bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative and Positive mRNA Splicing Elements Act Competitively To Regulate Human Immunodeficiency Virus Type 1 Vif Gene Expression
Authors: Exline C. M. , Feng Z. , Stoltzfus C. M. 
Published: February 2008

ABSTRACT

Over 40 different human immunodeficiency virus type 1 (HIV-1) mRNAs are produced by alternative splicing of the primary HIV-1 RNA transcripts. In addition, approximately half of the viral RNA remains unspliced and is used as genomic RNA and as mRNA for the Gag and Pol gene products. Regulation of splicing at the HIV-1 3′ splice sites (3′ss) requires suboptimal polypyrimidine tracts, and positive or negative regulation occurs through the binding of cellular factors to
cis
-acting splicing regulatory elements. We have previously shown that splicing at HIV-1 3′ss A1, which produces single-spliced
vif
mRNA and promotes the inclusion of HIV exon 2 into both completely and incompletely spliced viral mRNAs, is increased by optimizing the 5′ splice site (5′ss) downstream of exon 2 (5′ss D2). Here we show that the mutations within 5′ss D2 that are predicted to lower or increase the affinity of the 5′ss for U1 snRNP result in reduced or increased Vif expression, respectively. Splicing at 5′ss D2 was not necessary for the effect of 5′ss D2 on Vif expression. In addition, we have found that mutations of the GGGG motif proximal to the 5′ss D2 increase exon 2 inclusion and Vif expression. Finally, we report the presence of a novel exonic splicing enhancer (ESE) element within the 5′-proximal region of exon 2 that facilitates both exon inclusion and Vif expression. This ESE binds specifically to the cellular SR protein SRp75. Our results suggest that the 5′ss D2, the proximal GGGG silencer, and the ESE act competitively to determine the level of
vif
mRNA splicing and Vif expression. We propose that these positive and negative splicing elements act together to allow the accumulation of
vif
mRNA and unspliced HIV-1 mRNA, compatible with optimal virus replication.
Genital Ulcers Facilitate Rapid Viral Entry and Dissemination following Intravaginal Inoculation with Cell-Associated Simian Immunodeficiency Virus SIVmac239
Authors: Weiler Andrea M. , Li Qingsheng , Duan Lijie , Kaizu Masahiko , Weisgrau Kim L. , Friedrich Thomas C. , Reynolds Matthew R. , Haase Ashley T. , Rakasz Eva G. 
Published: February 2008

ABSTRACT
Here we report the results of studies in the simian immunodeficiency virus (SIV)-rhesus macaque model of intravaginal transmission of human immunodeficiency virus type 1 in the setting of genital ulcerative diseases. We document preferential association of vRNA with induced ulcers during the first days of infection and show that allogeneic cells of the inoculum traffic from the vaginal lumen to lymphatic tissues. This surprisingly rapid systemic dissemination in this cell-associated SIV challenge model thus reveals the challenges of preventing transmission in the setting of genital ulcerative diseases and illustrates the utility of this animal model in tests of strategies aimed at reducing transmission under these conditions.
Role of Cellular Phosphatase cdc25C in Herpes Simplex Virus 1 Replication
Authors: Smith-Donald Benjamin A. , Durand Lizette O. , Roizman Bernard 
Published: February 2008

ABSTRACT

Earlier studies have shown that in herpes simplex virus 1-infected cells, ICP22 upregulates the accumulation of a subset of γ
2
proteins exemplified by the products of the U
L
38, U
L
41, and U
S
11 genes. The ICP22-dependent process involves degradation of cyclins A and B1, the stabilization and activation of cdc2, physical interaction of activated cdc2 with the U
L
42 DNA synthesis processivity factor, and recruitment and phosphorylation of topoisomerase IIα by the cdc2/U
L
42 complex. Activation of cdc2, the first step in the process, is a key function of the mitotic phosphatase cdc25C. To define the role of cdc25C, we probed some features of the ICP22-dependent pathway of upregulation of γ
2
genes in cdc25C
−/−
cells and in cdc25C
+/+
cells derived from sibling mice. We report that cyclin B1 turned over in cdc25C
+/+
or cdc25C
−/−
cells at the same rate, that cdc2 increased in amount, and that U
S
11 and U
L
38 proteins and infectious virus accumulated in smaller amounts than in wild-type infected cells. The reduction in U
L
38 protein accumulation and virus was greater in cdc25C
−/−
cells infected with virus lacking ICP22 than in cells infected with wild-type virus. We conclude that cdc25C phosphatase plays a role in viral replication and that this role extends beyond its function of activating cdc2 for initiation of the ICP22-dependent cascade for upregulation of γ
2
gene expression.
The Interaction of Herpes Simplex Virus 1 Regulatory Protein ICP22 with the cdc25C Phosphatase Is Enabled In Vitro by Viral Protein Kinases U
S
3 and U
L
13
Authors: Smith-Donald Benjamin A. , Roizman Bernard 
Published: February 2008

