bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue-Specific Splicing of the Herpes Simplex Virus Type 1 Latency-Associated Transcript (LAT) Intron in LAT Transgenic Mice
Authors: Gussow Anne M. , Giordani Nicole V. , Tran Robert K. , Imai Yumi , Kwiatkowski Dacia L. , Rall Glenn F. , Margolis Todd P. , Bloom David C. 
Published: September 2006

ABSTRACT

To study the regulation of herpes simplex virus type 1 (HSV-1) latency-associated transcript (LAT) expression and processing in the absence of other
cis
and
trans
viral functions, a transgenic mouse containing the region encompassing the LAT promoter (LAP1) and the LAT 5′ exon through the 2.0-kb intron was created. LAT expression was detectable by reverse transcriptase PCR (RT-PCR) in a number of tissues, including the dorsal root ganglia (DRG), trigeminal ganglia (TG), brain, skin, liver, and kidney. However, when the accumulation of the 2.0-kb LAT intron was analyzed at the cellular level by in situ hybridization, little or no detectable accumulation was observed in the brain, spinal cord, kidney, or foot, although the 2.0-kb LAT intron was detected at high levels (over 90% of neurons) in the DRG and TG. Northern blot analysis detected the stable 2.0-kb LAT intron only in the sensory ganglia. When relative amounts of the spliced and unspliced LAT within the brain, liver, kidney, spinal cord, TG, and DRG were analyzed by real-time RT-PCR, splicing of the 2.0-kb LAT intron was significantly more efficient in the sensory ganglia than in other tissues. Finally, infection of both transgenic mice and nontransgenic littermates with HSV-1 revealed no differences in lytic replication, establishment of latency, or reactivation, suggesting that expression of the LAT transgene in
trans
has no significant effect on those functions. Taken together, these data indicate that the regulation of expression and processing of LAT RNA within the mouse is highly cell-type specific and occurs in the absence of other viral
cis
- and
trans
-acting factors.
Cidofovir Resistance in Vaccinia Virus Is Linked to Diminished Virulencein Mice
Authors: Andrei Graciela , Gammon Don B. , Fiten Pierre , De Clercq Erik , Opdenakker Ghislain , Snoeck Robert , Evans David H. 
Published: September 2006

ABSTRACT

Cidofovir
[(
S
)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (HPMPC)]
is recognized as a promising drug for the treatment of poxvirus
infections, but drug resistance can arise by a mechanism that is poorly
understood. We show here that in vitro selection for high
levels of resistance to HPMPC produces viruses encoding two
substitution mutations in the virus DNA polymerase (
E9L
) gene.
These mutations are located within the regions of the gene encoding the
3′-5′ exonuclease (A314T) and polymerase (A684V)
catalytic domains. These mutant viruses exhibited cross-resistance to
other nucleoside phosphonate drugs, while they remained sensitive to
other unrelated DNA polymerase inhibitors. Marker rescue experiments
were used to transfer A314T and/or A684V alleles into a vaccinia virus
Western Reserve strain. Either mutation alone could confer a drug
resistance phenotype, although the degree of resistance was
significantly lower than when virus encoded both mutations. The A684V
substitution, but not the A314T change, also conferred a spontaneous
mutator phenotype. All of the HPMPC-resistant recombinant viruses
exhibited reduced virulence in mice, demonstrating that these
E9L
mutations are inextricably linked to reduced fitness in
vivo. HPMPC, at a dose of 50 mg/kg of body weight/day for 5 days, still
protected mice against intranasal challenge with the drug-resistant
virus with A314T and A684V mutations. Our studies show that proposed
drug therapies offer a reasonable likelihood of controlling
orthopoxvirus infections, even if the viruses encode drug resistance
markers.
An Antiviral Peptide Inhibitor That Is Active against Picornavirus 2A Proteinases but Not Cellular Caspases
Authors: Deszcz Luiza , Cencic Regina , Sousa Carla , Kuechler Ernst , Skern Tim 
Published: September 2006

