bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analytical and Biological Considerations in the Measurement of Cell-Associated CCR5 and CXCR4 mRNA and Protein
Authors: Campbell D. E. , Lai J. P. , Tustin N. B. , Riedel E. , Tustin R. , Taylor J. , Murray J. , Douglas S. D. 
Published: May 2010

ABSTRACT
The accurate measurement of T cell-associated CC chemokine receptor type 5 (CCR5) and CXC chemokine receptor type 4 (CXCR4) expression, including expression of CCR5 and CXCR4 mRNA as an immune measure of immunologic response to highly active antiretroviral therapy (HAART) and newer agents, including entry inhibitors, is essential. Previous studies have reported alterations in lymphocyte cell membrane CCR5 expression that were related to blood collection and cell separation media. Clinical trials often require the transport of specimens to central laboratories for evaluation, resulting in significant time delays between specimen procurement and analysis. This study shows that CCR5 expression on naïve and memory T cells is influenced by blood collection media and specimen age. Peripheral blood collected in Streck Vacutainer tubes containing a cell stabilizer and fixative was found to improve detection of CCR5 expression compared to specimens collected in K2 EDTA anticoagulant. The selection of flow cytometry gating strategies for the identification of naïve and memory T-helper cells can also significantly influence the sensitivity of detection of CCR5 expression. Procedural methods are described that allow for the optimal measurement of naïve and memory T-helper cell CCR5 and CXCR4 expression as well as the quantitation of CCR5 and CXCR4 mRNA.
Multicenter Study of Clinical Performance of the 3M Rapid Detection RSV Test
Authors: Ginocchio Christine C. , Swierkosz Ella , McAdam Alexander J. , Marcon Mario , Storch Gregory A. , Valsamakis Alexandra , Juretschko Stefan , Romero José , Yen-Lieberman Belinda 
Published: May 2010

ABSTRACT

This multicenter study evaluated the clinical performance of the 3M Rapid Detection RSV test (3MRSV) compared to a composite reference standard of R-Mix culture and direct specimen immunofluorescence for detection of respiratory syncytial virus (RSV). The performance of the BinaxNOW RSV test was also evaluated using this reference standard. In a secondary analysis, discordant results were arbitrated using the Gen-Probe/Prodesse ProFlu+ reverse transcription-PCR (RT-PCR) assay. Subjects were stratified into three groups as follows: group 1 (G1), all ages; G2, subjects <22 years old (FDA-cleared ages for 3MRSV testing); and G3, subjects <5 years old (FDA-cleared ages for BinaxNOW RSV testing). A total of 1,306 specimens (G1,
n
= 1,306; G2,
n
= 1,140; G3,
n
= 953) from subjects of all ages presenting with respiratory symptoms met study criteria for analysis. Sensitivities, specificities, positive predictive values, and negative predictive values of 3MRSV for G1 were 86.5%, 95.8%, 91.4%, and 93.2%, respectively, and those for G2 were 87.3%, 95.6%, 92.4%, and 92.5%, respectively. For those samples analyzed by both 3MRSV and BinaxNOW, the 3MRSV was more sensitive (G1, 86.3%; G2, 87.2%; and G3, 89.9%) than was BinaxNOW (G1, 70.84%; G2, 72.0%; and G3, 72.4%) (
P
< 0.05). Specificities for RSV detection from nasopharyngeal (NP) aspirates and NP swabs for all groups were comparable for 3MRSV and BinaxNOW, but 3MRSV was less specific than BinaxNOW when nasal washes/aspirates were tested (
P
< 0.05). The 3MRSV assay performed well for the detection of RSV, and the overall assay performance was superior to that of BinaxNOW. The 3MRSV reader eliminated user misinterpretation and provided test result and quality control documentation.
Phylogenetic Analysis of Rubella Viruses Involved in Congenital Rubella Infections in France between 1995 and 2009
Authors: Vauloup-Fellous Christelle , Hübschen Judith M. , Abernathy Emily S. , Icenogle Joseph , Gaidot Nicolas , Dubreuil Pascal , Parent-du-Châtelet Isabelle , Grangeot-Keros Liliane , Muller Claude P. 
Published: May 2010

