bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple-Locus Variable-Number Tandem-Repeat Analysis for Longitudinal Survey of Sources of
Pseudomonas aeruginosa
Infection in Cystic Fibrosis Patients
Authors: Vu-Thien Hoang , Corbineau Gaëlle , Hormigos Katia , Fauroux Brigitte , Corvol Harriet , Clément Annick , Vergnaud Gilles , Pourcel Christine 
Published: August 2007

ABSTRACT

In order to identify the source of infection by
Pseudomonas aeruginosa
in patients with cystic fibrosis (CF), systematic genotyping of isolates is necessary. Multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) was used to survey the sources of
P. aeruginosa
infections in a French (Paris, France) pediatric CF center. Between January 2004 and December 2006, 108 patients ages 2 to 21 years who were regularly monitored at the center provided sputum for culture.
P. aeruginosa
was detected in 46 children, 17 of whom had primary colonization. A total of 163 isolates were recovered. MLVA was improved from a previously published method by the addition of new, informative, and easily typeable markers. Upon genotyping with 15 VNTRs, a total of 39 lineages composed of indistinguishable or closely related isolates, were observed. One of them corresponds to “clone C,” which is widely distributed in Europe, and another corresponds to reference strain PA14. Six patients were colonized with two different strains, and the remaining 40 patients were colonized with a single strain. Strains from seven lineages were shared by at least two and up to four patients among a total of 20 patients. The study demonstrates that MLVA is an efficient, easy, and rapid molecular method for epidemiological surveillance for
P. aeruginosa
infection. The resulting data and strain genetic profiles can be queried on
http://bacterial-genotyping.igmors.u-psud.fr
.
Capsule Gene Analysis of Invasive
Haemophilus influenzae
: Accuracy of Serotyping and Prevalence of IS
1016
among Nontypeable Isolates
Authors: Satola Sarah W. , Collins Julie T. , Napier Ruth , Farley Monica M. 
Published: August 2007

ABSTRACT

We evaluated the accuracy of serologic capsule typing by analyzing capsule genes and related markers among invasive
Haemophilus influenzae
isolates before and after the introduction of
H. influenzae
serotype b (Hib) conjugate vaccines. Three hundred and sixty invasive
H. influenzae
isolates were collected as part of Active Bacterial Core surveillance within the Georgia Emerging Infections Program between 1 January 1989 and 31 July 1998. All isolates were biotyped, serotyped by slide agglutination serotyping (SAST), and evaluated using PCR capsule typing. Nontypeable
H. influenzae
(NTHi) isolates were probed with Hib
cap
-gene-containing plasmid pUO38 and with IS
1016
; a subset was examined with phosphoglucose isomerase (
pgi
) genotyping and pulsed-field gel electrophoresis (PFGE). Discrepancies between SAST and PCR capsule typing were found for 64/360 (17.5%) of the isolates; 48 encapsulated by SAST were NTHi by PCR, 8 NTHi by SAST were encapsulated by PCR, 6 encapsulated by SAST were a different capsule type by PCR, and 2 encapsulated by SAST were capsule-deficient Hib variants (Hib-minus). None of the PCR-confirmed NTHi isolates demonstrated homology with residual capsule gene sequences; 19/201 (9.5%) had evidence of IS
1016
, an insertion element associated with division I
H. influenzae
capsule serotypes. The majority of IS
1016
-positive NTHi were biotypes I and V and showed some genetic relatedness by PFGE. In conclusion, PCR capsule typing was more accurate than SAST and Hib-minus variants were rare. IS
1016
was present in 9.5% of NTHi isolates, suggesting that this subset may be more closely related to encapsulated organisms. A better understanding of NTHi may contribute to vaccine development.
Bordetella pertussis
Strains Circulating in Europe in 1999 to 2004 as Determined by Pulsed-Field Gel Electrophoresis
Authors: Hallander Hans , Advani Abdolreza , Riffelmann Marion , von König Carl H. W. , Caro Valerie , Guiso Nicole , Mooi Frits R. , Gzyl Anna , Kaltoft Margit S. , Fry Norman K. , Mertsola Jussi , He Qiushui 
Published: August 2007

