bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of Genomic Island 3 and Genetic Variability of Chilean Field Strains of Brucella abortus
Authors: Céspedes Sandra , Salgado Paulina , Valenzuela Patricio , Vidal Roberto , Oñate Angel A. 
Published: May 2011

ABSTRACT

One of the capabilities developed by bacteria is the ability to gain large fragments of DNA from other bacteria or to lose portions of their own genomes. Among these exchangeable fragments are the genomic islands (GIs). Nine GIs have been identified in
Brucella
, and genomic island 3 (GI-3) is shared by two pathogenic species,
B. melitensis
and
B. abortus
. GI-3 encodes mostly unknown proteins. One of the aims of this study was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of
B. abortus
from Chile to determine whether these isolates are clonally related. Furthermore, we focused on the characterization of GI-3, studying its organization and the genetic conservation of the GI-3 sequence using techniques such as tiling-path PCR (TP-PCR) and restriction fragment length polymorphism-PCR (RFLP-PCR). Our results, after PFGE was performed on 69 field isolates of
B. abortus
from Chile, showed that the strains were genetically homogeneous. To increase the power of genetic discrimination among these strains, we used multiple locus variable-number tandem-repeat (VNTR) analysis with 16 loci (MLVA-16). The results obtained by MLVA-16 showed that the strains of
B. abortus
were genetically heterogeneous and that most of them clustered according to their geographic origin. Of the genetic loci studied, panel 2B was the one describing the highest diversity in the analysis, as well as locus Bruce19 in panel 2A. In relation to the study of GI-3, our experimental analysis by TP-PCR identified and confirmed that GI-3 is present in all wild strains of
B. abortus
, demonstrating the high stability of gene cluster GI-3 in Chilean field strains.
Comparative Evaluation of Three Commercial Identification Systems Using Common and Rare Bloodstream Yeast Isolates
Authors: Meletiadis Joseph , Arabatzis Michael , Bompola Maria , Tsiveriotis Konstantinos , Hini Stavroula , Petinaki Efthymia , Velegraki Aristea , Zerva Loukia 
Published: May 2011

ABSTRACT
The commercial yeast identification systems API ID32C, Auxacolor, and Vitek were evaluated using 251 molecularly identified bloodstream isolates and 2 reference strains, representing a total of 35 species (6 common and 29 rare). Correct identification rates were higher for common species (Auxacolor, 95%; API ID32C, 94%; Vitek, 92%) than for rare species (Auxacolor, 43%; API ID32C, 56%; Vitek, 64%). All systems performed equally among the former, and Vitek performed best among the latter.
Prospective Study of Congenital Toxoplasmosis Screening with Use of IgG Avidity and Multiplex Nested PCR Methods
Authors: Yamada Hideto , Nishikawa Akira , Yamamoto Tomohiro , Mizue Yuka , Yamada Takashi , Morizane Mayumi , Tairaku Shinya , Nishihira Jun 
Published: May 2011

ABSTRACT

Acute infection with
Toxoplasma gondii
during pregnancy can cause congenital toxoplasmosis. The aim of this study was to evaluate whether screening with the use of IgG avidity and multiplex nested PCR methods was effective to detect a high-risk pregnancy. In a prospective study, serum
T. gondii
IgG avidity was measured in consecutive 146 pregnant women testing positive for
T. gondii
antibody and either positive or equivocal for IgM. Multiplex nested PCR for
T. gondii
DNA on amniotic fluid, maternal blood, and umbilical cord blood were performed with informed consent. A total of 51 (34.9%) women presented with low IgG avidity (<30%), 15 (10.3%) presented with borderline avidity (30 to 35%), and 80 (54.8%) presented with high avidity (>35%) indices. Amniotic fluid obtained at amniocentesis or birth yielded positive PCR results in nine women with low IgG avidity indices. Of these nine women, three had congenital toxoplasmosis. None of women with high or border line IgG avidity indices had a positive PCR result in the amniotic fluid or congenital toxoplasmosis. No congenital toxoplasmosis was detected in women whose amniotic fluids yielded negative PCR results. Ingestion of raw or undercooked meat was found to be the main risk factor for acute
T. gondii
infection. Congenital toxoplasmosis screening with a combination of IgG avidity in the maternal blood and multiplex nested PCR in the amniotic fluid was useful for detecting a high risk pregnancy and diagnosing congenital toxoplasmosis.
Avidity Index for Anti-HIV Antibodies: Comparison between Third- and Fourth-Generation Automated Immunoassays
Authors: Suligoi Barbara , Rodella Anna , Raimondo Mariangela , Regine Vincenza , Terlenghi Luigina , Manca Nino , Casari Salvatore , Camoni Laura , Salfa Maria Cristina , Galli Claudio 
Published: May 2011