ABSTRACT

Earlier studies have shown that ICP22 and the U
L
13 protein kinase but not the U
S
3 kinase are required for optimal expression of a subset of late (γ
2
) genes exemplified by U
L
38, U
L
41, and U
S
11. In primate cells, ICP22 mediates the disappearance of inactive isoforms of cdc2 and degradation of cyclins A and B1. Active cdc2 acquires a new partner, the viral DNA synthesis processivity factor U
L
42. The cdc2-U
L
42 complex recruits and phosphorylates topoisomerase IIα for efficient expression of the γ
2
genes listed above. In uninfected cells, the cdc25C phosphatase activates cdc2 by removing two inhibitory phosphates. The accompanying report shows that in the absence of cdc25C, the rate of degradation of cyclin B1 is similar to that occurring in infected wild-type mouse embryo fibroblast cells but the levels of cdc2 increase, and the accumulation of a subset of late proteins and virus yields are reduced. This report links ICP22 with cdc25C. We show that in infected cells, ICP22 and U
S
3 protein kinase mediate the phosphorylation of cdc25C at its C-terminal domain. In in vitro assays with purified components, both U
L
13 and U
S
3 viral kinases phosphorylate cdc25C and ICP22. cdc25C also interacts with cdc2. However, in infected cells, the ability of cdc25C to activate cdc2 by dephosphorylation of the inactive cdc2 protein is reduced. Coupled with the phosphorylation of cdc25C by the U
S
3 kinase, the results raise the possibility that herpes simplex virus 1 diverts cdc25C to perform functions other than those performed in uninfected cells.
Antiviral Therapy during Primary Simian Immunodeficiency Virus Infection Fails To Prevent Acute Loss of CD4
+
T Cells in Gut Mucosa but Enhances Their Rapid Restoration through Central Memory T Cells
Authors: Verhoeven David , Sankaran Sumathi , Silvey Melanie , Dandekar Satya 
Published: February 2008

ABSTRACT

Gut-associated lymphoid tissue (GALT) is an early target of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) and a site for severe CD4
+
T-cell depletion. Although antiretroviral therapy (ART) is effective in suppressing HIV replication and restoring CD4
+
T cells in peripheral blood, restoration in GALT is delayed. The role of restored CD4
+
T-cell help in GALT during ART and its impact on antiviral CD8
+
T-cell responses have not been investigated. Using the SIV model, we investigated gut CD4
+
T-cell restoration in infected macaques, initiating ART during either the primary stage (1 week postinfection), prior to acute CD4
+
cell loss (PSI), or during the chronic stage at 10 weeks postinfection (CSI). ART led to viral suppression in GALT and peripheral blood mononuclear cells of PSI and CSI animals at comparable levels. CSI animals had incomplete CD4
+
T-cell restoration in GALT. In PSI animals, ART did not prevent acute CD4
+
T-cell loss by 2 weeks postinfection in GALT but supported rapid and complete CD4
+
T-cell restoration thereafter. This correlated with an accumulation of central memory CD4
+
T cells and better suppression of inflammation. Restoration of CD4
+
T cells in GALT correlated with qualitative changes in SIV gag-specific CD8
+
T-cell responses, with a dominance of interleukin-2-producing responses in PSI animals, while both CSI macaques and untreated SIV-infected controls were dominated by gamma interferon responses. Thus, central memory CD4
+
T-cell levels and qualitative antiviral CD8
+
T-cell responses, independent of viral suppression, were the immune correlates of gut mucosal immune restoration during ART.
The Specificities of Kaposi's Sarcoma-Associated Herpesvirus-Encoded E3 Ubiquitin Ligases Are Determined by the Positions of Lysine or Cysteine Residues within the Intracytoplasmic Domains of Their Targets
Authors: Cadwell Ken , Coscoy Laurent 
Published: February 2008

