bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species-Level Molecular Identification of Invasive “
Streptococcus milleri
” Group Clinical Isolates by Nucleic Acid Sequencing in a Centralized Regional Microbiology Laboratory
Authors: Daley Peter , Church Deirdre L. , Gregson Daniel B. , Elsayed Sameer 
Published: June 2005

ABSTRACT

Organisms belonging to the “
Streptococcus milleri
” group are important invasive human pathogens. A detailed understanding of their pathogenesis in human infection has only recently been facilitated by the use of molecular methods to study this group of organisms.
Multicenter Evaluation of a Semiautomated, Standardized Assay for Detection of Hepatitis B Virus DNA in Blood Donations
Authors: Romanò Luisa , Velati Claudio , Baruffi Lorella , Fomiatti Laura , Colucci Giuseppe , Zanetti Alessandro R. ,   the Italian Group for the Study of Transfusion Transmissible Diseases
Published: June 2005

ABSTRACT
We evaluated the COBAS Ampliscreen hepatitis B virus (HBV) test using standards, seroconversion panels, consecutive donations, and samples from patients with abnormal alanine aminotransferase and chronic hepatitis C. Specificity was 100% and sensitivity was 20 IU/ml. In seroconversion panels, HBV DNA was detected up to 4 to 18 days before HBsAg, suggesting that this assay is useful in shortening the infectious window phase.
First Identification of
Clostridium celerecrescens
in Liquid Drained from an Abscess
Authors: Glazunova Olga O. , Raoult Didier , Roux Véronique 
Published: June 2005

ABSTRACT

We present the first report on the characterization of
Clostridium celerecrescens
isolated from liquid drained via abscess puncture from a 45-year-old man. The organism was identified by sequence comparison of 16S rRNA genes.
Human Immunodeficiency Virus Type 1 Vpr Impairs Dendritic Cell Maturation and T-Cell Activation: Implications for Viral Immune Escape
Authors: Majumder Biswanath , Janket Michelle L. , Schafer Elizabeth A. , Schaubert Keri , Huang Xiao-Li , Kan-Mitchell June , Rinaldo Charles R. , Ayyavoo Velpandi 
Published: June 2005

ABSTRACTAntigen presentation and T-cell activation are dynamic processes involving signaling molecules present in both APCs and T cells. Effective APC function and T-cell activation can be compromised by viral immune evasion strategies, including those of human immunodeficiency virus type 1 (HIV-1). In this study, we determined the effects of HIV-1 Vpr on one of the initial target of the virus, dendritic cells (DC), by investigating DC maturation, cytokine profiling, and CD8-specific T-cell stimulation function followed by a second signal. Vpr impaired the expression of CD80, CD83, and CD86 at the transcriptional level without altering normal cellular transcription. Cytokine profiling indicated that the presence of Vpr inhibited production of interleukin 12 (IL-12) and upregulated IL-10, whereas IL-6 and IL-1β were unaltered. Furthermore, DC infected with HIV-1vpr+significantly reduced the activation of antigen-specific memory and recall cytotoxic-T-lymphocyte responses. Taken together, these results indicate that HIV-1 Vpr may in part be responsible for HIV-1 immune evasion by inhibiting the maturation of costimulatory molecules and cytokines essential for immune activation.
Regulation of the Translation Initiation Factor eIF4F by Multiple Mechanisms in Human Cytomegalovirus-Infected Cells
Authors: Walsh Derek , Perez Cesar , Notary Joanna , Mohr Ian 
Published: June 2005

ABSTRACT
As a viral opportunistic pathogen associated with serious disease among the immunocompromised and congenital defects in newborns, human cytomegalovirus (HCMV) must engage the translational machinery within its host cell to synthesize the viral proteins required for its productive growth. However, unlike many viruses, HCMV does not suppress the translation of host polypeptides. Here, we examine how HCMV regulates the cellular cap recognition complex eIF4F, a critical component of the cellular translation initiation apparatus that recruits the 40S ribosome to the 5′ end of the mRNA. This study establishes that the cap binding protein eIF4E, together with the translational repressor 4E-BP1, are both phosphorylated early in the productive viral growth cycle and that the activity of the cellular eIF4E kinase, mnk, is critical for efficient viral replication. Furthermore, HCMV replication also induces an increase in the overall abundance of eIF4F components and promotes assembly of eIF4F complexes. Notably, increasing the abundance of select eIF4F core components and associated factors alters the ratio of active eIF4F complexes in relation to the 4E-BP1 translational repressor, illustrating a new strategy through which members of the herpesvirus family enhance eIF4F activity during their replicative cycle.
Role of the Hypervariable Hinge Region of Phosphoprotein P of Vesicular Stomatitis Virus in Viral RNA Synthesis and Assembly of Infectious Virus Particles
Authors: Das Subash C. , Pattnaik Asit K. 
Published: June 2005