ABSTRACT

The development of assays for detecting recent HIV infections has become crucial for analyzing trends in infection in different populations, both for surveillance and prevention activities. The anti-HIV avidity index (AI), measured with third-generation immunoassays (which detect anti-HIV antibody), has been shown to be an accurate tool for discriminating recent HIV infections (<6 months) from established infections (≥6 months). We compared a third-generation immunoassay (AxSYM HIV 1/2 gO; Abbott Diagnostics) to a fourth-generation immunoassay (Architect HIV Ag/Ab Combo; Abbott Diagnostics; which detects anti-HIV antibody and p24 antigen) in terms of AI performance in distinguishing between recent and established HIV infections. A total of 142 samples from 75 HIV-infected individuals with an estimated date of seroconversion were assayed. The two assays showed the same accuracy in identifying a recent infection (91.5%), using an AI cutoff of 0.80, although Architect HIV Ag/Ab Combo was slightly more sensitive (89.4% versus 84.8%;
P
> 0.05) and yet less specific (93.4% versus 97.4%;
P
> 0.05). The correlation between assays was high (
r
= 0.87). When 20 specimens falling in the gray zone around the cutoff point (0.75 ≤ AI ≤ 0.84) were excluded, the accuracy of AI with Architect HIV Ag/Ab Combo was 94.7%, and the concordance between the two assays was 99.2%. The anti-HIV AI is a serological marker that accurately discriminates recent from established HIV infections. It can be successfully applied on fully automated fourth-generation HIV Ab/Ag immunoassays, which have several advantages, including increased throughput, high reproducibility, no need for specific technical skills, and easy comparability of results obtained in different settings.
Canine Distemper Virus Matrix Protein Influences Particle Infectivity, Particle Composition, and Envelope Distribution in Polarized Epithelial Cells and Modulates Virulence
Authors: Dietzel Erik , Anderson Danielle E. , Castan Alexandre , von Messling Veronika , Maisner Andrea 
Published: May 2011

ABSTRACT
In paramyxoviruses, the matrix (M) protein mediates the interaction between the envelope and internal proteins during particle assembly and egress. In measles virus (MeV), M mutations, such as those found in subacute sclerosing panencephalitis (SSPE) strains, and differences in vaccine and wild-type M proteins can affect the strength of interaction with the envelope glycoproteins, assembly efficiency, and spread. However, the contribution of the M protein to the replication and pathogenesis of the closely related canine distemper virus (CDV) has not been characterized. To this end this, we generated a recombinant wild-type CDV carrying a vaccine strain M protein. The recombinant virus retained the parental growth phenotype in VerodogSLAMtag cells, but displayed an increased particle-to-infectivity ratio very similar to that of the vaccine strain, likely due to inefficient H protein incorporation. Even though infectious virus was released only from the apical surface, consistent with the release polarity of the wild-type CDV strain, envelope protein distribution in polarized epithelial cells reproduced the bipolar pattern seen in vaccine strain-infected cells. Most notably, the chimeric virus was completely attenuated in ferrets and caused only a mild and transient leukopenia, indicating that the differences in particle infectivity and envelope protein sorting mediated by the vaccine M protein contribute importantly to vaccine strain attenuation.
Gene-Specific Contributions to Mumps Virus Neurovirulence and Neuroattenuation
Authors: Sauder Christian J. , Zhang Cheryl X. , Ngo Laurie , Werner Kellie , Lemon Ken , Duprex W. Paul , Malik Tahir , Carbone Kathryn , Rubin Steven A. 
Published: May 2011