ABSTRACT

Rubella is an acute infectious disease that normally has a mild clinical course. However, infections during pregnancy, especially before week 12 of gestation (WG), can cause severe birth defects known as congenital rubella syndrome (CRS). The aim of this study was to perform genotyping and molecular characterization of rubella viruses involved in congenital infections in France over the past 15 years (1995 to 2009). Amniotic fluid (AF) specimens (
n
= 80) from pregnant women with congenital rubella infections (CRI) before week 20 of gestation, and a few other samples available from children/newborns with CRS (
n
= 26), were analyzed. The coding region of the rubella virus E1 gene was amplified directly from clinical specimens by reverse transcriptase PCR, and the resulting DNA fragments were sequenced. Sequences were assigned to genotypes by phylogenetic analysis with rubella virus reference sequences. Sufficient E1 gene sequences were obtained from 56 cases. Phylogenetic analysis of the sequences showed that at least five different genotypes (1E, 1G, 1B, 2B, and 1h) were present in France and were involved in congenital infections, with a strong predominance of genotype 1E (87%). This is one of the very few comprehensive studies of rubella viruses involved in CRI. The results indicated that over the past 15 years, multiple introductions of the dominant genotype E caused most of the CRI cases in France. A few sporadic cases were due to other genotypes (1B, 1G, 1h, 2B).
Salmonella enterica
Serovar Virchow Bacteremia Presenting as Typhoid-Like Illness in an Immunocompetent Patient
Authors: Eckerle Isabella , Zimmermann Stefan , Kapaun Annette , Junghanss Thomas 
Published: May 2010

ABSTRACT

We report a typhoid-like illness with fever and altered consciousness in a 22-year-old man with growth of
Salmonella enterica
serovar Virchow in blood and stool culture. Bacteremia and invasive disease due to non-typhoid salmonellae (NTS) are known in severely immunocompromised patients, but so far have not been described in immunocompetent adults.
Correlation of Parasite Load Determined by Quantitative PCR to Clinical Outcome in a Heart Transplant Patient with Disseminated Toxoplasmosis
Authors: Patrat-Delon Solène , Gangneux Jean-Pierre , Lavoué Sylvain , Lelong Bernard , Guiguen Claude , le Tulzo Yves , Robert-Gangneux Florence 
Published: May 2010

ABSTRACTDisseminated toxoplasmosis is a life-threatening infection in transplant recipients, which results either from reactivation of latent infection or from organ-transmitted primary infection. Preventive measures and diagnostic screening methods differ between countries and are related to the seroprevalence ofToxoplasmaspp. in the general population. Here we report a case of disseminated toxoplasmosis in a heart transplant recipient with previous immunity that occurred after cotrimoxazole prophylaxis for the prevention ofPneumocystis jiroveciipneumonia was stopped. Quantitative PCR proved useful for the diagnosis and monitoring ofToxoplasmainfection. Decreasing parasitic burdens in sequential samples of cerebrospinal fluid, blood, and bronchoalveolar lavage fluid correlated with a favorable outcome and allowed modulation of the immunosuppressive drug regimen. The duration of anti-Toxoplasmatreatment and the need for maintenance prophylaxis are discussed, as well as prophylaxis for solid-organ transplant recipients. Although a rare event in heart transplant recipients,Toxoplasmareactivation must be investigated promptly, since early treatment improves the prognosis.
In Vivo
Acquisition of a Plasmid-Mediated
bla
KPC-2
Gene among Clonal Isolates of
Serratia marcescens
Authors: Tsakris Athanassios , Voulgari Evangelia , Poulou Aggeliki , Kimouli Maria , Pournaras Spyros , Ranellou Kyriaki , Kosmopoulou Olga , Petropoulou Dimitra 
Published: May 2010

ABSTRACT

Three patients admitted to a Greek hospital were infected with
Serratia marcescens
isolates that exhibited reduced susceptibility to carbapenems and harbored
Klebsiella pneumoniae
carbapenemase (KPC) enzymes. In two of these cases, the patients were initially infected by carbapenem-susceptible
S. marcescens
isolates. Molecular typing and plasmid analysis suggested that all three patients had clonally indistinguishable isolates of
S. marcescens
that acquired a plasmid-mediated
bla
KPC-2
gene during the hospitalization.
Pepscan Mapping of Viral Hemorrhagic Septicemia Virus Glycoprotein G Major Lineal Determinants Implicated in Triggering Host Cell Antiviral Responses Mediated by Type I Interferon
Authors: Chico V. , Martinez-Lopez A. , Ortega-Villaizan M. , Falco A. , Perez L. , Coll J. M. , Estepa A. 
Published: May 2010

