bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotyping of
Chlamydophila psittaci
by Real-Time PCR and High-Resolution Melt Analysis
Authors: Mitchell Stephanie L. , Wolff Bernard J. , Thacker W. Lanier , Ciembor Paula G. , Gregory Christopher R. , Everett Karin D. E. , Ritchie Branson W. , Winchell Jonas M. 
Published: November 2008

ABSTRACT

Human infection with
Chlamydophila
(
Chlamydia
)
psittaci
can lead to psittacosis, a disease that occasionally results in severe pneumonia and other medical complications.
C. psittaci
is currently grouped into seven avian genotypes: A through F and E/B. Serological testing, outer membrane protein A (
ompA
) gene sequencing, and restriction fragment length polymorphism analysis are currently used for distinguishing these genotypes. Although accurate, these methods are time-consuming and require multiple confirmatory tests. By targeting the
ompA
gene, a real-time PCR assay has been developed to rapidly detect and genotype
C. psittaci
by light-upon-extension chemistry and high-resolution melt analysis. Using this assay, we screened 169 animal specimens; 98 were positive for
C. psittaci
(71.4% genotype A, 3.1% genotype B, 4.1% genotype E, and 21.4% unable to be typed). This test may provide insight into the distribution of each genotype among specific hosts and provide epidemiological and epizootiological data in human and mammalian/avian cases. This diagnostic assay may also have veterinary applications during chlamydial outbreaks, particularly with respect to identifying the sources and tracking the movements of a particular genotype when multiple animal facilities are affected.
Double-Stranded RNA Analog Poly(I:C) Inhibits Human Immunodeficiency Virus Amplification in Dendritic Cells via Type I Interferon-Mediated Activation of APOBEC3G
Authors: Trapp Susanna , Derby Nina R. , Singer Rachel , Shaw Andrew , Williams Vennansha G. , Turville Stuart G. , Bess Julian W. , Lifson Jeffrey D. , Robbiani Melissa 
Published: November 2008

ABSTRACT

Human immunodeficiency virus (HIV) is taken up by and replicates in immature dendritic cells (imDCs), which can then transfer virus to T cells, amplifying the infection. Strategies known to boost DC function were tested for their ability to overcome this exploitation when added after HIV exposure. Poly(I:C), but not single-stranded RNA (ssRNA) or a standard DC maturation cocktail, elicited type I interferon (IFN) and interleukin-12 (IL-12) p70 production and the appearance of unique small (15- to 20-kDa) fragments of APOBEC3G (A3G) and impeded HIV
Bal
replication in imDCs when added up to 60 h after virus exposure. Comparable effects were mediated by recombinant alpha/beta IFN (IFN-α/β). Neutralizing the anti-IFN-α/β receptor reversed poly(I:C)-induced inhibition of HIV replication and blocked the appearance of the small A3G proteins. The poly(I:C)-induced appearance of small A3G proteins was not accompanied by significant differences in A3G mRNA or A3G monomer expression. Small interfering RNA (siRNA) knockdown of A3G could not be used to reverse the poly(I:C)-induced protective effect, since siRNAs nonspecifically activated the DCs, inducing the appearance of the small A3G proteins and inhibiting HIV infection. Notably, the appearance of small A3G proteins coincided with the shift of high-molecular-mass inactive A3G complexes to the low-molecular-mass (LMM) active A3G complexes. The unique immune stimulation by poly(I:C) with its antiviral effects on imDCs marked by the expression of IFN-α/β and active LMM A3G renders poly(I:C) a promising novel strategy to combat early HIV infection in vivo.
Coadministration of Cidofovir and Smallpox Vaccine Reduced Vaccination Side Effects but Interfered with Vaccine-Elicited Immune Responses and Immunity to Monkeypox
Authors: Wei Huiyong , Huang Dan , Fortman Jeff , Wang Richard , Shao Linyun , Chen Zheng W. 
Published: November 2008