ABSTRACT

Clinical isolates of
Bordetella pertussis
collected during the year 2004 (
n
= 153) in eight European countries, Denmark, Finland, France, Germany, The Netherlands, Poland, Sweden, and United Kingdom, were analyzed by pulsed-field gel electrophoresis (PFGE), and their PFGE profiles were compared with those of isolates collected in 1999 (
n
= 102). The 255 isolates produced 59 distinct PFGE profiles. Among the 153 isolates from 2004, 36 profiles were found, while within the 102 isolates from 1999, 33 profiles were detected. One PFGE profile, BpSR11, was dominant (30% to 50%) in all countries except Denmark (10%) and Poland (0%). In comparison with 1999, there was an increase in BpSR11 prevalence in Finland in 2004 from 5% to 40%, coinciding with a major incidence peak. Some other PFGE profiles seemed to be associated with limited dissemination. Poland was the only country in which the most common actual European PFGE profiles were not found. In a dendrogram analysis, all common PFGE profiles were identified within PFGE group IV, and BpSR11 clustered together with PFGE subgroup IVβ. Compared to the 1999 isolates, PFGE group V representative for pertactin variant
prn3
strains had disappeared, and a new cluster was seen. In conclusion, some PFGE profiles, such as BpSR11, evidently have a higher capacity to spread, suggesting increased fitness to the present immunological environment. It is therefore of major interest to continue with surveillance programs of
B. pertussis
isolates, as both waning vaccine-derived immunity and strain variation may play a role in the persistence of pertussis.
Large-Scale Human Immunodeficiency Virus Rapid Test Evaluation in a Low-Prevalence Ugandan Blood Bank Population
Authors: Eller Leigh A. , Eller Michael A. , Ouma Benson J. , Kataaha Peter , Bagaya Bernard S. , Olemukan Robert L. , Erima Simon , Kawala Lilian , de Souza Mark S. , Kibuuka Hannah , Wabwire-Mangen Fred , Peel Sheila A. , O'Connell Robert J. , Robb Merlin L. , Michael Nelson L. 
Published: August 2007

ABSTRACTThe use of rapid tests for human immunodeficiency virus (HIV) has become standard in HIV testing algorithms employed in resource-limited settings. We report an extensive HIV rapid test validation study conducted among Ugandan blood bank donors at low risk for HIV infection. The operational characteristics of four readily available commercial HIV rapid test kits were first determined with 940 donor samples and were used to select a serial testing algorithm. Uni-Gold Recombigen HIV was used as the screening test, followed by HIV-1/2 STAT-PAK for reactive samples. OraQuick HIV-1 testing was performed if the first two test results were discordant. This algorithm was then tested with 5,252 blood donor samples, and the results were compared to those of enzyme immunoassays (EIAs) and Western blotting. The unadjusted algorithm sensitivity and specificity were 98.6 and 99.9%, respectively. The adjusted sensitivity and specificity were 100 and 99.96%, respectively. This HIV testing algorithm is a suitable alternative to EIAs and Western blotting for Ugandan blood donors.
Validation of Nasopharyngeal Sampling and Culture Techniques for Detection of
Streptococcus pneumoniae
in Children in Kenya
Authors: Abdullahi Osman , Wanjiru Eva , Musyimi Robert , Glass Nina , Scott J. Anthony G. 
Published: August 2007

ABSTRACT
We compared nasopharyngeal swabs against nasal wash cultures for detecting colonizing pneumococci and examined the effect of frozen storage in skim milk-tryptone-glucose-glycerin on culture. Among the 55 children with positive nasal wash cultures, swab cultures were positive for 47 (85%). Of the 96 swabs positive on direct plating, 94 (98%) were positive when recultured after freezing.
Evaluation of Pan-Dermatophyte Nested PCR in Diagnosis of Onychomycosis
Authors: Garg Jaya , Tilak Ragini , Singh Sanjay , Gulati Anil Kumar , Garg Atul , Prakash Pradyot , Nath Gopal 
Published: August 2007

ABSTRACT

In this study, nested PCR using novel primers targeting the pan-dermatophyte-specific sequence of the chitin synthase 1 gene (
CHS1
) was compared with KOH microscopy, culture isolation, and single-round PCR for diagnosis of 152 patients with clinically suspected onychomycosis. Results indicate that nested PCR may be considered the gold standard for the diagnosis of cases of onychomycosis for which the etiological agents are dermatophytes.
ORF73-Null Murine Gammaherpesvirus 68 Reveals Roles for mLANA and p53 in Virus Replication
Authors: Forrest J. Craig , Paden Clinton R. , Allen Robert D. , Collins Julie , Speck Samuel H. 
Published: August 2007