ABSTRACT

Surface glycoproteins of enveloped virus are potent elicitors of type I interferon (IFN)-mediated antiviral responses in a way that may be independent of the well-studied genome-mediated route. However, the viral glycoprotein determinants responsible for initiating the IFN response remain unidentified. In this study, we have used a collection of 60 synthetic 20-mer overlapping peptides (pepscan) spanning the full length of glycoprotein G (gpG) of viral hemorrhagic septicemia virus (VHSV) to investigate what regions of this protein are implicated in triggering the type I IFN-associated immune responses. Briefly, two regions with ability to increase severalfold the basal expression level of the IFN-stimulated
mx
gene and to restrict the spread of virus among responder cells were mapped to amino acid residues 280 to 310 and 340 to 370 of the gpG protein of VHSV. In addition, the results obtained suggest that an interaction between VHSV gpG and integrins might trigger the host IFN-mediated antiviral response after VHSV infection. Since it is known that type I IFN plays an important role in determining/modulating the protective-antigen-specific immune responses, the identification of viral glycoprotein determinants directly implicated in the type I IFN induction might be of special interest for designing new adjuvants and/or more-efficient and cost-effective viral vaccines as well as for improving our knowledge on how to stimulate the innate immune system.
The T=1 Capsid Protein of
Penicillium chrysogenum
Virus Is Formed by a Repeated Helix-Rich Core Indicative of Gene Duplication
Authors: Luque Daniel , González José M. , Garriga Damiá , Ghabrial Said A. , Havens Wendy M. , Trus Benes , Verdaguer Nuria , Carrascosa José L. , Castón José R. 
Published: May 2010

ABSTRACT

Penicillium chrysogenum
virus (PcV), a member of the
Chrysoviridae
family, is a double-stranded RNA (dsRNA) fungal virus with a multipartite genome, with each RNA molecule encapsidated in a separate particle. Chrysoviruses lack an extracellular route and are transmitted during sporogenesis and cell fusion. The PcV capsid, based on a T=1 lattice containing 60 subunits of the 982-amino-acid capsid protein, remains structurally undisturbed throughout the viral cycle, participates in genome metabolism, and isolates the virus genome from host defense mechanisms. Using three-dimensional cryoelectron microscopy, we determined the structure of the PcV virion at 8.0 Å resolution. The capsid protein has a high content of rod-like densities characteristic of α-helices, forming a repeated α-helical core indicative of gene duplication. Whereas the PcV capsid protein has two motifs with the same fold, most dsRNA virus capsid subunits consist of dimers of a single protein with similar folds. The spatial arrangement of the α-helical core resembles that found in the capsid protein of the L-A virus, a fungal totivirus with an undivided genome, suggesting a conserved basic fold. The encapsidated genome is organized in concentric shells; whereas the inner dsRNA shells are well defined, the outermost layer is dense due to numerous interactions with the inner capsid surface, specifically, six interacting areas per monomer. The outermost genome layer is arranged in an icosahedral cage, sufficiently well ordered to allow for modeling of an A-form dsRNA. The genome ordering might constitute a framework for dsRNA transcription at the capsid interior and/or have a structural role for capsid stability.
Deep Sequencing Reveals Highly Complex Dynamics of Human Cytomegalovirus Genotypes in Transplant Patients over Time
Authors: Görzer Irene , Guelly Christian , Trajanoski Slave , Puchhammer-Stöckl Elisabeth 
Published: May 2010

ABSTRACT
In lung transplant patients undergoing immunosuppression, more than one human cytomegalovirus (HCMV) genotype may emerge during follow-up, and this could be critical for the outcome of HCMV infection. Up to now, many cases of infection with multiple HCMV genotypes were probably overlooked due to the limitations of the current genotyping approaches. We have now analyzed mixed-genotype infections in 17 clinical samples from 9 lung transplant patients using the highly sensitive ultradeep-pyrosequencing (UDPS) technology. UDPS genotyping was performed at three variable HCMV genes, coding for glycoprotein N (gN), glycoprotein O (gO), and UL139. Simultaneous analysis of a mean of 10,430 sequence reads per amplicon allowed the relative amounts of distinct genotypes in the samples to be determined down to 0.1% to 1% abundance. Complex mixtures of up to six different HCMV genotypes per sample were observed. In all samples, no more than two major genotypes accounted for at least 88% of the HCMV DNA load, and these were often accompanied by up to four low-abundance genotypes at frequencies of 0.1% to 8.6%. No evidence for the emergence of new genotypes or sequence changes over time was observed. However, analysis of different samples withdrawn from the same patients at different time points revealed that the relative levels of replication of the individual HCMV genotypes changed within a mixed-genotype population upon reemergence of the virus. Our data show for the first time that, similar to what has been hypothesized for the murine model, HCMV reactivation in humans seems to occur stochastically.
Productive Replication of
vif
-Chimeric HIV-1 in Feline Cells
Authors: Stern Melissa A. , Hu Chunling , Saenz Dyana T. , Fadel Hind J. , Sims Olivia , Peretz Mary , Poeschla Eric M. 
Published: May 2010

