bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cervical Human Papillomavirus (HPV) Infection and HPV Type 16 Antibodies in South African Women
Authors: Marais Dianne J. , Constant Debbie , Allan Bruce , Carrara Henri , Hoffman Margaret , Shapiro Samuel , Morroni Chelsea , Williamson Anna-Lise 
Published: December 2007

ABSTRACTThere is a high incidence of cervical cancer in South African women. No large studies to assess human papillomavirus virus (HPV) infection or HPV type 16 (HPV-16) exposure have occurred in the region, a requirement for policy making with regards to HPV screening and the introduction of vaccines. Control women (n= 1,003) enrolled in a case control study of hormonal contraceptives and cervical cancer were tested for 27 cervical HPV types by reverse line blot analysis. The seroprevalence of HPV-16 immunoglobulin G (IgG) and IgA antibodies was assessed by a virus-like particle-based enzyme-linked immunoassay of 908 and 904 control women, respectively, and of 474 women with cervical cancer. The cervical HPV prevalence was 26.1%. The HPV-16 IgG seroprevalence was 44.4% and the HPV-16 IgA seroprevalence was 28.7% in control women, and these levels were significantly higher (61.8% and 52.7%, respectively) for women with cervical cancer (odds ratio [OR], 2.1 and 2.8, respectively). The cervical HPV prevalence showed an association with cervical disease, and the HPV-16 IgG prevalence decreased while the HPV-16 IgA prevalence increased with increasing age (P< 0.05). The prevalence of oncogenic HPV types (including HPV-16) decreased with age, whereas nononcogenic HPV types showed limited association with age. Multivariate analysis revealed cervical HPV infection to be associated with herpes simplex virus type 2 infection (OR, 1.7) and increasing years of education (OR, 1.9). HPV-16 IgG antibodies were inversely associated with current smoking status (OR, 0.6), and the presence of HPV-16 IgA antibodies was inversely associated with the use of alcohol (OR, 2.1) and inversely associated with the use of oral contraceptives (OR, 0.6). High levels of exposure to HPV, and particularly HPV-16, were evident in this population. The apparent increase of serum HPV-16 IgA with increasing age requires further investigation.
Treatment with Tigecycline of Recurrent Urosepsis Caused by Extended-Spectrum-β-Lactamase-Producing
Escherichia coli
Authors: Krueger Wolfgang A. , Kempf Volkhard A. J. , Peiffer Manou , Nagele Udo , Unertl Klaus E. , Schroeder Torsten H. 
Published: December 2007

ABSTRACT

A 25-year-old female was admitted to our intensive care unit with septic shock and multiorgan failure caused by extended-spectrum β-lactamase-producing
Escherichia coli
originating from the right renal pelvis. A 16-day course of treatment with meropenem reversed the septic condition, but the infection recurred thereafter. The patient recovered fully after therapy was changed to tigecycline.
Pathotypical Characterization and Molecular Epidemiology of Newcastle Disease Virus Isolates from Different Hosts in China from 1996 to 2005
Authors: Qin Zhuo-Ming , Tan Lei-Tao , Xu Huai-Ying , Ma Bao-Chen , Wang You-Ling , Yuan Xiao-Yuan , Liu Wen-Jun 
Published: December 2007

ABSTRACT

Thirty Newcastle disease virus (NDV) strains isolated from outbreaks in China during 1996 to 2005 were characterized pathotypically and genotypically. All strains except one were velogenic. An analysis of the variable region (nucleotides 47 to 420) of the F gene indicated that 6 isolates belonged to genotype II, 3 to genotype III, 1 (isolated from a pigeon) to genotype VI, and 20 to genotype VII. Isolates belonging to genotype VII were further divided into five subtypes, VIIa, VIIb, VIIc, VIId, and VIIe, and subtype VIId was made up of VIId1 to VIId5. These results showed that genotype VII isolates might have been the most prevalent in China during the past two decades. Genotype VII isolates shared high homology, but the homology was less than that between genotype VII viruses and the vaccine virus LaSota. Among these NDV isolates, 25 isolates had the velogenic motif
112
R/K-R-Q-K/R-R-F
117
that is consistent with results of the biological tests. However, four of five LaSota-type isolates that contained the lentogenic motif
112
G-R-Q-G-R-L
117
were velogenic, except SY/03, in the view of the biological test. The majority of genotype VII isolates had lost one or two N-glycosylation sites. Finally, a cross-protection experiment in which specific-pathogen-free chickens vaccinated with LaSota were challenged by six NDV isolates showed that more than three isolates were antigenic variants that could be responsible for recent outbreaks of Newcastle disease.
Discrimination of Herpes Simplex Virus Type 2 Strains by Nucleotide Sequence Variations
Authors: Kaneko Hisatoshi , Kawana Takashi , Ishioka Ken , Fukushima Eiko , Suzutani Tatsuo 
Published: December 2007