ABSTRACT
Gammaherpesviruses establish lifelong, latent infections in host lymphocytes, during which a limited subset of viral gene products facilitates maintenance of the viral episome. Among the gamma-2-herpesvirus (rhadinovirus) subfamily, this includes expression of the conserved ORF73-encoded LANA proteins. We previously demonstrated by loss-of-function mutagenesis that the murine gammaherpesvirus 68 (MHV68) ORF73 gene product, mLANA, is required for the establishment of latency following intranasal inoculation of mice (N. J. Moorman, D. O. Willer, and S. H. Speck, J. Virol. 77:10295-10303, 2003). mLANA-deficient viruses also exhibited a defect in acute virus replication in the lungs of infected mice. The latter observation led us to examine the role of mLANA in productive viral replication. We assessed the capacity of mLANA-deficient virus (73.Stop) to replicate in cell culture at low multiplicities of infection (MOIs) and found that 73.Stop growth was impaired in murine fibroblasts but not in Vero cells. A recombinant virus expressing an mLANA-green fluorescent protein (GFP) fusion revealed that mLANA is expressed throughout the virus replication cycle. In addition, 73.Stop infection of murine fibroblasts at high MOIs was substantially more cytotoxic than infection with a genetically repaired marker rescue virus (73.MR), a phenotype that correlated with enhanced kinetics of viral gene expression and increased activation of p53. Notably, augmented cell death, viral gene expression, and p53 induction were independent of viral DNA replication. Expression of a mLANA-GFP fusion protein in fibroblasts correlated with both reduced p53 stabilization and reduced cell death following treatment with p53-inducing agonists. In agreement, accentuated cell death associated with 73.Stop infection was reduced in p53-deficient murine embryonic fibroblasts. Additionally, replication of 73.Stop in p53-deficient cells was restored to levels comparable to those of 73.MR. More remarkably, the absence of p53 led to an overall delay in replication for both 73.Stop and 73.MR viruses, which correlated with delayed viral gene expression, indicating a role for p53 in MHV68 replication. Consistent with these findings, the expression of replication-promoting viral genes was positively influenced by p53 overexpression or treatment with the p53 agonist etoposide. Overall, these data demonstrate the importance of mLANA in MHV68 replication and suggest that LANA proteins limit the induction of cellular stress responses to regulate the viral gene expression cascade and limit host cell injury.
Hepatitis B Virus Replication Is Associated with an HBx-Dependent Mitochondrion-Regulated Increase in Cytosolic Calcium Levels
Authors: McClain Stephanie L. , Clippinger Amy J. , Lizzano Rebecca , Bouchard Michael J. 
Published: August 2007

ABSTRACT
The nonstructural hepatitis B virus (HBV) protein HBx has an important role in HBV replication and in HBV-associated liver disease. Many activities have been linked to HBx expression; however, the molecular mechanisms underlying many of these activities are unknown. One proposed HBx function is the regulation of cytosolic calcium. We analyzed calcium levels in HepG2 cells that expressed HBx or replicating HBV, and we demonstrated that HBx, expressed in the absence of other HBV proteins or in the context of HBV replication, elevates cytosolic calcium. We linked this elevation of cytosolic calcium to the association of HBx with the mitochondrial permeability transition pore.
Disease Duration Determines Canine Distemper Virus Neurovirulence
Authors: Bonami François , Rudd Penny A. , von Messling Veronika 
Published: August 2007

ABSTRACT

The
Morbillivirus
hemagglutinin (H) protein mediates attachment to the target cell. To evaluate its contribution to canine distemper virus neurovirulence, we exchanged the H proteins of the wild-type strains 5804P and A75 and assessed the pathogenesis of the chimeric viruses in ferrets. Both strains are lethal to ferrets; however, 5804P causes a 2-week disease without neurological signs, whereas A75 is associated with a longer disease course and neurological involvement. We observed that both H proteins supported neuroinvasion and the subsequent development of clinical neurological signs if given enough time, demonstrating that disease duration is the main neurovirulence determinant.
Role for Amino Acids
212
KLR
214
of Ebola Virus VP40 in Assembly and Budding
Authors: McCarthy Sarah E. , Johnson Reed F. , Zhang Yong-An , Sunyer J. Oriol , Harty Ronald N. 
Published: August 2007