ABSTRACT
Kaposi's sarcoma-associated herpesvirus encodes two homologous E3 ligases, MIR1 and MIR2, that mediate the ubiquitination and subsequent downregulation of several cell surface proteins, and in particular major histocompatibility complex class I (MHC-I) molecules. We have previously shown that, in addition to lysine ubiquitination, MIR1 has the unique ability of transferring ubiquitin onto MHC-I molecules lacking available lysine residues, in a cysteine-dependent manner. Here we report that MIR1 activity is maximal when either a lysine or cysteine residue is placed approximately 15 amino acids away from the transmembrane domain, whereas MIR2 preferentially targets residues, including cysteines, that are closer to the transmembrane domain. Thus MIR1 and -2 can distinguish their substrates based on the position of the lysine or cysteine residues, suggesting that these proteins have evolved to target different sets of surface molecules. These results indicate that the position of target residues within a substrate is an essential determinant of E3 ubiquitin ligase specificity.
The Role of T Cells in the Enhancement of Respiratory Syncytial Virus Infection Severity during Adult Reinfection of Neonatally Sensitized Mice
Authors: Tregoning John S. , Yamaguchi Yuko , Harker James , Wang Belinda , Openshaw Peter J. M. 
Published: February 2008

ABSTRACTRespiratory syncytial virus (RSV) is the major cause of infantile bronchiolitis and hospitalization. Severe RSV disease is associated with the development of wheezing in later life. In a mouse model of the delayed effects of RSV, the age at primary infection determines responses to reinfection in adulthood. During primary RSV infection, neonatal BALB/c mice developed only mild disease and recruited CD8 cells that were defective in gamma interferon production. Secondary reinfection of neonatally primed mice caused enhanced inflammation and profuse lung T-cell recruitment. CD4 cell depletion during secondary RSV challenge attenuated disease (measured by weight loss); depletion of CD8 cells also markedly attenuated disease severity but enhanced lung eosinophilia, and depletion of both CD4 and CD8 cells together completely abrogated weight loss. Depletion of CD8 (but not CD4) cells during primary neonatal infection was protective against weight loss during adult challenge. Therefore, T cells, in particular CD8 T cells, play a central role in the outcome of neonatal infection by enhancing disease during secondary challenge. These findings demonstrate a crucial role for T cells in the regulation of immune responses after neonatal infection.
Tobacco Rattle Virus 16-Kilodalton Protein Encodes a Suppressor of RNA Silencing That Allows Transient Viral Entry in Meristems
Authors: Martín-Hernández Ana M. , Baulcombe David C. 
Published: February 2008

ABSTRACT
RNA silencing is a host defense mechanism that limits the accumulation and spread of viruses in infected plants. Correspondingly, plant viruses encode suppressors of silencing. In the positive-strand RNA virus Tobacco rattle virus (TRV), the suppressor of silencing is a 16-kDa (16K) protein encoded by RNA1. The suppressor action of the 16K protein is transient and weaker than that of the P19 suppressor, encoded by tomato bushy stunt virus. Mutant TRV that does not produce its suppressor, unlike other suppressor-defective viruses, is competent to accumulate and spread systemically in the infected plant. However, this mutant virus does not exhibit the transient invasion of the meristem that is characteristic of the wild-type virus. Based on this analysis, we propose that the 16K suppressor of silencing allows TRV to transiently invade the meristem. Our data are consistent with a mechanism of long-term meristem virus exclusion that is dependent on a transient invasion of the meristem early in the infection cycle. This novel mechanism of meristem exclusion may be associated with the phenomenon of recovery in virus-infected plants in which upper leaves have little or no virus and are immune to secondary infection by the same virus.
CD4
+
Target Cell Availability Determines the Dynamics of Immune Escape and Reversion In Vivo
Authors: Petravic Janka , Loh Liyen , Kent Stephen J. , Davenport Miles P. 
Published: February 2008