ABSTRACT

The replication of many viruses is absolutely dependent on proteolytic cleavage. Infected cells also use this biological mechanism to induce programmed cell death in response to viral infection. Specific inhibitors for both viral and cellular proteases are therefore of vital importance. We have recently shown that the general caspase inhibitor zVAD.fmk inhibits not only caspases, but also the 2A

pro

of human rhinoviruses (HRVs) (L. Deszcz, J. Seipelt, E. Vassilieva, A. Roetzer, and E. Kuechler, FEBS Lett.
560:
51-55, 2004). Here, we describe a derivative of zVAD.fmk that inhibits HRV2 2A

pro

but that has no effect on caspase 9. This gain in specificity was achieved by replacing the aspartic acid of zVAD.fmk with methionine to generate zVAM.fmk. Methionine was chosen because an oligopeptide with methionine at the P1 position was a much better substrate than an oligopeptide with an alanine residue, which is found at the P1 position of the wild-type HRV2 2A

pro

cleavage site. zVAM.fmk inhibits the replication of HRV type 2 (HRV2), HRV14, and HRV16. In contrast to zVAD.fmk, however, zVAM.fmk did not inhibit apoptosis induced by puromycin in HeLa cells. zVAM.fmk inhibited in vitro the intermolecular cleavage of eukaryotic initiation factor 4GI (eIF4GI) by HRV2 2A

pro

at nanomolar concentrations. However, much higher concentrations of zVAM.fmk were required to inhibit HRV14 2A

pro

cleavage of eIF4GI. In contrast, intramolecular self-processing of HRV14 2A

pro

was much more susceptible to inhibition by zVAM.fmk than that of HRV2 2A

pro

, suggesting that zVAM.fmk inhibits HRV2 and HRV14 replication by targeting different reactions of the same proteinase.
Antibodies to gp350/220 Enhance the Ability of Epstein-Barr Virus To Infect Epithelial Cells
Authors: Turk Susan M. , Jiang Ru , Chesnokova Liudmila S. , Hutt-Fletcher Lindsey M. 
Published: September 2006

ABSTRACTEpstein-Barr virus (EBV) is a persistent, orally transmitted herpesvirus that replicates in B cells and epithelial cells and is associated with lymphoid and epithelial malignancies. The virus binds to CD21 on B cells via glycoprotein gp350/220 and infects efficiently. Infection of cultured epithelial cells has not typically been efficient but can occur in the absence of gp350/220 and CD21 and in vivo is thought to be important to the development of nasopharyngeal carcinoma. We report here that antibodies to gp350/220, which inhibit EBV infection of B cells, enhance infection of epithelial cells. The effect is not mediated by Fc receptor binding but is further enhanced by antibody cross-linking, which may patch gp350/220 in the virus envelope. Saliva from EBV-seropositive individuals has similar effects that can be reversed by depletion of antibody. The results are consistent with a model in which gp350/220 interferes with the access of other important players to the epithelial cell surface. The results may have implications for the development of nasopharyngeal carcinoma in high-risk populations in which elevated titers of antibody to EBV lytic cycle proteins are prognostic.
Mobilization of Full-Length Semliki Forest Virus Replicon by Retrovirus Particles
Authors: Piver Eric , Collin Christine , Renault Noémie , Bru Thierry , Pagès Jean-Christophe 
Published: September 2006

ABSTRACT

Conciliating biosafety with efficient gene transfer remains a constant concern in the development of retroviral vectors. Semliki Forest virus (SFV) replicons allow important retroviral vector production with interesting features. It is noteworthy that retroviruses have the ability to package Ψ
+
and, to some extent, Ψ
−
cellular RNAs. Therefore, it was important to study the retroviral transfer of highly abundant SFV genomes expressing retroviral proteins. Here, we show that full-length SFV-vector replicons, with or without Ψ, are efficiently packaged into retrovirus particles. Mechanistically, our data suggest that SFV packaging is the sum of its retroviral nucleocapsid-dependent recruitment together with a passive hijacking of membrane-anchored SFV replicon. A direct consequence of this phenomenon is the formation of particles harboring autonomous replicative abilities and contaminating vector preparations. Importantly, we confirm that retroviral SFV mobilization is not an exclusive feature of murine gamma retroviruses, since it is also observed using lentivectors.
Complementation of Human Immunodeficiency Virus Type 1 Replication by Intracellular Selection of
Escherichia coli
\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(tRNA_{3}^{Lys}\) \end{document} Supplied in
trans
Authors: McCulley Anna , Morrow Casey D. 
Published: September 2006

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) exclusively selects
tRNA
3

Lys

as the primer for the initiation of reverse transcription, even though both
tRNA
3