ABSTRACT
Mumps virus (MuV) is highly neurotropic and was the leading cause of aseptic meningitis in the Western Hemisphere prior to widespread use of live attenuated MuV vaccines. Due to the absence of markers of virus neuroattenuation and neurovirulence, ensuring mumps vaccine safety has proven problematic, as demonstrated by the occurrence of aseptic meningitis in recipients of certain vaccine strains. Here we examined the genetic basis of MuV neuroattenuation and neurovirulence by generating a series of recombinant viruses consisting of combinations of genes derived from a cDNA clone of the neurovirulent wild-type 88-1961 strain (r88) and from a cDNA clone of the highly attenuated Jeryl Lynn vaccine strain (rJL). Testing of these viruses in rats demonstrated the ability of several individual rJL genes and gene combinations to significantly neuroattenuate r88, with the greatest effect imparted by the rJL nucleoprotein/matrix protein combination. Interestingly, no tested combination of r88 genes, including the nucleoprotein/matrix protein combination, was able to convert rJL into a highly neurovirulent virus, highlighting mechanistic differences between processes involved in neuroattenuation and neurovirulence.
Identification of a Novel Neuropathogenic Theiler's Murine Encephalomyelitis Virus
Authors: Buckwalter Matthew R. , Nga Phan Thi , Gouilh Meriadeg Ar , Fiette Laurence , Bureau Jean-Francois , Laird Melissa E. , Buchrieser Julian , Ozden Simona , Cheval Justine , Eloit Marc , Manuguerra Jean-Claude , Gessain Antoine , Brey Paul T. , Fontanet Arnaud , Albert Matthew L. 
Published: May 2011

ABSTRACT
Theiler's murine encephalitis viruses (TMEV) are divided into two subgroups based on their neurovirulence. Persistent strains resemble Theiler's original viruses (referred to as the TO subgroup), which largely induce a subclinical polioencephalomyelitis during the acute phase of the disease and can persist in the spinal cord of susceptible animals, inducing a chronic demyelinating disease. In contrast, members of the neurovirulent subgroup cause an acute encephalitis characterized by the rapid onset of paralysis and death within days following intracranial inoculation. We report herein the characterization of a novel neurovirulent strain of TMEV, identified using pyrosequencing technology and referred to as NIHE. Complete coverage of the NIHE viral genome was obtained, and it shares <90% nucleotide sequence identity to known TMEV strains irrespective of subgroup, with the greatest sequence variability being observed in genes encoding the leader and capsid proteins. The histopathological analysis of infected brain and spinal cord demonstrate inflammatory lesions and neuronal necrosis during acute infection with no evidence of viral persistence or chronic disease. Intriguingly, genetic analysis indicates the putative expression of the L* protein, considered a hallmark of strains within the persistent subgroup. Thus, the identification and characterization of a novel neurovirulent TMEV strain sharing features previously associated with both subgroups will lead to a deeper understanding of the evolution of TMEV strains and new insights into the determinants of neurovirulence.
HIV Gag-Leucine Zipper Chimeras Form ABCE1-Containing Intermediates and RNase-Resistant Immature Capsids Similar to Those Formed by Wild-Type HIV-1 Gag
Authors: Klein Kevin C. , Reed Jonathan C. , Tanaka Motoko , Nguyen Veronica T. , Giri Samina , Lingappa Jaisri R. 
Published: May 2011

ABSTRACT

During HIV-1 assembly, Gag polypeptides multimerize to form an immature capsid and also package HIV-1 genomic RNA. Assembling Gag forms immature capsids by progressing through a stepwise pathway of assembly intermediates containing the cellular ATPase ABCE1, which facilitates capsid formation. The NC domain of Gag is required for ABCE1 binding, acting either directly or indirectly. NC is also critical for Gag multimerization and RNA binding. Previous studies of GagZip chimeric proteins in which NC was replaced with a heterologous leucine zipper that promotes protein dimerization but not RNA binding established that the RNA binding properties of NC are dispensable for capsid formation
per se
. Here we utilized GagZip proteins to address the question of whether the RNA binding properties of NC are required for ABCE1 binding and for the formation of ABCE1-containing capsid assembly intermediates. We found that assembly-competent HIV-1 GagZip proteins formed ABCE1-containing intermediates, while assembly-incompetent HIV-1 GagZip proteins harboring mutations in residues critical for leucine zipper dimerization did not. Thus, these data suggest that ABCE1 does not bind to NC directly or through an RNA bridge, and they support a model in which dimerization of Gag, mediated by NC or a zipper, results in exposure of an ABCE1-binding domain located elsewhere in Gag, outside NC. Additionally, we demonstrated that immature capsids formed by GagZip proteins are insensitive to RNase A, as expected. However, unexpectedly, immature HIV-1 capsids were almost as insensitive to RNase A as GagZip capsids, suggesting that RNA is not a structural element holding together immature wild-type HIV-1 capsids.
Beta Interferon Controls West Nile Virus Infection and Pathogenesis in Mice
Authors: Lazear Helen M. , Pinto Amelia K. , Vogt Matthew R. , Gale Michael , Diamond Michael S. 
Published: May 2011