ABSTRACT

Infections with human immunodeficiency virus (HIV) and the closely related monkey viruses simian-human immunodeficiency virus (SHIV) and simian immunodeficiency virus (SIV) are characterized by progressive waves of immune responses, followed by viral mutation and “immune escape.” However, escape mutation usually leads to lower replicative fitness, and in the absence of immune pressure, an escape mutant (EM) virus “reverts” to the wild-type phenotype. Analysis of the dynamics of immune escape and reversion has suggested it is a mechanism for identifying the immunogens best capable of controlling viremia. We have analyzed and modeled data of the dynamics of wild-type (WT) and EM viruses during SHIV infection of macaques. Modeling suggests that the dynamics of reversion and immune escape should be determined by the availability of target cells for infection. Consistent with this suggestion, we find that the rate of reversion of cytotoxic T-lymphocyte (CTL) EM virus strongly correlates with the number of CD4
+
T cells available for infection. This phenomenon also affects the rate of immune escape, since this rate is determined by the balance of CTL killing and the WT fitness advantage. This analysis predicts that the optimal timing for the selection of immune escape variants will be immediately after the peak of viremia and that the development of escape variants at later times will lead to slower selection. This has important implications for comparative studies of immune escape and reversion in different infections and for identifying epitopes with high fitness cost for use as vaccine targets.
Genome Analysis of a
Glossina pallidipes
Salivary Gland Hypertrophy Virus Reveals a Novel, Large, Double-Stranded Circular DNA Virus
Authors: Abd-Alla Adly M. M. , Cousserans François , Parker Andrew G. , Jehle Johannes A. , Parker Nicolas J. , Vlak Just M. , Robinson Alan S. , Bergoin Max 
Published: February 2008

ABSTRACT

Several species of tsetse flies can be infected by the
Glossina pallidipes
salivary gland hypertrophy virus (GpSGHV). Infection causes salivary gland hypertrophy and also significantly reduces the fecundity of the infected flies. To better understand the molecular basis underlying the pathogenesis of this unusual virus, we sequenced and analyzed its genome. The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally on both strands with a gene density of one per 1.2 kb. It has a high A+T content of 72%. About 3% of the GpSGHV genome is composed of 15 sequence repeats, distributed throughout the genome. Although sharing the same morphological features (enveloped rod-shaped nucleocapsid) as baculoviruses, nudiviruses, and nimaviruses, analysis of its genome revealed that GpSGHV differs significantly from these viruses at the level of its genes. Sequence comparisons indicated that only 23% of GpSGHV genes displayed moderate homologies to genes from other invertebrate viruses, principally baculoviruses and entomopoxviruses. Most strikingly, the GpSGHV genome encodes homologues to the four baculoviral per os infectivity factors (p74 [pif-0], pif-1, pif-2, and pif-3). The DNA polymerase encoded by GpSGHV is of type B and appears to be phylogenetically distant from all DNA polymerases encoded by large double-stranded DNA viruses. The majority of the remaining ORFs could not be assigned by sequence comparison. Furthermore, no homologues to DNA-dependent RNA polymerase subunits were detected. Taken together, these data indicate that GpSGHV is the prototype member of a novel group of insect viruses.
Identification of a Coronavirus Transcription Enhancer
Authors: Moreno José L. , Zúñiga Sonia , Enjuanes Luis , Sola Isabel 
Published: February 2008

ABSTRACT

Coronavirus
(CoV) transcription includes a discontinuous mechanism during the synthesis of sub-genome-length minus-strand RNAs leading to a collection of mRNAs in which the 5′ terminal leader sequence is fused to contiguous genome sequences. It has been previously shown that transcription-regulating sequences (TRSs) preceding each gene regulate transcription. Base pairing between the leader TRS (TRS-L) and the complement of the body TRS (cTRS-B) in the nascent RNA is a determinant factor during CoV transcription. In fact, in transmissible gastroenteritis CoV, a good correlation has been observed between subgenomic mRNA (sg mRNA) levels and the free energy (ΔG) of TRS-L and cTRS-B duplex formation. The only exception was sg mRNA N, the most abundant sg mRNA during viral infection in spite of its minimum ΔG associated with duplex formation. We postulated that additional factors should regulate transcription of sg mRNA N. In this report, we have described a novel transcription regulation mechanism operating in CoV by which a 9-nucleotide (nt) sequence located 449 nt upstream of the N gene TRS core sequence (CS-N) interacts with a complementary sequence just upstream of CS-N, specifically increasing the accumulation of sg mRNA N. Alteration of this complementarity in mutant replicon genomes showed a correlation between the predicted stability of the base pairing between 9-nt sequences and the accumulation of sg mRNA N. This interaction is exclusively conserved in group 1a CoVs, the only CoV subgroup in which the N gene is not the most 3′ gene in the viral genome. This is the first time that a long-distance RNA-RNA interaction regulating transcriptional activity specifically enhancing the transcription of one gene has been described to occur in CoVs.
Hybrid Iteration Method for Fixed Points of Nonexpansive Mappings in Arbitrary Banach Spaces
Authors: Osilike MO , Isiogugu FO , Nwokoro PU 
Published: February 2008