ABSTRACTWhile the smallpox vaccine, Dryvax or Dryvax-derived ACAM2000, holds potential for public immunization against the spread of smallpox by bioterror, there is serious concern about Dryvax-mediated side effects. Here, we report that a single-dose vaccination regimen comprised of Dryvax and an antiviral agent, cidofovir, could reduce vaccinia viral loads after vaccination and significantly control Dryvax vaccination side effects. However, coadministration of cidofovir and Dryvax also reduced vaccine-elicited immune responses of antibody and T effector cells despite the fact that the reduced priming could be boosted as a recall response after monkeypox virus challenge. Evaluations of four different aspects of vaccine efficacy showed that coadministration of cidofovir and Dryvax compromised the Dryvax-induced immunity against monkeypox, although the covaccinated monkeys exhibited measurable protection against monkeypox compared to that of naïve controls. Thus, the single-dose coadministration of cidofovir and Dryvax effectively controlled vaccination side effects but significantly compromised vaccine-elicited immune responses and vaccine-induced immunity to monkeypox.
Human Immunodeficiency Virus Type 1 Env Trimer Immunization of Macaques and Impact of Priming with Viral Vector or Stabilized Core Protein
Authors: Mörner Andreas , Douagi Iyadh , Forsell Mattias N. E. , Sundling Christopher , Dosenovic Pia , O'Dell Sijy , Dey Barna , Kwong Peter D. , Voss Gerald , Thorstensson Rigmor , Mascola John R. , Wyatt Richard T. , Karlsson Hedestam Gunilla B. 
Published: November 2008

ABSTRACT

Currently there is limited information about the quality of immune responses elicited by candidate human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env)-based immunogens in primates. Here we describe a comprehensive analysis of neutralizing antibody and T-cell responses obtained in cynomolgus macaques by three selected immunization regimens. We used the previously described YU2-based gp140 protein trimers administered in an adjuvant, preceded by two distinct priming strategies: either alphavirus replicon particles expressing matched gp140 trimers or gp120 core proteins stabilized in the CD4-bound conformation. The rationale for priming with replicon particles was to evaluate the impact of the expression platform on trimer immunogenicity. The stable core proteins were chosen in an attempt to expand selectively lymphocytes recognizing common determinants between the core and trimers to broaden the immune response. The results presented here demonstrate that the platform by which Env trimers were delivered in the priming (either protein or replicon vector) had little impact on the overall immune response. In contrast, priming with stable core proteins followed by a trimer boost strikingly focused the T-cell response on the core sequences of HIV-1 Env. The specificity of the T-cell response was distinctly different from that of the responses obtained in animals immunized with trimers alone and was shown to be mediated by CD4
+
T cells. However, this regimen showed limited or no improvement in the neutralizing antibody responses, suggesting that further immunogen design efforts are required to successfully focus the B-cell response on conserved neutralizing determinants of HIV-1 Env.
A Single Amino Acid Substitution in a Segment of the CA Protein within Gag That Has Similarity to Human Immunodeficiency Virus Type 1 Blocks Infectivity of a Human Endogenous Retrovirus K Provirus in the Human Genome
Authors: Heslin David J. , Murcia Pablo , Arnaud Frederick , Van Doorslaer Koenraad , Palmarini Massimo , Lenz Jack 
Published: November 2008

ABSTRACT

Human endogenous retrovirus K (HERV-K) is the most intact retrovirus in the human genome. However, no single HERV-K provirus in the human genome today appears to be infectious. Since the Gag protein is the central component for the production of retrovirus particles, we investigated the abilities of Gag from two HERV-K proviruses to support production of virus-like particles and viral infectivity. HERV-K113 has full-length open reading frames for all viral proteins, while HERV-K101 has a full-length
gag
open reading frame and is expressed in human male germ cell tumors. The Gag of HERV-K101 allowed production of viral particles and infectivity, although at lower levels than observed with a consensus sequence Gag. Thus, including HERV-K109, at least two HERV-K proviruses in human genome today have functional Gag proteins. In contrast, HERV-K113 Gag supported only very low levels of particle production, and no infectivity was detectable due to a single amino acid substitution (I516M) near the extreme C terminus of the CA protein within Gag. The sequence of this portion of HERV-K CA showed similarities to that of human immunodeficiency virus type 1 and other primate immunodeficiency viruses. The extreme C terminus of CA may be a general determinant of retrovirus particle production. In addition, precise mapping of the defects in HERV-K proviruses as was done here identifies the key polymorphisms that need to be analyzed to assess the possible existence of infectious HERV-K alleles within the human population.
Optimization of Human Immunodeficiency Virus Gag Expression by Newcastle Disease Virus Vectors for the Induction of Potent Immune Responses
Authors: Carnero Elena , Li Wenjing , Borderia Antonio V. , Moltedo Bruno , Moran Thomas , García-Sastre Adolfo 
Published: November 2008