ABSTRACT

Studies with mice lacking the common plasma membrane receptor for type I interferon (
IFN-αβR
−
/
−
) have revealed that IFN signaling restricts tropism, dissemination, and lethality after infection with West Nile virus (WNV) or several other pathogenic viruses. However, the specific functions of individual IFN subtypes remain uncertain. Here, using
IFN-β
−
/
−
mice, we defined the antiviral and immunomodulatory function of this IFN subtype in restricting viral infection.
IFN-β
−
/
−
mice were more vulnerable to WNV infection than wild-type mice, succumbing more quickly and with greater overall mortality, although the phenotype was less severe than that of
IFN-αβR
−
/
−
mice. The increased susceptibility of
IFN-β
−
/
−
mice was accompanied by enhanced viral replication in different tissues. Consistent with a direct role for IFN-β in control of WNV replication, viral titers in
ex vivo
cultures of macrophages, dendritic cells, fibroblasts, and cerebellar granule cell neurons, but not cortical neurons, from
IFN-β
−
/
−
mice were greater than in wild-type cells. Although detailed immunological analysis revealed no major deficits in the quality or quantity of WNV-specific antibodies or CD8
+
T cells, we observed an altered CD4
+
CD25
+
FoxP3
+
regulatory T cell response, with greater numbers after infection. Collectively, these results suggest that IFN-β controls WNV pathogenesis by restricting infection in key cell types and by modulating T cell regulatory networks.
Binding Interactions between Soluble HIV Envelope Glycoproteins and Quaternary-Structure-Specific Monoclonal Antibodies PG9 and PG16
Authors: Davenport Thaddeus M. , Friend Della , Ellingson Katharine , Xu Hengyu , Caldwell Zachary , Sellhorn George , Kraft Zane , Strong Roland K. , Stamatatos Leonidas 
Published: May 2011

ABSTRACTPG9 and PG16 are antibodies isolated from a subject infected with HIV-1 and display broad anti-HIV neutralizing activities. They recognize overlapping epitopes, which are preferentially expressed on the membrane-anchored trimeric form of the HIV envelope glycoprotein (Env). PG9 and PG16 were reported not to bind to soluble mimetics of Env. The engineering of soluble Env proteins on which the PG9 and PG16 epitopes are optimally exposed will support efforts to elicit broad anti-HIV neutralizing antibodies by immunization. Here, we identified several soluble gp140 Env proteins that are recognized by PG9 and PG16, and we investigated the molecular details of those binding interactions. The IgG versions of PG9 and PG16 recognize the soluble trimeric gp140 form less efficiently than the corresponding monomeric gp140 form. In contrast, the Fab versions of PG9 and PG16 recognized the monomeric and trimeric gp140 forms with identical binding kinetics and with binding affinities similar to the high binding affinity of the anti-V3 antibody 447D to its epitope. Our data also indicate that, depending on the Env backbone, the interactions of PG9 and PG16 with gp140 may be facilitated by the presence of the gp41 ectodomain and are independent of the proper enzymatic cleavage of gp140 into gp120 and gp41. The identification of soluble Env proteins that express the PG9 and PG16 epitopes and the detailed characterization of the molecular interactions between these two antibodies and their ligands provide important and novel information that will assist in improving the engineering of future Env immunogens.
Canonical NF-κB Activation Is Essential for Epstein-Barr Virus Latent Membrane Protein 1 TES2/CTAR2 Gene Regulation
Authors: Gewurz Benjamin E. , Mar Jessica C. , Padi Megha , Zhao Bo , Shinners Nicholas P. , Takasaki Kaoru , Bedoya Edward , Zou James Y. , Cahir-Mcfarland Ellen , Quackenbush John , Kieff Elliott 
Published: May 2011