ABSTRACT
We determined the polymorphous 400-bp regions in UL53, US1, and US4 for the discrimination of herpes simplex virus type 2 (HSV-2) strains. Thirty-six HSV-2 clinical strains could be differentiated into 35 groups using these three regions and into 36 groups by additional analysis of three noncoding regions previously reported as polymorphous.
Differences in Potential for Selection of Clindamycin-Resistant Mutants Between Inducible
erm
(A) and
erm
(C)
Staphylococcus aureus
Genes
Authors: Daurel Claire , Huet Corinne , Dhalluin Anne , Bes Michèle , Etienne Jerome , Leclercq Roland 
Published: December 2007

ABSTRACT

In staphylococci, inducible macrolide-lincosamide-streptogramin B (MLS
B
) resistance is conferred by the
erm
(C) or
erm
(A) gene. This phenotype is characterized by the erythromycin-clindamycin “D-zone” test. Although clindamycin appears active in vitro, exposure of MLS
B
-inducible
Staphylococcus aureus
to this antibiotic may result in the selection of clindamycin-resistant mutants, either in vitro or in vivo. We have compared the frequencies of mutation to clindamycin resistance for 28 isolates of
S. aureus
inducibly resistant to erythromycin and bearing the
erm
(C) (
n
= 18) or
erm
(A) (
n
= 10) gene. Seven isolates susceptible to erythromycin or bearing the
msr
(A) gene (efflux) were used as controls. The frequencies of mutation to clindamycin resistance for the
erm
(A) isolates (mean ± standard deviation, 3.4 × 10
−8
± 2.4 × 10
−8
) were only slightly higher than those for the controls (1.1 × 10
−8
± 6.4 × 10
−9
). By contrast,
erm
(C) isolates displayed a mean frequency of mutation to clindamycin resistance (4.7 × 10
−7
± 5.5 × 10
−7
) 14-fold higher than that of the
S. aureus
isolates with
erm
(A). The difference was also observed, although to a lower extent, when
erm
(C) and
erm
(A) were cloned into
S. aureus
RN4220. We conclude that
erm
(C) and
erm
(A) have different genetic potentials for selection of clindamycin-resistant mutants. By the disk diffusion method,
erm
(C) and
erm
(A) isolates could be distinguished on the basis of high- and low-level resistance to oleandomycin, respectively.
Heterogeneity of Hemolysin Expression during Neonatal
Streptococcus agalactiae
Sepsis
Authors: Sigge Anja , Schmid Manuel , Mauerer Stefanie , Spellerberg Barbara 
Published: December 2007

ABSTRACT

The β-hemolysin of
Streptococcus agalactiae
is a major virulence factor; consequently, nonhemolytic strains rarely cause infections. We report on a case of neonatal sepsis caused by a strain displaying heterogeneous hemolysin expression. It was detected by the simultaneous isolation of hemolytic and nonhemolytic colonies from cultures of the infant's blood.
Candida bracarensis
Detected among Isolates of
Candida glabrata
by Peptide Nucleic Acid Fluorescence In Situ Hybridization: Susceptibility Data and Documentation of Presumed Infection
Authors: Bishop Justin A. , Chase Nancy , Magill Shelley S. , Kurtzman Cletus P. , Fiandaca Mark J. , Merz William G. 
Published: December 2007