ABSTRACT
The phosphoprotein (P protein) of vesicular stomatitis virus (VSV) is an essential subunit of the viral RNA-dependent RNA polymerase and has multiple functions residing in its different domains. In the present study, we examined the role of the hypervariable hinge region of P protein in viral RNA synthesis and recovery of infectious VSV by using transposon-mediated insertion mutagenesis and deletion mutagenesis. We observed that insertions of 19-amino-acid linker sequences at various positions within this region affected replication and transcription functions of the P protein to various degrees. Interestingly, one insertion mutant was completely defective in both transcription and replication. Using a series of deletion mutants spanning the hinge region of the protein, we observed that amino acid residues 201 through 220 are required for the activity of P protein in both replication and transcription. Neither insertion nor deletion had any effect on the interaction of P protein with N or L proteins. Infectious VSVs with a deletion in the hinge region possessed retarded growth characteristics and exhibited small-plaque morphology. Interestingly, VSV containing one P protein deletion mutant (PΔ7, with amino acids 141 through 200 deleted), which possessed significant levels of replication and transcription activity, could be amplified only by passage in cells expressing the wild-type P protein. We conclude that the hypervariable hinge region of the P protein plays an important role in viral RNA synthesis. Furthermore, our results provide a previously unidentified function for the P protein: it plays a critical role in the assembly of infectious VSV.
Longitudinal Assessment of Human Immunodeficiency Virus Type 1 (HIV-1)-Specific Gamma Interferon Responses during the First Year of Life in HIV-1-Infected Infants
Authors: Lohman Barbara L. , Slyker Jennifer A. , Richardson Barbra A. , Farquhar Carey , Mabuka Jenniffer M. , Crudder Christopher , Dong Tao , Obimbo Elizabeth , Mbori-Ngacha Dorothy , Overbaugh Julie , Rowland-Jones Sarah , John-Stewart Grace 
Published: June 2005

ABSTRACTHuman immunodeficiency virus type 1 (HIV-1) infection results in different patterns of viral replication in pediatric compared to adult populations. The role of early HIV-1-specific responses in viral control has not been well defined, because most studies of HIV-1-infected infants have been retrospective or cross-sectional. We evaluated the association between HIV-1-specific gamma interferon (IFN-γ) release from the cells of infants of 1 to 3 months of age and peak viral loads and mortality in the first year of life among 61 Kenyan HIV-1-infected infants. At 1 month, responses were detected in 7/12 (58%) and 6/21 (29%) of infants infected in utero and peripartum, respectively (P= 0.09), and in ∼50% of infants thereafter. Peaks of HIV-specific spot-forming units (SFU) increased significantly with age in all infants, from 251/106peripheral blood mononuclear cells (PBMC) at 1 month of age to 501/106PBMC at 12 months of age (P= 0.03), although when limited to infants who survived to 1 year, the increase in peak HIV-specific SFU was no longer significant (P= 0.18). Over the first year of life, infants with IFN-γ responses at 1 month had peak plasma viral loads, rates of decline of viral load, and mortality risk similar to those of infants who lacked responses at 1 month. The strength and breadth of IFN-γ responses at 1 month were not significantly associated with viral containment or mortality. These results suggest that, in contrast to HIV-1-infected adults, in whom strong cytotoxic T lymphocyte responses in primary infection are associated with reductions in viremia, HIV-1-infected neonates generate HIV-1-specific CD8+-T-cell responses early in life that are not clearly associated with improved clinical outcomes.
Promoters, Transcripts, and Regulatory Proteins of Mungbean Yellow Mosaic Geminivirus
Authors: Shivaprasad P. V. , Akbergenov Rashid , Trinks Daniela , Rajeswaran R. , Veluthambi K. , Hohn Thomas , Pooggin Mikhail M. 
Published: June 2005