ABSTRACT

Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) transforms rodent fibroblasts and is expressed in most EBV-associated malignancies. LMP1 (
t
ransformation
e
ffector
s
ite 2 [TES2]/C-terminal activation region 2 [CTAR2]) activates NF-κB, p38, Jun N-terminal protein kinase (JNK), extracellular signal-regulated kinase (ERK), and interferon regulatory factor 7 (IRF7) pathways. We have investigated LMP1 TES2 genome-wide RNA effects at 4 time points after LMP1 TES2 expression in HEK-293 cells. By using a false discovery rate (FDR) of <0.001 after correction for multiple hypotheses, LMP1 TES2 caused >2-fold changes in 1,916 mRNAs; 1,479 RNAs were upregulated and 437 were downregulated. In contrast to tumor necrosis factor alpha (TNF-α) stimulation, which transiently upregulates many target genes, LMP1 TES2 maintained most RNA effects through the time course, despite robust and sustained induction of negative feedback regulators, such as IκBα and A20. LMP1 TES2-regulated RNAs encode many NF-κB signaling proteins and secondary interacting proteins. Consequently, many LMP1 TES2-regulated RNAs encode proteins that form an extensive interactome. Gene set enrichment analyses found LMP1 TES2-upregulated genes to be significantly enriched for pathways in cancer, B- and T-cell receptor signaling, and Toll-like receptor signaling. Surprisingly, LMP1 TES2 and IκBα superrepressor coexpression decreased LMP1 TES2 RNA effects to only 5 RNAs, with FDRs of <0.001-fold and >2-fold changes. Thus, canonical NF-κB activation is critical for almost all LMP1 TES2 RNA effects in HEK-293 cells and a more significant therapeutic target than previously appreciated.
Identification and Expression Analysis of Herpes B Virus-Encoded Small RNAs
Authors: Amen Melanie A. , Griffiths Anthony 
Published: May 2011

ABSTRACT
Herpes B virus (BV) naturally infects macaque monkeys and is genetically similar to herpes simplex virus (HSV). Zoonotic infection of humans can cause encephalitis and if untreated has a fatality rate of ∼80%. The frequent use of macaques in biomedical research emphasizes the need to understand the molecular basis of BV pathogenesis with a view toward improving safety for those working with macaques. MicroRNAs (miRNAs) are small noncoding RNAs that regulate the expression of mRNAs bearing complementary target sequences and are employed by viruses to control viral and host gene expression. Using deep sequencing and validation by expression in transfected cells, we identified 12 novel BV-encoded miRNAs expressed in lytically infected cells and 4 in latently infected trigeminal ganglia (TG). Using quantitative reverse transcription-PCR (RT-qPCR), we found that most of the miRNAs exhibited a high level of abundance throughout infection. Further analyses showed that some miRNAs could be generated from multiple transcripts with different kinetic classes, possibly explaining detection throughout infection. Interestingly, miRNAs were detected at early times in the absence of viral gene expression and were present in purified virions. In TG, despite similar amounts of viral DNA per ganglion, it was notable that the relative amount of each miRNA varied between ganglia. The majority of the miRNAs are encoded by the regions that exhibit the most sequence differences between BV and HSV. Additionally, there is no sequence conservation between BV- and HSV-encoded miRNAs, which may be important for the differences in the human diseases caused by BV and HSV.
Identification of Amino Acid Residues Important for Heparan Sulfate Proteoglycan Interaction within Variable Region 3 of the Feline Immunodeficiency Virus Surface Glycoprotein
Authors: Hu Qiong-Ying , Fink Elizabeth , Happer Meaghan , Elder John H. 
Published: May 2011

ABSTRACTHeparan sulfate proteoglycans (HSPGs) act as binding receptors or attachment factors for the viral envelope of many viruses, including strains of HIV and feline immunodeficiency virus (FIV). The FIV gp95 glycoprotein (SU) from laboratory-adapted strains (tissue culture adapted [TCA]) such as FIV-34TF10 can bind to HSPG, whereas SU from field strains (FS) such as FIV-PPR cannot. Previous studies indicate that SU-HSPG interactions occur within the V3 loop. We utilized a series of nested V3 peptides to further map the HSPG binding sites and found that both sides of the predicted V3 loop stem were critical for the binding but not the CXCR4 binding domain near the predicted tip of the V3 loop. Neutralization assays for TCA strain entry using the same set of V3 peptides showed that peptides targeting CXCR4 or HSPG binding sites can block infection, supporting the V3 loop as a critical neutralization target. Site-directed mutagenesis identified two highly conserved arginines, R379 and R389, on the N-terminal side of the V3 stem as critical for the contact between SU and HSPG. Residues K407, K409, K410, and K412 on the C-terminal side of the V3 stem form a second nonconserved domain necessary for HSPG binding, consistent with the observed specificity distinctions with FS FIV. Our findings discriminate structural determinants important for HSPG and CXCR4 binding by FIV SU and thus further define the importance of the V3 loop for virus entry and infection.