Lys

and
tRNA
1,2

Lys

are found in HIV-1 virions. Alteration of the HIV-1 primer-binding site (PBS) to be complementary to alternate tRNAs results in the use of those tRNAs for replication, indicating that primer complementarity with the PBS is an important determinant of primer selection. In previous studies, we have exploited this fact to develop a system in which yeast (
Saccharomyces cerevisiae
) tRNA
Phe
is provided in
trans
to complement the replication of HIV-1 with a PBS complementary to yeast tRNA
Phe
. Recent studies have demonstrated that the presence of lysyl-tRNA synthetase in HIV-1 virions might account for the preference for the selection of
tRNA
3

Lys

in HIV-1 replication. To establish a complementation system more reflective of HIV-1 primer selection, we have altered the HIV-1 PBS to be complementary to the
Escherichia coli tRNA
3

Lys

, which shares near identity with mammalian
tRNA
3

Lys

except in the 3′-terminal 18-nucleotide sequence that binds to the PBS.
E. coli tRNA
3

Lys

expressed from a plasmid was aminoacylated in mammalian cells. Cotransfection of cells with a plasmid that encodes
E. coli tRNA
3

Lys

and a plasmid encoding an HIV-1 provirus with a PBS complementary to
E. coli tRNA
3

Lys

resulted in the production of infectious virus. A comparison of the two complementation systems revealed that higher levels of intracellular
E. coli tRNA
3

Lys

than of yeast tRNA
Phe
were needed to achieve equal levels of infectious virus, indicating that there was no preferential selection of
E. coli tRNA
3

Lys

. To examine the specificity of tRNA
Lys
selection,
E. coli tRNA
3

Lys

was modified to
tRNA
1,2

Lys

. This tRNA was also aminoacylated when expressed in mammalian cells and complemented the infectivity of HIV-1 at levels similar to those seen for
E. coli tRNA
3

Lys

. Additional mutations in the anticodon of
E. coli tRNA
3

Lys

were constructed; these mutations did not significantly correlate with the capacity of the tRNA primer to complement infectivity of HIV-1, even though they had a drastic effect on the aminoacylation of the tRNAs. The results of these studies demonstrate that
E. coli tRNA
3

Lys

provided in
trans
can complement HIV-1 genomes with the PBS altered to
E. coli tRNA
3

Lys

. However, the capacity of
tRNA
3

Lys

to interact with lysyl-tRNA synthetase does not entirely explain the enhanced preference for selection of
tRNA
3

Lys

for the replication of HIV-1.
A Full-Genome Phylogenetic Analysis of Varicella-Zoster Virus Reveals a Novel Origin of Replication-Based Genotyping Scheme and Evidence of Recombination between Major Circulating Clades
Authors: Peters Geoffrey A. , Tyler Shaun D. , Grose Charles , Severini Alberto , Gray Michael J. , Upton Chris , Tipples Graham A. 
Published: September 2006

ABSTRACTVaricella-zoster virus (VZV) is a remarkably stable virus that until recently was thought to exhibit near-universal genetic homogeneity among circulating wild-type strains. In recent years, the expanding knowledge of VZV genetics has led to a number of groups proposing sequence-based typing schemes, but no study has yet examined the relationships between VZV genotypes at a full-genome level. A central hypothesis of this study is that VZV has coevolved with humankind. In this study, 11 additional full VZV genomic sequences are presented, bringing the current number of complete genomic sequences publicly available to 18. The full-genome alignment contained strains representing four distinct clades, but the possibility exists that a fifth clade comprised of African and Asian-like isolates was not represented. A consolidated VZV genotyping scheme employing the origin-associated region between reiteration region R4 and open reading frames (ORFs) 63 and 70 is described, one which accurately categorizes strains into one of four clades related to the geographic origin of the isolates. The full-genome alignment also provided evidence for recombination having occurred between the major circulating VZV clades. One Canadian clinical isolate was primarily Asian-like in origin, with most of the genome showing strong sequence identity to the Japanese-like clade B, with the exceptions being two putative recombination regions, located in ORFs 14 to 17 and ORFs 22 to 26, which showed clear similarity to the European/North American clade A. The very low rate of single-nucleotide polymorphisms scattered across the genome made full-genome sequencing the only definitive method for identifying specific VZV recombination events.
Inhibition of Hendra Virus Fusion
Authors: Porotto M. , Doctor L. , Carta P. , Fornabaio M. , Greengard O. , Kellogg G. E. , Moscona A. 
Published: September 2006

