-4 protein was detected by enzyme-linked immunosorbent assay (ELISA) in HeLa cells inoculated with either strain of chimeric virus. Lysates of HeLa cells inoculated with either chimeric virus induced the proliferation of the mIL-4-requiring murine MC-9 cell line, demonstrating biological activity of the CVB3-expressed mIL-4. Reverse transcription (RT)-PCR analysis of viral RNA derived from sequential passaging of CVB3/0-mIL4/47 in HeLa cells demonstrated deletion of the mIL-4 coding sequence occurring by the fourth passage, while similar analysis of CVB3-PL2-mIL4/46 RNA demonstrated detection of the mIL-4 coding sequence in the virus population through 10 generations in HeLa cells. mIL-4 protein levels determined by ELISA were consistent with the stability and loss data determined by RT-PCR analysis of the passaged viral genomes. Studies of insert stability of CVB3-PL2-mIL4/46 during replication in mice showed the presence of the viral mIL-4 insert in pancreas, heart, and liver at 14 days postinfection. Comparison of the murine antibody responses to CVB3-PL2-mIL4/46 and the parental CVB3/0 strain demonstrated an increased level of CVB3-binding serum immunoglobulin G1 in mice inoculated with CVB3-PL2-mIL4/46.
Specific Ablation of Antiviral Gene Expression in Macrophages by Antibody-Dependent Enhancement of Ross River Virus Infection
Authors: Lidbury Brett A. , Mahalingam Surendran 
Published: July 2002

ABSTRACTRoss River virus (RRV) is an indigenous Australian arthropod-borne alphavirus responsible for epidemic polyarthritis (EPA), myalgia, and lethargy in humans. Macrophages and monocytes have been associated with human RRV disease, and previous studies have shown that RRV is capable of infecting macrophages via both a natural virus receptor and by Fc receptor-mediated antibody-dependent enhancement (ADE). Similar to other viruses, such as human immunodeficiency virus and dengue virus, ADE infection results in dramatic RRV growth increases for in vitro macrophage cultures. This study demonstrates that RRV could resist lipopolysaccharide (LPS)-induced antiviral activity in macrophage cultures when infection was via the ADE pathway. Investigation of this infection pathway found that RRV was able to suppress the transcription and translation of key antiviral genes (tumor necrosis factor and inducible nitric oxide synthase) in LPS-stimulated macrophages by disrupting the transcription into mRNA of the genes coding for the associated transcription factors IRF-1 and NF-κB. The transcription of non-antiviral control genes was not perturbed by RRV-ADE infection, and de novo protein synthesis also was not significantly affected in RRV-ADE infected cells. The ADE pathway of infection allowed RRV to specifically target antiviral genes in macrophages, resulting in unrestricted virus replication. As ADE has been observed for several virus families and associated with disease and adverse vaccination outcomes, these findings may have broad relevance to viral disease formation and antiviral vaccination strategies.
Influenza Virus Assembly: Effect of Influenza Virus Glycoproteins on the Membrane Association of M1 Protein
Authors: Ali Ayub , Avalos Roy T. , Ponimaskin Evgeni , Nayak Debi P. 
Published: July 2002

ABSTRACT
Influenza virus matrix protein (M1), a critical protein required for virus assembly and budding, is presumed to interact with viral glycoproteins on the outer side and viral ribonucleoprotein on the inner side. However, because of the inherent membrane-binding ability of M1 protein, it has been difficult to demonstrate the specific interaction of M1 protein with hemagglutinin (HA) or neuraminidase (NA), the influenza virus envelope glycoproteins. Using Triton X-100 (TX-100) detergent treatment of membrane fractions and floatation in sucrose gradients, we observed that the membrane-bound M1 protein expressed alone or coexpressed with heterologous Sendai virus F was totally TX-100 soluble but the membrane-bound M1 protein expressed in the presence of HA and NA was predominantly detergent resistant and floated to the top of the density gradient. Furthermore, both the cytoplasmic tail and the transmembrane domain of HA facilitated binding of M1 to detergent-resistant membranes. Analysis of the membrane association of M1 in the early and late phases of the influenza virus infectious cycle revealed that the interaction of M1 with mature glycoproteins which associated with the detergent-resistant lipid rafts was responsible for the detergent resistance of membrane-bound M1. Immunofluorescence analysis by confocal microscopy also demonstrated that, in influenza virus-infected cells, a fraction of M1 protein colocalized with HA and associated with the HA in transit to the plasma membrane via the exocytic pathway. Similar results for colocalization were obtained when M1 and HA were coexpressed and HA transport was blocked by monensin treatment. These studies indicate that both HA and NA interact with influenza virus M1 and that HA associates with M1 via its cytoplasmic tail and transmembrane domain.