ABSTRACT

Molecular taxonomic studies have revealed new
Candida
species among phenotypically delineated species, the best example being
Candida dubliniensis
. This study was designed to determine the occurrence of two new molecularly defined species,
Candida bracarensis
and
Candida nivariensis
, which are closely related to and identified as
Candida glabrata
by phenotypic assays. A total of 137 recent clinical isolates of
C. glabrata
identified by phenotypic characteristics was tested with
C. bracarensis
and
C. nivariensis
species-specific peptide nucleic acid fluorescence in situ hybridization probes. Three of 137 (2.2%) isolates were positive with the
C. bracarensis
probe, whereas the control strain, but none of the clinical isolates, was positive with the
C. nivariensis
probe. D1/D2 sequencing confirmed the identification of the three isolates as representing
C. bracarensis
. Clinically, one
C. bracarensis
isolate was recovered from a presumed infection, a polymicrobial pelvic abscess in a patient with perforated diverticulitis. The other two isolates were recovered from two adult oncology patients who were only colonized.
C. bracarensis
was white on CHROMagar Candida, had variable API-20C patterns that overlapped with
C. nivariensis
and some
C. glabrata
isolates, and had variable results with a rapid trehalose assay. Interestingly, an isolate from one of the colonized oncology patients was resistant to fluconazole, itraconazole, voriconazole, and posaconazole in vitro. In summary,
C. bracarensis
was detected among clinical isolates of
C. glabrata
, while
C. nivariensis
was not. One
C. bracarensis
isolate causing a presumed deep infection was recovered, and another isolate was azole resistant. Whether clinical laboratories should identify
C. bracarensis
will require more data.
Multiple Displacement Amplification Enables Large-Scale Clonal Analysis following Retroviral Gene Therapy
Authors: Bleier S. , Maier P. , Allgayer H. , Wenz F. , Zeller W. J. , Fruehauf S. , Laufs S. 
Published: December 2007

ABSTRACT
Analysis of the fate of retrovirally transduced cells after transplantation is often hampered by the scarcity of available DNA. We evaluated a promising method for whole-genome amplification, called multiple displacement amplification (MDA), with respect to even and accurate representation of retrovirally transduced genomic DNA. We proved that MDA is a suitable method to subsequently quantify engraftment efficiencies by quantitative real-time PCR by analyzing retrovirally transduced DNA in a background of untransduced DNA and retroviral integrations found in primary material from a retroviral transplantation model. The portion of these retroviral integrations in the amplified samples was 1.02-fold (range 0.2, to 2.1-fold) the portion determined in the original genomic DNA. Integration site analysis by ligation-mediated PCR (LM-PCR) is essential for the detection of retroviral integrations. The combination of MDA and LM-PCR showed an increase in the sensitivity of integration site analysis, as a specific integration site could be detected in a background of untransduced DNA, while the transduced DNA made up only 0.001%. These results show for the first time that MDA enables large-scale sensitive detection and reliable quantification of retrovirally transduced human genomic DNA and therefore facilitates follow-up analysis in gene therapy studies even from the smallest amounts of starting material.
Structure of the Receptor-Binding Protein of Bacteriophage Det7: a Podoviral Tail Spike in a Myovirus
Authors: Walter Monika , Fiedler Christian , Grassl Renate , Biebl Manfred , Rachel Reinhard , Hermo-Parrado X. Lois , Llamas-Saiz Antonio L. , Seckler Robert , Miller Stefan , van Raaij Mark J. 
Published: December 2007

ABSTRACT

A new
Salmonella enterica
phage, Det7, was isolated from sewage and shown by electron microscopy to belong to the
Myoviridae
morphogroup of bacteriophages. Det7 contains a 75-kDa protein with 50% overall sequence identity to the tail spike endorhamnosidase of podovirus P22. Adsorption of myoviruses to their bacterial hosts is normally mediated by long and short tail fibers attached to a contractile tail, whereas podoviruses do not contain fibers but attach to host cells through stubby tail spikes attached to a very short, noncontractile tail. The amino-terminal 150 residues of the Det7 protein lack homology to the P22 tail spike and are probably responsible for binding to the base plate of the myoviral tail. Det7 tail spike lacking this putative particle-binding domain was purified from
Escherichia coli
, and well-diffracting crystals of the protein were obtained. The structure, determined by molecular replacement and refined at a 1.6-Å resolution, is very similar to that of bacteriophage P22 tail spike. Fluorescence titrations with an octasaccharide suggest Det7 tail spike to bind its receptor lipopolysaccharide somewhat less tightly than the P22 tail spike. The Det7 tail spike is even more resistant to thermal unfolding than the already exceptionally stable homologue from P22. Folding and assembly of both trimeric proteins are equally temperature sensitive and equally slow. Despite the close structural, biochemical, and sequence similarities between both proteins, the Det7 tail spike lacks both carboxy-terminal cysteines previously proposed to form a transient disulfide during P22 tail spike assembly. Our data suggest receptor-binding module exchange between podoviruses and myoviruses in the course of bacteriophage evolution.
A Repetitive Region of Gammaherpesvirus Genomic DNA Is a Ligand for Induction of Type I Interferon
Authors: Sanchez David Jesse , Miranda Daniel , Arumugaswami Vaithilingaraja , Hwang Seungmin , Singer Adam E. , Senaati Ashkon , Shahangian Arash , Song Moon Jung , Sun Ren , Cheng Genhong 
Published: December 2007