ABSTRACTOne attractive strategy for the development of a human immunodeficiency virus (HIV) vaccine is the use of viral vectors with a proven safety profile and an absence of preexisting immunity in humans, such as Newcastle disease virus (NDV). Several NDV vaccine vectors have been generated, and their immunogenicities have been investigated with different animal models. However, a systematic study to evaluate the optimal insertion site of the foreign antigens into NDV that results in enhanced immune responses specific to the antigen has not yet been conducted. In this article, we describe the ability of NDV expressing HIV Gag to generate a Gag-specific immune response in mice. We also have determined the optimal insertion site into the NDV genome by generating recombinant NDV-HIVGag viruses in which HIVgagwas located at different transcriptional positions throughout the NDV viral genome. All recombinant viruses were viable, grew to similar titers in embryonated chicken eggs, and expressed Gag in a stable manner. Our in vivo experiments revealed that higher HIV Gag protein expression positively correlates with an enhanced CD8+T-cell-mediated immune response and protective immunity against challenge with vaccinia virus expressing HIV Gag. We also inserted a codon-optimized version of HIVgagin the described best location, between the P and M genes. Virus expressing the codon-optimized version of HIVgaginduced a higher expression of the protein and an enhanced immune response against HIV Gag in mice. These results indicate that strategies directed toward increasing antigen expression by NDV result in enhanced immunogenicity and vaccine efficacy.
The Mdm2 Ubiquitin Ligase Enhances Transcriptional Activity of Human Papillomavirus E2
Authors: Gammoh Noor , Gardiol Daniela , Massimi Paola , Banks Lawrence 
Published: November 2008

ABSTRACT
The regulation of human papillomavirus (HPV) gene expression by the E2 protein is a critical feature of the viral life cycle. Previous studies have shown an important role in transcription for the ubiquitin-proteasome pathway, but its role in HPV gene expression has not been addressed. We now show that HPV E2 requires an active proteasome for its optimal transcriptional activator function. This involves an interaction with the Mdm2 ubiquitin ligase, which together with E2 acts synergistically to activate the HPV type 16 promoter. We also show that HPV E2 recruits Mdm2 onto HPV promoter sequences, providing an explanation for this cooperative activity.
African Swine Fever Virus Blocks the Host Cell Antiviral Inflammatory Response through a Direct Inhibition of PKC-θ-Mediated p300 Transactivation
Authors: Granja Aitor G. , Sánchez Elena G. , Sabina Prado , Fresno Manuel , Revilla Yolanda 
Published: November 2008

ABSTRACTDuring a viral infection, reprogramming of the host cell gene expression pattern is required to establish an adequate antiviral response. The transcriptional coactivators p300 and CREB binding protein (CBP) play a central role in this regulation by promoting the assembly of transcription enhancer complexes to specific promoters of immune and proinflammatory genes. Here we show that the protein A238L encoded by African swine fever virus counteracts the host cell inflammatory response through the control of p300 transactivation during the viral infection. We demonstrate that A238L inhibits the expression of the inflammatory regulators cyclooxygenase-2 (COX-2) and tumor necrosis factor alpha (TNF-α) by preventing the recruitment of p300 to the enhanceosomes formed on their promoters. Furthermore, we report that A238L inhibits p300 activity during the viral infection and that its amino-terminal transactivation domain is essential in the A238L-mediated inhibition of the inflammatory response. Importantly, we found that the residue serine 384 of p300 is required for the viral protein to accomplish its inhibitory function and that ectopically expressed PKC-θ completely reverts this inhibition, thus indicating that this signaling pathway is disrupted by A238L during the viral infection. Furthermore, we show here that A238L does not affect PKC-θ enzymatic activity, but the molecular mechanism of this viral inhibition relies on the lack of interaction between PKC-θ and p300. These findings shed new light on how viruses alter the host cell antiviral gene expression pattern through the blockade of the p300 activity, which represents a new and sophisticated viral mechanism to evade the inflammatory and immune defense responses.
The C-Terminal Domains of Adenovirus Serotype 5 Protein IX Assemble into an Antiparallel Structure on the Facets of the Capsid
Authors: Fabry Céline M. S. , Rosa-Calatrava Manuel , Moriscot Christine , Ruigrok Rob W. H. , Boulanger Pierre , Schoehn Guy 
Published: November 2008