ABSTRACT

Geminiviruses package circular single-stranded DNA and replicate in the nucleus via a double-stranded intermediate. This intermediate also serves as a template for bidirectional transcription by polymerase II. Here, we map promoters and transcripts and characterize regulatory proteins of
Mungbean yellow mosaic virus-Vigna
(MYMV), a bipartite geminivirus in the genus
Begomovirus
. The following new features, which might also apply to other begomoviruses, were revealed in MYMV. The leftward and rightward promoters on DNA-B share the transcription activator AC2-responsive region, which does not overlap the common region that is nearly identical in the two DNA components. The transcription unit for BC1 (movement protein) includes a conserved, leader-based intron. Besides negative-feedback regulation of its own leftward promoter on DNA-A, the replication protein AC1, in cooperation with AC2, synergistically transactivates the rightward promoter, which drives a dicistronic transcription unit for the coat protein AV1. AC2 and the replication enhancer AC3 are expressed from one dicistronic transcript driven by a strong promoter mapped within the upstream AC1 gene. Early and constitutive expression of AC2 is consistent with its essential dual function as an activator of viral transcription and a suppressor of silencing.
Isolation of a Bovine Plasma Fibronectin-Containing Complex Which Inhibits the Expression of Bovine Leukemia Virus p24
Authors: van den Heuvel Marianne J. , Jefferson Barbara J. , Jacobs Robert M. 
Published: June 2005

ABSTRACT
Bovine leukemia virus (BLV) is a deltaretrovirus that infects cattle worldwide. In agriculturally intensive regions, approximately 30% of dairy cows are BLV infected. Like the human T-cell leukemia virus (HTLV), there is a lengthy period of viral quiescence after initial infection with BLV. Unlike HTLV, BLV resides predominantly in B cells. Lymphoma is observed in less than 10% of BLV-infected adult cattle. Although viremia is undetectable in vivo, BLV-infected peripheral blood mononuclear cells readily become productive when cultured in vitro. Productivity is markedly diminished when cultures are supplemented with bovine plasma. This inhibitory activity of bovine plasma has been attributed to the “plasma blocking factor” (PBF). Here, we describe the purification of a PBF whose activity was resistant to heating to 65°C for 10 min and was attributable to a fibronectin-containing complex of approximately 320 kDa under nonreducing conditions. By use of two-dimensional polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization-time of flight (mass spectrometry), a protein with a size of 220 kDa and a pI of 5.4 was identified as a member of the fibronectin group of molecules. Both the purified protein and the commercially available bovine fibronectin inhibited BLV production in naturally infected peripheral blood mononuclear cells, although the fibronectin was less biologically active.
Development of a Novel System To Study Hepatitis Delta Virus Genome Replication
Authors: Chang Jinhong , Gudima Severin O. , Tarn Chi , Nie Xingcao , Taylor John M. 
Published: June 2005

ABSTRACT

Hepatitis delta virus (HDV) genome replication requires the virus-encoded small delta protein (δAg). During replication, nucleotide sequence changes accumulate on the HDV RNA, leading to the translation of δAg species that are nonfunctional or even inhibitory. A replication system was devised where all δAg was conditionally provided from a separate and unchanging source. A line of human embryonic kidney cells was stably transfected with a single copy of cDNA encoding small δAg, with expression under tetracycline (TET) control. Next, HDV genome replication was initiated in these cells by transfection with a mutated RNA unable to express δAg. Thus, replication of this RNA was under control of the TET-inducible δAg. In the absence of TET, there was sufficient δAg to allow a low level of HDV replication that could be maintained for at least 1 year. When TET was added, both δAg and genomic RNA increased dramatically within 2 days. With clones of such cells, designated 293-HDV, the burst of HDV RNA replication interfered with cell cycling. Within 2 days, there was a fivefold enhancement of G
1
/G
0
cells relative to both S and G
2
/M cells, and by 6 days, there was extensive cell detachment and death. These findings and those of other studies that are under way demonstrate the potential applications of this experimental system.
Differential Sensitivity of Murine Leukemia Virus to APOBEC3-Mediated Inhibition Is Governed by Virion Exclusion
Authors: Doehle Brian P. , Schäfer Alexandra , Wiegand Heather L. , Bogerd Hal P. , Cullen Bryan R. 
Published: June 2005