ABSTRACT
Innate immune responses against viral infection, especially the induction of type I interferon, are critical for limiting the replication of the virus. Although it has been shown that DNA can induce type I interferon, to date no natural DNA ligand of a virus that induces type I interferon has been described. Here we screened the genome of murine gammaherpesvirus 68 with mutations at various genomic locations to map the region of DNA that induces type I interferon. A repetitive region termed the 100-base-pair repeat region is a ligand that is both necessary and sufficient for the viral genomic DNA to induce type I interferon. A region colinear with this ligand in the genome of Kaposi's sarcoma-associated herpesvirus also induces type I interferon. We have thus defined a repetitive region of the genomes of gammaherpesviruses as the first natural DNA virus ligand that induces type I interferon.
Antiretroviral Activity of Ancestral TRIM5α
Authors: Goldschmidt Valérie , Ciuffi Angela , Ortiz Millan , Brawand David , Muñoz Miguel , Kaessmann Henrik , Telenti Amalio 
Published: December 2007

ABSTRACT

The antiretroviral protein TRIM5α is known to have evolved different restriction capacities against various retroviruses, driven by positive Darwinian selection. However, how these different specificities have evolved in the primate lineages is not fully understood. Here we used ancestral protein resurrection to estimate the evolution of antiviral restriction specificities of TRIM5α on the primate lineage leading to humans. We used TRIM5α coding sequences from 24 primates for the reconstruction of ancestral
TRIM5α
sequences using maximum-likelihood and Bayesian approaches. Ancestral sequences were transduced into HeLa and CRFK cells. Stable cell lines were generated and used to test restriction of a panel of extant retroviruses (human immunodeficiency virus type 1 [HIV-1] and HIV-2, simian immunodeficiency virus [SIV] variants SIV
mac
and SIV
agm
, and murine leukemia virus [MLV] variants N-MLV and B-MLV). The resurrected TRIM5α variant from the common ancestor of Old World primates (Old World monkeys and apes, ∼25 million years before present) was effective against present day HIV-1. In contrast to the HIV-1 restriction pattern, we show that the restriction efficacy against other retroviruses, such as a murine oncoretrovirus (N-MLV), is higher for more recent resurrected hominoid variants. Ancestral TRIM5α variants have generally limited efficacy against HIV-2, SIV
agm
, and SIV
mac
. Our study sheds new light on the evolution of the intrinsic antiviral defense machinery and illustrates the utility of functional evolutionary reconstruction for characterizing recently emerged protein differences.
Global Transcriptional Responses of
Pseudomonas aeruginosa
to Phage PRR1 Infection
Authors: Ravantti Janne J. , Ruokoranta Tanja M. , Alapuranen A. Marika , Bamford Dennis H. 
Published: December 2007

ABSTRACT

The infectious cycles of viruses are known to cause dramatic changes to host cell function. The development of microarray technology has provided means to monitor host cell responses to viral infection at the level of global changes in mRNA levels. We have applied this methodology to investigate gene expression changes caused by a small, icosahedral, single-stranded-RNA phage, PRR1 (a member of the
Leviviridae
family), on its host,
Pseudomonas aeruginosa
, at different times during its growth cycle. Viral infection in this system resulted in changes in expression levels of <4% of
P. aeruginosa
genes. Interestingly, the number of genes affected by viral infection was significantly lower than the number of genes affected by changes in growth conditions during the experiment. Compared with a similar study that focused on the complex, double-stranded-DNA bacterial virus PRD1, it was evident that there were no universal responses to viral infection. However, in both cases, translation was affected in infected cells.
The Essential Human Cytomegalovirus Gene UL52 Is Required for Cleavage-Packaging of the Viral Genome
Authors: Borst Eva Maria , Wagner Karen , Binz Anne , Sodeik Beate , Messerle Martin 
Published: December 2007