ABSTRACT
Adenovirus serotype 5 protein IX (pIX) has two domains connected by a flexible linker. Three N-terminal domains form triskelions on the capsid facets that cement hexons together, and the C-terminal domains of four monomers form complexes toward the facet periphery. Here we present a cryoelectron microscopy structure of recombinant adenovirus with a peptide tag added to the C terminus of pIX. The structure, made up by several C termini of pIX, is longer at both ends than the wild-type protein, and Fabs directed against the tag bind to both ends of the oligomer, demonstrating that the pIX C termini associate in an antiparallel manner.
Structural Plasticity and Rapid Evolution in a Viral RNA Revealed by In Vivo Genetic Selection
Authors: Guo Rong , Lin Wai , Zhang Jiuchun , Simon Anne E. , Kushner David B. 
Published: November 2008

ABSTRACT

Satellite RNAs usually lack substantial homology with their helper viruses. The 356-nucleotide satC of Turnip crinkle virus (TCV) is unusual in that its 3′-half shares high sequence similarity with the TCV 3′ end. Computer modeling, structure probing, and/or compensatory mutagenesis identified four hairpins and three pseudoknots in this TCV region that participate in replication and/or translation. Two hairpins and two pseudoknots have been confirmed as important for satC replication. One portion of the related 3′ end of satC that remains poorly characterized corresponds to juxtaposed TCV hairpins H4a and H4b and pseudoknot ψ
3
, which are required for the TCV-specific requirement of translation (V. A. Stupina et al., RNA 14:2379-2393, 2008). Replacement of satC H4a with randomized sequence and scoring for fitness in plants by in vivo genetic selection (SELEX) resulted in winning sequences that contain an H4a-like stem-loop, which can have additional upstream sequence composing a portion of the stem. SELEX of the combined H4a and H4b region in satC generated three distinct groups of winning sequences. One group models into two stem-loops similar to H4a and H4b of TCV. However, the selected sequences in the other two groups model into single hairpins. Evolution of these single-hairpin SELEX winners in plants resulted in satC that can accumulate to wild-type (wt) levels in protoplasts but remain less fit in planta when competed against wt satC. These data indicate that two highly distinct RNA conformations in the H4a and H4b region can mediate satC fitness in protoplasts.
The Response of a Stochastically Forced ENSO Model to Observed Off-Equatorial Wind Stress Forcing
Authors: McGregor Shayne , Holbrook Neil J. , Power Scott B. 
Published: November 2008

AbstractThis study investigates the response of a stochastically forced coupled atmosphere–ocean model of the equatorial Pacific to off-equatorial wind stress anomaly forcing. The intermediate-complexity coupled ENSO model comprises a linear, first baroclinic mode, ocean shallow water model with a steady-state, two–pressure level (250 and 750 mb) atmospheric component that has been linearized about a state of rest on the β plane. Estimates of observed equatorial region stochastic forcing are calculated from NCEP–NCAR reanalysis surface winds for the period 1950–2006 using singular value decomposition. The stochastic forcing is applied to the model both with and without off-equatorial region wind stress anomalies (i.e., poleward of 12.5° latitude). It is found that the multiyear changes in the equatorial Pacific thermocline depth “background state” induced by off-equatorial forcing can affect the amplitude of modeled sea surface temperature anomalies by up to 1°C. Moreover, off-equatorial wind stress anomalies increased the modeled amplitude of the two biggest El Niño events in the twentieth century (1982/83 and 1997/98) by more than 0.5°C, resulting in a more realistic modeled response. These equatorial changes driven by off-equatorial region wind stress anomalies are highly predictable to two years in advance and may be useful as a physical basis to enhance multiyear probabilistic predictions of ENSO indices.
How Early Can Fetal Heart Pulsations Be Detected Reliably Using Modern Ultrasound Equipment?
Authors: Ramsey Elisabeth , Shilitto Jayne 
Published: November 2008