ABSTRACT

Nonprimate animal models of HIV-1 infection are prevented by missing cellular cofactors and by antiviral actions of species-specific host defense factors. These blocks are profound in rodents but may be less abundant in certain Carnivora. Here, we enabled productive, spreading replication and passage of HIV-1 in feline cells. Feline fibroblasts, T-cell lines, and primary peripheral blood mononuclear cells supported early and late HIV-1 life cycle phases in a manner equivalent to that of human cells, except that produced virions had low infectivity. Stable expression of feline immunodeficiency virus (FIV) Vif-green fluorescent protein (GFP) in HIV-1 entry receptor-complemented feline (CrFK) cells enabled robust spreading HIV-1 replication. FIV Vif colocalized with feline APOBEC3 (fA3) proteins, targeted them for degradation, and prevented G→A hypermutation of the HIV-1 cDNA by fA3CH and fA3H. HIV-1 Vif was inactive against fA3s as expected and even paradoxically augmented restriction in some assays. In an interesting contrast, simian immunodeficiency virus SIVmac Vif had substantial anti-fA3 activities, which were complete against fA3CH and partial against fA3H. Moreover, both primate lentiviral Vifs colocalized with fA3s and could be pulled down from cell lysates by fA3CH. HIV-1 molecular clones that encode FIV Vif or SIVmac Vif (HIV-1
VF
and HIV-1
VS
) were then constructed. These viruses replicated productively in HIV-1 receptor-expressing CrFK cells and could be passaged serially to uninfected cells. Thus, with the exception of entry receptors, the cat genome can supply the dependency factors needed by HIV-1, and a main restriction can be countered by
vif
chimerism. The results raise the possibility that the domestic cat could yield an animal model of HIV-1 infection.
Oligomerization of Ebola Virus VP40 Is Essential for Particle Morphogenesis and Regulation of Viral Transcription
Authors: Hoenen T. , Biedenkopf N. , Zielecki F. , Jung S. , Groseth A. , Feldmann H. , Becker S. 
Published: May 2010

ABSTRACT
The morphogenesis and budding of virus particles represent an important stage in the life cycle of viruses. For Ebola virus, this process is driven by its major matrix protein, VP40. Like the matrix proteins of many other nonsegmented, negative-strand RNA viruses, VP40 has been demonstrated to oligomerize and to occur in at least two distinct oligomeric states: hexamers and octamers, which are composed of antiparallel dimers. While it has been shown that VP40 oligomers are essential for the viral life cycle, their function is completely unknown. Here we have identified two amino acids essential for oligomerization of VP40, the mutation of which blocked virus-like particle production. Consistent with this observation, oligomerization-deficient VP40 also showed impaired intracellular transport to budding sites and reduced binding to cellular membranes. However, other biological functions, such as the interaction of VP40 with the nucleoprotein, NP, remained undisturbed. Furthermore, both wild-type VP40 and oligomerization-deficient VP40 were found to negatively regulate viral genome replication, a novel function of VP40, which we have recently reported. Interestingly, while wild-type VP40 was also able to negatively regulate viral genome transcription, oligomerization-deficient VP40 was no longer able to fulfill this function, indicating that regulation of viral replication and transcription by VP40 are mechanistically distinct processes. These data indicate that VP40 oligomerization not only is a prerequisite for intracellular transport of VP40 and efficient membrane binding, and as a consequence virion morphogenesis, but also plays a critical role in the regulation of viral transcription by VP40.
Interferon Regulatory Factor 3 Attenuates Reovirus Myocarditis and Contributes to Viral Clearance
Authors: Holm Geoffrey H. , Pruijssers Andrea J. , Li Lianna , Danthi Pranav , Sherry Barbara , Dermody Terence S. 
Published: May 2010