ABSTRACT

Ebola virus VP40 is able to produce virus-like particles (VLPs) in the absence of other viral proteins. At least three domains within VP40 are thought to be required for efficient VLP release: the late domain (L-domain), membrane association domain (M-domain), and self-interaction domain (I-domain). While the L-domain of Ebola VP40 has been well characterized, the exact mechanism by which VP40 mediates budding through the M- and I-domains remains unclear. To identify additional domains important for VP40 assembly/budding, amino acids
212
KLR
214
were targeted for mutagenesis based on the published crystal structure of VP40. These residues are part of a loop connecting two beta sheets in the C-terminal region and thus are potentially important for overall structure and/or oligomerization of VP40. A series of alanine substitutions were generated in the KLR region of VP40, and these mutants were examined for VLP budding, intracellular localization, and oligomerization. Our results indicated that (i)
212
KLR
214
residues of VP40 are important for efficient release of VP40 VLPs, with Leu213 being the most critical; (ii) VP40 KLR mutants displayed altered patterns of cellular localization compared to that of wild-type VP40 (VP40-WT); and (iii) self-assembly of VP40 KLR mutants into oligomers was altered compared to that of VP40-WT. These results suggest that
12
KLR
214
residues of VP40 are important for proper assembly/oligomerization of VP40 which subsequently leads to efficient budding of VLPs.
Cross-Priming of Cytotoxic T Cells Dictates Antigen Requisites for Modified Vaccinia Virus Ankara Vector Vaccines
Authors: Gasteiger Georg , Kastenmuller Wolfgang , Ljapoci Ronny , Sutter Gerd , Drexler Ingo 
Published: August 2007

ABSTRACTRecombinant vaccines based on modified vaccinia virus Ankara (MVA) have an excellent record concerning safety and immunogenicity and are currently being evaluated in numerous clinical studies for immunotherapy of infectious diseases and cancer. However, knowledge about the biological properties of target antigens to efficiently induce MVA vaccine-mediated immunity in vivo is sparse. Here, we examined distinct antigen presentation pathways and different antigen formulations contained in MVA vaccines for their capability to induce cytotoxic CD8+T-cell (CTL) responses. Strikingly, we found that CTL responses against MVA-produced antigens were dominated by cross-priming in vivo, despite the ability of the virus to efficiently infect professional antigen-presenting cells such as dendritic cells. Moreover, stable mature protein was preferred to preprocessed antigen as the substrate for cross-priming. Our data are essential for improved MVA vaccine design, as they demonstrate the need for optimal adjustment of the target antigen properties to the intrinsic requirements of the delivering vector system.
Pol-Specific CD8
+
T Cells Recognize Simian Immunodeficiency Virus-Infected Cells Prior to Nef-Mediated Major Histocompatibility Complex Class I Downregulation
Authors: Sacha Jonah B. , Chung Chungwon , Reed Jason , Jonas Anna K. , Bean Alexander T. , Spencer Sean P. , Lee Wonhee , Vojnov Lara , Rudersdorf Richard , Friedrich Thomas C. , Wilson Nancy A. , Lifson Jeffrey D. , Watkins David I. 
Published: August 2007

ABSTRACT

Effective, vaccine-induced CD8
+
T-cell responses should recognize infected cells early enough to prevent production of progeny virions. We have recently shown that Gag-specific CD8
+
T cells recognize simian immunodeficiency virus-infected cells at 2 h postinfection, whereas Env-specific CD8
+
T cells do not recognize infected cells until much later in infection. However, it remains unknown when other proteins present in the viral particle are presented to CD8
+
T cells after infection. To address this issue, we explored CD8
+
T-cell recognition of epitopes derived from two other relatively large virion proteins, Pol and Nef. Surprisingly, infected cells efficiently presented CD8
+
T-cell epitopes from virion-derived Pol proteins within 2 h of infection. In contrast, Nef-specific CD8
+
T cells did not recognize infected cells until 12 h postinfection. Additionally, we show that SIVmac239 Nef downregulated surface major histocompatibility complex class I (MHC-I) molecules beginning at 12 h postinfection, concomitant with presentation of Nef-derived CD8
+
T-cell epitopes. Finally, Pol-specific CD8
+
T cells eliminated infected cells as early as 6 h postinfection, well before MHC-I downregulation, suggesting a previously underappreciated antiviral role for Pol-specific CD8
+
T cells.
Viral Sequence Evolution in Acute Hepatitis C Virus Infection
Authors: Kuntzen Thomas , Timm Joerg , Berical Andrew , Lewis-Ximenez Lia L. , Jones Andrea , Nolan Brian , Schulze zur Wiesch Julian , Li Bin , Schneidewind Arne , Kim Arthur Y. , Chung Raymond T. , Lauer Georg M. , Allen Todd M. 
Published: August 2007