ABSTRACT
Hendra virus (HeV) is a recently identified paramyxovirus that is fatal in humans and could be used as an agent of bioterrorism. The HeV receptor-binding protein (G) is required in order for the fusion protein (F) to mediate fusion, and analysis of the triggering/activation of HeV F by G should lead to strategies for interfering with this key step in viral entry. HeV F, once triggered by the receptor-bound G, by analogy with other paramyxovirus F proteins, undergoes multistep conformational changes leading to a six-helix bundle (6HB) structure that accomplishes fusion of the viral and cellular membranes. The ectodomain of paramyxovirus F proteins contains two conserved heptad repeat regions (HRN and HRC) near the fusion peptide and the transmembrane domains, respectively. Peptides derived from the HRN and HRC regions of F are proposed to inhibit fusion by preventing F, after the initial triggering step, from forming the 6HB structure that is required for fusion. HeV peptides have previously been found to be effective at inhibiting HeV fusion. However, we found that a human parainfluenza virus 3 F-peptide is more effective at inhibiting HeV fusion than the comparable HeV-derived peptide.
Resistance to Alpha/Beta Interferon Is a Determinant of West Nile Virus Replication Fitness and Virulence
Authors: Keller Brian C. , Fredericksen Brenda L. , Samuel Melanie A. , Mock Richard E. , Mason Peter W. , Diamond Michael S. , Gale Michael 
Published: September 2006

ABSTRACT
The
emergence of West Nile virus (WNV) in the Western Hemisphere is marked
by the spread of pathogenic lineage I strains, which differ from
typically avirulent lineage II strains. To begin to understand the
virus-host interactions that may influence the phenotypic properties of
divergent lineage I and II viruses, we compared the genetic,
pathogenic, and alpha/beta interferon
(IFN-α/β)-regulatory properties of a lineage II isolate
from Madagascar (MAD78) with those of a new lineage I isolate from
Texas (TX02). Full genome sequence analysis revealed that MAD78
clustered, albeit distantly, with other lineage II strains, while TX02
clustered with emergent North American isolates, more specifically with
other Texas strains. Compared to TX02, MAD78 replicated at low levels
in cultured human cells, was highly sensitive to the antiviral actions
of IFN in vitro, and demonstrated a completely avirulent phenotype in
wild-type mice. In contrast to TX02 and other pathogenic forms of WNV,
MAD78 was defective in its ability to disrupt IFN-induced JAK-STAT
signaling, including the activation of Tyk2 and downstream
phosphorylation and nuclear translocation of STAT1 and STAT2. However,
replication of MAD78 was rescued in cells with a nonfunctional
IFN-α/β receptor (IFNAR). Consistent with this finding,
the virulence of MAD78 was unmasked upon infection of mice lacking
IFNAR. Thus, control of the innate host response and IFN actions is a
key feature of WNV pathogenesis and replication
fitness.
Complete-Genome Phylogenetic Approach to Varicella-Zoster Virus Evolution: Genetic Divergence and Evidence for Recombination
Authors: Norberg Peter , Liljeqvist Jan-Åke , Bergström Tomas , Sammons Scott , Schmid D. Scott , Loparev Vladimir N. 
Published: September 2006

ABSTRACT
Recent studies of varicella-zoster virus (VZV) DNA sequence variation, involving large numbers of globally distributed clinical isolates, suggest that this virus has diverged into at least three distinct genotypes designated European (E), Japanese (J), and mosaic (M). In the present study, we determined and analyzed the complete genomic sequences of two M VZV strains and compared them to the sequences of three E strains and two J strains retrieved from GenBank (including the Oka vaccine preparation, V-Oka). Except for a few polymorphic tandem repeat regions, the whole genome, representing approximately 125,000 nucleotides, is highly conserved, presenting a genetic similarity between the E and J genotypes of approximately 99.85%. These analyses revealed that VZV strains distinctly segregate into at least four genotypes (E, J, M1, and M2) in phylogenetic trees supported by high bootstrap values. Separate analyses of informative sites revealed that the tree topology was dependent on the region of the VZV genome used to determine the phylogeny; collectively, these results indicate the observed strain variation is likely to have resulted, at least in part, from interstrain recombination. Recombination analyses suggest that strains belonging to the M1 and M2 genotypes are mosaic recombinant strains that originated from ancestral isolates belonging to the E and J genotypes through recombination on multiple occasions. Furthermore, evidence of more recent recombination events between M1 and M2 strains is present in six segments of the VZV genome. As such, interstrain recombination in dually infected cells seems to figure prominently in the evolutionary history of VZV, a feature it has in common with other herpesviruses. In addition, we report here six novel genomic targets located in open reading frames 51 to 58 suitable for genotyping of clinical VZV isolates.
Revealing Domain Structure through Linker-Scanning Analysis of the Murine Leukemia Virus (MuLV) RNase H and MuLV and Human Immunodeficiency Virus Type 1 Integrase Proteins
Authors: Puglia Jennifer , Wang Tan , Smith-Snyder Christine , Cote Marie , Scher Michael , Pelletier Joelle N. , John Sinu , Jonsson Colleen B. , Roth Monica J. 
Published: September 2006