Background: Current national guidelines for the use of ultrasound in early pregnancy state that the embryonic heartbeat should be identified when the embryo measures 6 mm in length (RCOG/RCR 1995). Failure to visualise heart pulsations in embryos measuring 6 mm or less requires patients to wait 7 days for a repeat scan. Anecdotally, there is evidence to suggest that it is usually possible to see embryonic heart pulsation much earlier using modern ultrasound equipment. The aim of this study was to identify the smallest length of embryo when it is possible to always visualise heart pulsations during an ultrasound examination. Method: This was a prospective observational study of women attending the early pregnancy unit of a large teaching hospital. Women were invited to participate when a clinically indicated ultrasound examination revealed an intrauterine pregnancy with an embryo measuring 6 mm or less. All women were symptomatic, i.e. they presented with pain and/or bleeding in early pregnancy. The presence or absence of discernible embryonic cardiac activity was recorded at the initial ultrasound examination, and any follow-up ultrasound examination, along with the crown rump length (CRL) of the embryo. Results: The study sample consisted of 95 embryos with CRL range 1·2–6 mm. Visible heart pulsations were seen in 80 (84%) embryos at the initial examination. In 15 embryos, no discernible heart pulsation was noted; in all 15 cases, these pregnancies went on to miscarry: this was confirmed at a follow-up examination 7 days later. Conclusion: In early pregnancy ultrasound, cardiac activity should be visualized in all live embryos as soon as the embryo can be identified reliably. The absence of heart pulsations in very small embryos is indicative of pregnancy demise, regardless of the actual size of the embryo.
Protein disulfide isomerases are antibody targets during immune-mediated tumor destruction
Authors: Fonseca Catia , Soiffer Robert , Ho Vincent , Vanneman Matthew , Jinushi Masahisa , Ritz Jerome , Neuberg Donna , Stone Richard , DeAngelo Dan , Dranoff Glenn 
Published: November 2008

Abstract
The identification of cancer antigens that contribute to transformation and are linked with immune-mediated tumor destruction is an important goal for immunotherapy. Toward this end, we screened a murine renal cell carcinoma cDNA expression library with sera from mice vaccinated with irradiated tumor cells engineered to secrete granulocyte macrophage colony-stimulating factor (GM-CSF). Multiple nonmutated, overexpressed proteins that function in tumor cell migration, protein/nucleic acid homeostasis, metabolism, and stress responses were detected. Among these, the most frequently recognized clone was protein disulfide isomerase (PDI). High titer antibodies to human PDI were similarly induced in an acute myeloid leukemia patient who achieved a complete response after vac-cination with irradiated, autologous GM-CSF–secreting tumor cells in the setting of nonmyeloablative allogeneic bone marrow transplantation. Moreover, ERp5, a closely related disulfide isomerase involved in major histocompatibility complex (MHC) class I chain-related protein A (MICA) shedding, also evoked potent humoral reactions in diverse solid and hematologic malignancy patients who responded to GM-CSF–secreting tumor cell vaccines or antibody blockade of cytotoxic T lymphocyte–associated antigen 4 (CTLA-4). Together, these findings reveal the unexpected immunogenicity of PDIs and raise the possibility that these gene products might serve as targets for therapeutic monoclonal antibodies.
Altered levels of cytokines and inflammatory mediators in plasma and leukocytes of sickle cell anemia patients and effects of hydroxyurea therapy
Authors: Lanaro C , Franco-Penteado C F , Albuqueque D M , Saad S T O , Conran N , Costa F F 
Published: November 2008

AbstractInflammation, cell adhesion to vascular endothelium, and endothelial injury contribute to sickle cell anemia (SCA) vaso-occlusion. Although alterations in inflammatory cytokines and biomarkers have been related, reports have been conflicting, and a conclusive role for these molecules in the disease remains to be established. Furthermore, the effect of hydroxyurea therapy (HU) on the release of inflammatory mediators is not understood. This study aimed to determine plasma levels and leukocyte gene expressions of inflammatory mediators in healthy controls, steady-state SCA patients, and SCA patients on HU therapy. TNF-α, IL-8, and PGE2 levels were significantly higher in the plasma of SCA individuals when compared with control individuals. HU therapy was associated with a significant reversal of augmented TNF-α and, interestingly, increased plasma anti-inflammatory IL-10. IFN-γ, IL-10, cyclooxygenase 2 (COX-2), and inducible NO synthase (iNOS) gene expressions were unaltered in SCA mononuclear cells (MC); however, gene expressions of TNF-α, IL-8, and the protective enzyme heme oxygenase-1 (HO-1) were significantly higher. HU therapy was not associated with significantly altered SCA MC inflammatory gene expression, although COX-2 mRNA expression was decreased. In SCA neutrophils, gene expressions of IL-8, IFN-γ, iNOS, and HO-1 were significantly higher than those of control subjects. Patients on HU demonstrated lower iNOS and higher IL-10 neutrophil gene expressions. Taken together, data suggest that alterations in the gene expressions and productions of a number of pro- and anti-inflammatory mediators are present in SCA and importantly, in those patients on HU therapy. Knowledge of these pathways may contribute to further the understanding of the pathophysiology of this disease.