ABSTRACT
While members of the APOBEC3 family of human intrinsic resistance factors are able to restrict the replication of Vif-deficient forms of human immunodeficiency virus type 1 (HIV-1), they are unable to block replication of wild-type HIV-1 due to the action of Vif, which induces their degradation. In contrast, HIV-1 Vif is unable to block inhibition mediated by APOBEC3 proteins expressed by several heterologous species, including mice. Here, we have asked whether the simple retrovirus murine leukemia virus (MLV) is sensitive to restriction by the cognate murine or heterologous, human APOBEC3 proteins. We demonstrate that MLV is highly sensitive to inhibition by human APOBEC3G and APOBEC3B but resistant to inhibition by murine APOBEC3 or by other human APOBEC3 proteins, including APOBEC3F. This sensitivity fully correlates with the ability of these proteins to be packaged into MLV virion particles: i.e., human APOBEC3G and APOBEC3B are packaged while murine APOBEC3 and human APOBEC3F are excluded. Moreover, this packaging in turn correlates with the differential ability of these APOBEC3 proteins to bind MLV Gag. Together, these data suggest that MLV Gag has evolved to avoid binding, and hence virion packaging, of the cognate murine APOBEC3 protein but that MLV infectivity is still restricted by certain heterologous APOBEC3 proteins that retain this ability. Moreover, these results suggest that APOBEC3 proteins may help prevent the zoonotic infection of humans by simple retroviruses and provide a mechanism for how simple retroviruses can avoid inhibition by APOBEC3 family members.
An Interplay between Hypervariable Region 1 of the Hepatitis C Virus E2 Glycoprotein, the Scavenger Receptor BI, and High-Density Lipoprotein Promotes both Enhancement of Infection and Protection against Neutralizing Antibodies
Authors: Bartosch Birke , Verney Géraldine , Dreux Marlène , Donot Peggy , Morice Yoann , Penin François , Pawlotsky Jean-Michel , Lavillette Dimitri , Cosset Francois-Loïc 
Published: June 2005

ABSTRACT
Hepatitis C virus (HCV) circulates in the bloodstream in different forms, including complexes with immunoglobulins and/or lipoproteins. To address the significance of such associations, we produced or treated HCV pseudoparticles (HCVpp), a valid model of HCV cell entry and its inhibition, with naïve or patient-derived sera. We demonstrate that infection of hepatocarcinoma cells by HCVpp is increased more than 10-fold by human serum factors, of which high-density lipoprotein (HDL) is a major component. Infection enhancement requires scavenger receptor BI, a molecule known to mediate HDL uptake into cells as well as HCVpp entry, and involves conserved amino acid positions in hypervariable region 1 (HVR1) of the E2 glycoprotein. Additionally, we show that the interaction with human serum or HDL, but not with low-density lipoprotein, leads to the protection of HCVpp from neutralizing antibodies, including monoclonal antibodies and antibodies present in patient sera. Finally, the deletion or mutation of HVR1 in HCVpp abolishes infection enhancement and leads to increased sensitivity to neutralizing antibodies/sera compared to that of parental HCVpp. Altogether, these results assign to HVR1 new roles which are complementary in helping HCV to survive within its host. Besides immune escape by mutation, HRV1 can mediate the enhancement of cell entry and the protection of virions from neutralizing antibodies. By preserving a balance between these functions, HVR1 may be essential for the viral persistence of HCV.
Avian Sarcoma and Leukosis Virus Cytopathic Effect in the Absence of TVB Death Domain Signaling
Authors: Klucking Sara , Collins Asha S. , Young John A. T. 
Published: June 2005

ABSTRACT
The cytopathic effect (CPE) seen with some subgroups of avian sarcoma and leukosis virus (ASLV) is associated with viral Env activation of the death-promoting activity of TVB (a tumor necrosis factor receptor-related receptor that is most closely related to mammalian TNF-related apoptosis-inducing ligand [TRAIL] receptors) and with viral superinfection leading to unintegrated viral DNA (UVD) accumulation, which is presumed to activate a cellular DNA damage response. In this study, we employed cells that express signaling-deficient ASLV receptors to demonstrate that an ASLV CPE can be uncoupled from the death-promoting functions of the TVB receptor. However, these cell-killing events were associated with much higher levels of viral superinfection and DNA accumulation than those seen when the virus used signaling-competent TVB receptors. These findings suggest that a putative cellular DNA damage response that is activated by UVD accumulation might act in concert with the death-signaling pathways activated by Env-TVB interactions to trigger cell death. Such a model is consistent with the well-established synergy that exists between TRAIL-signaling pathways and DNA damage responses which is currently being exploited in cancer therapy regimens.
Innate STAT1-Dependent Genomic Response of Neurons to the Antiviral Cytokine Alpha Interferon
Authors: Wang Jianping , Campbell Iain L. 
Published: June 2005