ABSTRACT

Linker-scanning libraries were generated within the 3′ terminus of the Moloney murine leukemia virus (M-MuLV)
pol
gene encoding the connection-RNase H domains of reverse transcriptase (RT) as well as the structurally related M-MuLV and human immunodeficiency virus type 1 (HIV-1) integrase (IN) proteins. Mutations within the M-MuLV proviral vectors were Tn
7
based and resulted in 15-bp insertions. Mutations within an HIV-1 IN bacterial expression vector were based on Tn
5
and resulted in 57-bp insertions. The effects of the insertions were examined in vivo (M-MuLV) and in vitro (HIV-1). A total of 178 individual M-MuLV constructs were analyzed; 40 in-frame insertions within RT connection-RNase H, 108 in-frame insertions within IN, 13 insertions encoding stop codons within RNase H, and 17 insertions encoding stop codons within IN. For HIV-1 IN, 56 mutants were analyzed. In both M-MuLV and HIV-1 IN, regions are identified which functionally tolerate multiple-linker insertions. For MuLV, these correspond to the RT-IN proteolytic junction, the junction between the IN core and C terminus, and the C terminus of IN. For HIV-1 IN, in addition to the junction between the IN core and C terminus and the C terminus of IN, insertions between the N terminus and core domains maintained integration and disintegration activity. Of the 40 in-frame insertions within the M-MuLV RT connection-RNase H domains, only the three C-terminal insertions mapping to the RT-IN proteolytic junction were viable. These results correlate with deletion studies mapping the domain and subdomain boundaries of RT and IN. Importantly, these genetic footprints provide a means to identify nonessential regions within RT and IN for targeted gene therapy applications.
High Frequency of Genetic Recombination Is a Common Feature of Primate Lentivirus Replication
Authors: Chen Jianbo , Powell Douglas , Hu Wei-Shau 
Published: September 2006

ABSTRACT

Recent studies indicate that human immunodeficiency virus type 1 (HIV-1) recombines at exceedingly high rates, approximately 1 order of magnitude more frequently than simple gammaretroviruses such as murine leukemia virus and spleen necrosis virus. We hypothesize that this high frequency of genetic recombination is a common feature of primate lentiviruses. Alternatively, it is possible that HIV-1 is unique among primate lentiviruses in possessing high recombination rates. Among other primate lentiviruses, only the molecular mechanisms of HIV-2 replication have been extensively studied. There are reported differences between the replication mechanisms of HIV-1 and those of HIV-2, such as preferences for RNA packaging in
cis
and properties of reverse transcriptase and RNase H activities. These biological disparities could lead to differences in recombination rates between the two viruses. Currently, HIV-1 is the only primate lentivirus in which recombination rates have been measured. To test our hypothesis, we established recombination systems to measure the recombination rates of two other primate lentiviruses, HIV-2 and simian immunodeficiency virus from African green monkeys (SIVagm), in one round of viral replication. We determined that, for markers separated by 588, 288, and 90 bp, HIV-2 recombined at rates of 7.4%, 5.5%, and 2.4%, respectively, whereas SIVagm recombined at rates of 7.8%, 5.6%, and 2.7%, respectively. These high recombination rates are within the same range as the previously measured HIV-1 recombination rates. Taken together, our results indicate that HIV-1, HIV-2, and SIVagm all possess high recombination frequencies; hence, the high recombination potential is most likely a common feature of primate lentivirus replication.