ABSTRACTApoptosis is a pathological hallmark of encephalitis and myocarditis caused by reovirus in newborn mice. In cell culture models, the antiviral transcription factor interferon regulatory factor 3 (IRF-3) enhances reovirus-induced apoptosis following activation via retinoic acid inducible gene I and interferon promoter-stimulating factor 1. To determine the role of IRF-3 in reovirus disease, we infected newborn IRF-3+/+and IRF-3−/−mice perorally with mildly virulent strain type 1 Lang (T1L) and fully virulent strain type 3 SA+ (T3SA+) and monitored infected animals for survival. Both wild-type and IRF-3−/−mice succumbed with equivalent frequencies to infection with T3SA+. However, the absence of IRF-3 was associated with significantly decreased survival rates following infection with T1L. The two virus strains achieved similar peak titers in IRF-3+/+and IRF-3−/−mice in the intestine, brain, heart, liver, and spleen. However, by day 12 postinoculation, titers in all organs examined were 10- to 100-fold higher in IRF-3−/−mice than those in wild-type mice. Increased titers were associated with marked pathological changes in all organs examined, especially in the heart, where absence of IRF-3 resulted in severe myocarditis. Cellular and humoral immune responses were equivalent in wild-type and IRF-3−/−animals, suggesting that IRF-3 functions independently of the adaptive immune response to enhance reovirus clearance. Thus, IRF-3 serves to facilitate virus clearance and prevent tissue injury in response to reovirus infection.
Opposing Effects of a Tyrosine-Based Sorting Motif and a PDZ-Binding Motif Regulate Human T-Lymphotropic Virus Type 1 Envelope Trafficking
Authors: Ilinskaya Anna , Heidecker Gisela , Derse David 
Published: May 2010

ABSTRACTHuman T-lymphotropic virus type 1 (HTLV-1) envelope (Env) glycoprotein mediates binding of the virus to its receptor on the surface of target cells and subsequent fusion of virus and cell membranes. To better understand the mechanisms that control HTLV-1 Env trafficking and activity, we have examined two protein-protein interaction motifs in the cytoplasmic domain of Env. One is the sequence YSLI, which matches the consensus YXXΦ motifs that are known to interact with various adaptor protein complexes; the other is the sequence ESSL at the C terminus of Env, which matches the consensus PDZ-binding motif. We show here that mutations that destroy the YXXΦ motif increased Env expression on the cell surface and increased cell-cell fusion activity. In contrast, mutation of the PDZ-binding motif greatly diminished Env expression in cells, which could be restored to wild-type levels either by mutating the YXXΦ motif or by silencing AP2 and AP3, suggesting that interactions with PDZ proteins oppose an Env degradation pathway mediated by AP2 and AP3. Silencing of the PDZ protein hDlg1 did not affect Env expression, suggesting that hDlg1 is not a binding partner for Env. Substitution of the YSLI sequence in HTLV-1 Env with YXXΦ elements from other cell or virus membrane-spanning proteins resulted in alterations in Env accumulation in cells, incorporation into virions, and virion infectivity. Env variants containing YXXΦ motifs that are predicted to have high-affinity interaction with AP2 accumulated to lower steady-state levels. Interestingly, mutations that destroy the YXXΦ motif resulted in viruses that were not infectious by cell-free or cell-associated routes of infection. Unlike YXXΦ, the function of the PDZ-binding motif manifests itself only in the producer cells; AP2 silencing restored the incorporation of PDZ-deficient Env into virus-like particles (VLPs) and the infectivity of these VLPs to wild-type levels.
APOBEC3G Generates Nonsense Mutations in Human T-Cell Leukemia Virus Type 1 Proviral Genomes
In Vivo
Authors: Fan Jun , Ma Guangyong , Nosaka Kisato , Tanabe Junko , Satou Yorifumi , Koito Atsushi , Wain-Hobson Simon , Vartanian Jean-Pierre , Matsuoka Masao 
Published: May 2010

ABSTRACT

Human T-cell leukemia virus type 1 (HTLV-1) induces cell proliferation after infection, leading to efficient transmission by cell-to-cell contact. After a long latent period, a fraction of carriers develop adult T-cell leukemia (ATL). Genetic changes in the
tax
gene in ATL cells were reported in about 10% of ATL cases. To determine genetic changes that may occur throughout the provirus, we determined the entire sequence of the HTLV-1 provirus in 60 ATL cases. Abortive genetic changes, including deletions, insertions, and nonsense mutations, were frequent in all viral genes except the
HBZ
gene, which is transcribed from the minus strand of the virus. G-to-A base substitutions were the most frequent mutations in ATL cells. The sequence context of G-to-A mutations was in accordance with the preferred target sequence of human APOBEC3G (hA3G). The target sequences of hA3G were less frequent in the plus strand of the
HBZ
coding region than in other coding regions of the HTLV-1 provirus. Nonsense mutations in viral genes including
tax
were also observed in proviruses from asymptomatic carriers, indicating that these mutations were generated during reverse transcription and prior to oncogenesis. The fact that hA3G targets the minus strand during reverse transcription explains why the
HBZ
gene is not susceptible to such nonsense mutations. HTLV-1-infected cells likely take advantage of hA3G to escape from the host immune system by losing expression of viral proteins.