AbstractWe prove that recent results of Wang (2007) concerning the iterative approximation of fixed points of nonexpansive mappings using a hybrid iteration method in Hilbert spaces can be extended to arbitrary Banach spaces without the strong monotonicity assumption imposed on the hybrid operator.
The ENIAC Forecasts: A Re-creation
Authors: Lynch Peter 
Published: February 2008

The numerical forecasts made in 1950 using the Electronic Numerical Integrator and Computer (ENIAC) paved the way for the remarkable advances that have been made over the past half-century in weather prediction and climate modeling. We review the circumstances in which the forecasts were made, the nature of the ENIAC machine, and the roles of the people involved. The basis for the forecasts was the barotropic vorticity equation, and the initial data were prepared manually from standard weather charts. Now that the NCEP-NCAR reanalysis extends back to 1948, the initial height fields for the forecasts are readily available in digital form. We describe the reconstruction of the forecasts using reanalyzed data.
Were the ENIAC forecasts any good? To date, no objective verification of the four integrations has been available. A comparison of the original and reconstructed forecasts shows them to be in good agreement. Quantitative verification of the forecasts yields surprising results. On the basis of root-mean-square errors, persistence beats the forecast in three of the four cases. The mean error, or bias, is smaller for persistence in all four cases. However, when SI scores are compared, all four forecasts show skill and three are substantially better than persistence.
A small modification of the prediction equation, in which the streamfunction replaces the geopotential height as the prognostic variable, can be implemented without any computational penalty. The modified equation yields slightly improved forecasts in all four cases.
Comparison of Cutaneous and Transosseous Electromagnetic Position Sensors in the Assessment of Tibial Rotation in a Cadaveric Model
Authors: Magit David P. , McGarry Michelle , Tibone James E. , Lee Thay Q. 
Published: February 2008

Background Recent studies have highlighted the growing interest in validating anatomic anterior cruciate ligament reconstructions. A simple method of measuring tibial rotation is necessary to provide an objective clinical assessment of restoration of normal knee kinematics after various anterior cruciate ligament reconstructive techniques. Objective To validate a new method of measuring tibial rotation by comparing cutaneous with transosseous electromagnetic position sensors during a simulated standard knee examination. Study Design Controlled laboratory study. Methods Eight thawed, fresh-frozen cadaveric knee specimens with skin and soft tissues preserved were mounted on the femoral side in neutral rotation by a rigid clamp, allowing 6 degrees of freedom of the knee joint. With the knee fixed at 30° of flexion, a series of maximal manual internal and external tibial rotations were performed and measured with an electromagnetic tracking system that measures 6 degrees of freedom in a Cartesian coordinate system. During each series of measurements, a cutaneous transmitter was fixed overlying the tibial tuberosity. Simultaneously, a second transducer was rigidly fixed to a transosseous pin placed just distal to the tibial tubercle. Measurements were repeated at 90° of flexion. Differences in measurements were assessed. Results No significant differences were found with maximal internal and external rotation between cutaneous and transosseous measurements at 30° of knee flexion (13.0° vs 14.5°, P = .4) or at 90° of flexion (11.2° vs 12.9°, P = .5). Correlation ( R) between cutaneous and transosseous measurements at 30° was .97 ( P = .00009) and at 90° was .99 ( P < .00001). The accuracy of cutaneous measurements using transosseous as the known was 1.6° ± 1.3°. Repeatability of cutaneous measurements was 0.8° ± 0.4°. The repeatability of transosseous measurements was 1.0° ± 0.5°. Conclusion No significant differences were found at either 30° or 90° of flexion when measuring tibial rotation using cutaneous versus transosseous electromagnetic position sensors. Clinical Relevance The ability to measure knee rotation using cutaneous electromagnetic position sensors represents a promising new method for assessing various clinical conditions and surgical outcomes.