ABSTRACTAlpha/beta interferons (IFNs-α/β) are cytokines that play an essential role in the host defense against viral infection. Our previous studies have shown that the key IFN signaling molecule STAT1 is highly elevated and activated in central nervous system neurons during viral infection and in transgenic mice with astrocyte production of IFN-α (glial fibrillary acidic protein [GFAP]-IFN-α), suggesting that neurons are a very responsive target cell population for IFNs. To elucidate the genomic response of neurons to IFN-α, we undertook studies both in vitro and in vivo. Gene chip analysis was applied to RNA from IFN-α-treated or untreated primary cortical neuronal cultures derived from embryonic day 15 fetal wild-type or STAT1 knockout (KO) mice. The expression of 51 known and 5 unknown genes was increased significantly by more than twofold after exposure of wild-type but not STAT1 KO neurons to IFN-α. Some more highly expressed genes included IFN-induced 15-kDa protein, ubiquitin-specific protease 18, glucocorticoid attenuated response genes, IFN-induced GTPases, and the chemokine CXCL10. For several of these genes, the gene chip findings were confirmed by RNase protection assays. In addition, examination of the expression of some of these selected genes revealed that they were increased in neurons in the brain of either GFAP-IFN-α mice or mice infected with lymphocytic choriomeningitis virus. In conclusion, our study revealed a robust STAT1-dependent genomic response of neurons to IFN-α, highlighting an innate potential of these cells to defend against viral infection in the brain.
Herpes Simplex Virus ICP27 Activation of Stress Kinases JNK and p38
Authors: Hargett Danna , McLean Tim , Bachenheimer Steven L. 
Published: June 2005

ABSTRACTWe previously reported that herpes simplex virus type 1 (HSV-1) can activate the stress-activated protein kinases (SAPKs) p38 and JNK. In the present study, we undertook a comprehensive and comparative analysis of the requirements for viral protein synthesis in the activation of JNK and p38. Infection with the UL36 mutanttsB7 or with UV-irradiated virus indicated that both JNK and p38 activation required viral gene expression. Cycloheximide reversal or phosphonoacetic acid treatment of wild-type virus-infected cells as well as infection with the ICP4 mutantvi13 indicated that only the immediate-early class of viral proteins were required for SAPK activation. Infection with ICP4, ICP27, or ICP0 mutant viruses indicated that only ICP27 was necessary. Additionally, we determined that in the context of virus infection ICP27 was sufficient for SAPK activation and activation of the p38 targets Mnk1 and MK2 by infecting with mutants deleted for various combinations of immediate-early proteins. Specifically, thed100 (0−/4−) andd103 (4−/22−/47−) mutants activated p38 and JNK, while thed106 (4−/22−/27−/47−) andd107 (4−/27−) mutants did not. Finally, infections with a series of ICP27 mutants demonstrated that the functional domain of ICP27 required for activation was located in the region encompassing amino acids 20 to 65 near the N terminus of the protein and that the C-terminal transactivation activity of ICP27 was not necessary.
Mobilization and Mechanism of Transcription of Integrated Self-Inactivating Lentiviral Vectors
Authors: Hanawa Hideki , Persons Derek A. , Nienhuis Arthur W. 
Published: June 2005

ABSTRACT
Permanent genetic modification of replicating primitive hematopoietic cells by an integrated vector has many potential therapeutic applications. Both oncoretroviral and lentiviral vectors have a predilection for integration into transcriptionally active genes, creating the potential for promoter activation or gene disruption. The use of self-inactivating (SIN) vectors in which a deletion of the enhancer and promoter sequences from the 3′ long terminal repeat (LTR) is copied over into the 5′ LTR during vector integration is designed to improve safety by reducing the risk of mobilization of the vector genome and the influence of the LTR on nearby cellular promoters. Our results indicate that SIN vectors are mobilized in cells expressing lentiviral proteins, with the frequency of mobilization influenced by features of the vector design. The mechanism of transcription of integrated vector genomes was evaluated using a promoter trap design with a vector encoding tat but lacking an upstream promoter in a cell line in which drug resistance depended on tat expression. In six clones studied, all transcripts originated from cryptic promoters either upstream or within the vector genome. We estimate that approximately 1 in 3,000 integrated vector genomes is transcribed, leading to the inference that activation of cryptic promoters must depend on local features of chromatin structure and the constellation of nearby regulatory elements as well as the nature of the regulatory elements within the vector.