ABSTRACT

CD8
+
-T-cell responses play an important role in the containment and clearance of hepatitis C virus (HCV) infection, and an association between viral persistence and development of viral escape mutations has been postulated. While escape from CD8
+
-T-cell responses has been identified as a major driving force for the evolution of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV), a broader characterization of this relationship is needed in HCV infection. To determine the extent, kinetics, and driving forces of HCV sequence evolution, we sequenced the entire HCV genome longitudinally in four subjects monitored for up to 30 months after acute infection. For two subjects the transmission sources were also available. Of 53 total nonenvelope amino acid substitutions detected, a majority represented forward mutations away from the consensus sequence. In contrast to studies in HIV and SIV, however, only 11% of these were associated with detectable CD8
+
T-cell responses. Interestingly, 19% of nonenvelope mutations represented changes toward the consensus sequence, suggesting reversion in the absence of immune pressure upon transmission. Notably, the rate of evolution of forward and reverse mutations correlated with the conservation of each residue, which is indicative of structural constraints influencing the kinetics of viral evolution. Finally, the rate of sequence evolution was observed to decline over the course of infection, possibly reflective of diminishing selection pressure by dysfunctional CD8
+
T cells. Taken together, these data provide insight into the extent to which HCV is capable of evading early CD8
+
T-cell responses and support the hypothesis that dysfunction of CD8
+
T cells may be associated with failure to resolve HCV infections.
The Formation of Viroplasm-Like Structures by the Rotavirus NSP5 Protein Is Calcium Regulated and Directed by a C-Terminal Helical Domain
Authors: Sen Adrish , Sen Nandini , Mackow Erich R. 
Published: August 2007

ABSTRACT
The rotavirus NSP5 protein directs the formation of viroplasm-like structures (VLS) and is required for viroplasm formation within infected cells. In this report, we have defined signals within the C-terminal 21 amino acids of NSP5 that are required for VLS formation and that direct the insolubility and hyperphosphorylation of NSP5. Deleting C-terminal residues of NSP5 dramatically increased the solubility of N-terminally tagged NSP5 and prevented NSP5 hyperphosphorylation. Computer modeling and analysis of the NSP5 C terminus revealed the presence of an amphipathic α-helix spanning 21 C-terminal residues that is conserved among rotaviruses. Proline-scanning mutagenesis of the predicted helix revealed that single-amino-acid substitutions abolish NSP5 insolubility and hyperphosphorylation. Helix-disrupting NSP5 mutations also abolished localization of green fluorescent protein (GFP)-NSP5 fusions into VLS and directly correlate VLS formation with NSP5 insolubility. All mutations introduced into the hydrophobic face of the predicted NSP5 α-helix disrupted VLS formation, NSP5 insolubility, and the accumulation of hyperphosphorylated NSP5 isoforms. Some NSP5 mutants were highly soluble but still were hyperphosphorylated, indicating that NSP5 insolubility was not required for hyperphosphorylation. Expression of GFP containing the last 68 residues of NSP5 at its C terminus resulted in the formation of punctate VLS within cells. Interestingly, GFP-NSP5-C68 was diffusely dispersed in the cytoplasm when calcium was depleted from the medium, and after calcium resupplementation GFP-NSP5-C68 rapidly accumulated into punctate VLS. A potential calcium switch, formed by two tandem pseudo-EF-hand motifs (DxDxD), is present just upstream of the predicted α-helix. Mutagenesis of either DxDxD motif abolished the regulatory effect of calcium on VLS formation and resulted in the constitutive assembly of GFP-NSP5-C68 into punctate VLS. These results reveal specific residues within the NSP5 C-terminal domain that direct NSP5 hyperphosphorylation, insolubility, and VLS formation in addition to defining residues that constitute a calcium-dependent trigger of VLS formation. These studies identify functional determinants within the C terminus of NSP5 that regulate VLS formation and provide a target for inhibiting NSP5-directed VLS functions during rotavirus replication.