ABSTRACT
Replication of human cytomegalovirus (HCMV) produces large DNA concatemers of head-to-tail-linked viral genomes that upon packaging into capsids are cut into unit-length genomes. The mechanisms underlying cleavage-packaging and the subsequent steps prior to nuclear egress of DNA-filled capsids are incompletely understood. The hitherto uncharacterized product of the essential HCMV UL52 gene was proposed to participate in these processes. To investigate the function of pUL52, we constructed a ΔUL52 mutant as well as a complementing cell line. We found that replication of viral DNA was not impaired in noncomplementing cells infected with the ΔUL52 virus, but viral concatemers remained uncleaved. Since the subnuclear localization of the known cleavage-packaging proteins pUL56, pUL89, and pUL104 was unchanged in ΔUL52-infected fibroblasts, pUL52 does not seem to act via these proteins. Electron microscopy studies revealed only B capsids in the nuclei of ΔUL52-infected cells, indicating that the mutant virus has a defect in encapsidation of viral DNA. Generation of recombinant HCMV genomes encoding epitope-tagged pUL52 versions showed that only the N-terminally tagged pUL52 supported viral growth, suggesting that the C terminus is crucial for its function. pUL52 was expressed as a 75-kDa protein with true late kinetics. It localized preferentially to the nuclei of infected cells and was found to enclose the replication compartments. Taken together, our results demonstrate an essential role for pUL52 in cleavage-packaging of HCMV DNA. Given its unique subnuclear localization, the function of pUL52 might be distinct from that of other cleavage-packaging proteins.
Cellular Determinants of Hepatitis C Virus Assembly, Maturation, Degradation, and Secretion
Authors: Gastaminza Pablo , Cheng Guofeng , Wieland Stefan , Zhong Jin , Liao Wei , Chisari Francis V. 
Published: December 2007

ABSTRACTIntracellular infectious hepatitis C virus (HCV) particles display a distinctly higher buoyant density than do secreted virus particles, suggesting that the characteristic low density of extracellular HCV particles is acquired during viral egress. We took advantage of this difference to examine the determinants of assembly, maturation, degradation, and egress of infectious HCV particles. The results demonstrate that HCV assembly and maturation occur in the endoplasmic reticulum (ER) and post-ER compartments, respectively, and that both depend on microsomal transfer protein and apolipoprotein B, in a manner that parallels the formation of very-low-density lipoproteins (VLDL). In addition, they illustrate that only low-density particles are efficiently secreted and that immature particles are actively degraded, in a proteasome-independent manner, in a post-ER compartment of the cell. These results suggest that by coopting the VLDL assembly, maturation, degradation, and secretory machinery of the cell, HCV acquires its hepatocyte tropism and, by mimicry, its tendency to persist.
H5-Type Influenza Virus Hemagglutinin Is Functionally Recognized by the Natural Killer-Activating Receptor NKp44
Authors: Ho Joanna W. , Hershkovitz Oren , Peiris Malik , Zilka Alon , Bar-Ilan Ahuva , Nal Beatrice , Chu Kid , Kudelko Mateusz , Kam Yiu Wing , Achdout Hagit , Mandelboim Michal , Altmeyer Ralf , Mandelboim Ofer , Bruzzone Roberto , Porgador Angel 
Published: December 2007

ABSTRACTAntiviral immune defenses involve natural killer (NK) cells. We previously showed that the NK-activating receptor NKp44 is involved in the functional recognition of H1-type influenza virus strains by NK cells. In the present study, we investigated the interaction of NKp44 and the hemagglutinin of a primary influenza virus H5N1 isolate. Here we show that recombinant NKp44 recognizes H5-expressing cells and specifically interacts with soluble H5 hemagglutinin. H5-pseudotyped lentiviral particles bind to NK cells expressing NKp44. Following interaction with target cells expressing H5, pseudotyped lentiviral particles, or membrane-associated H5, NK cells show NKp44-mediated induced activity. These findings indicate that NKp44-H5 interactions induce functional NK activation.
Hepatitis C Virus Genotype 1a Growth and Induction of Autophagy
Authors: Ait-Goughoulte Malika , Kanda Tatsuo , Meyer Keith , Ryerse Jan S. , Ray Ratna B. , Ray Ranjit 
Published: December 2007

ABSTRACT
We have previously reported that immortalized human hepatocytes (IHH) support the generation of infectious hepatitis C virus (HCV) genotype 1a (clone H77). In the present study, we have investigated the growth of HCV genotype 1a (clone H77) through serial passages and accompanying changes in IHH in response to infection. Eleven serial passages of HCV genotype 1a (clone H77) in IHH were completed. Virus replication was ascertained from the presence of HCV-specific sequences, the detection of core antigen, the virus genome copy number, and the virus titer in IHH culture fluid. Electron microscopy suggested that HCV infection induces autophagic vacuole formation in IHH. Fluorescence microscopy displayed localization of autophagic markers, microtubule-associated protein-1 light chain-3 and Apg5, on the vacuoles of HCV-infected hepatocytes. Taken together, our results suggested that HCV genotype 1a (clone H77) can be serially passaged in IHH and that HCV infection induces an autophagic response in hepatocytes.