bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virus Infection Switches TLR-3-Positive Human Neurons To Become Strong Producers of Beta Interferon
Authors: Préhaud Christophe , Mégret Françoise , Lafage Mireille , Lafon Monique 
Published: September 2005

ABSTRACT

To study the capacity of human neurons to mount innate immunity responses to viral infections, we infected cells of a human postmitotic neuron-derivative cell line, NT2-N, with rabies virus (RABV) and herpes simplex type 1 (HSV-1). Changes in neuronal gene expression were analyzed by use of Affymetrix microarrays. Applying a twofold cutoff, RABV increased the transcription of 228 genes, and HSV-1 increased the transcription of 263 genes. The most striking difference between the two infections concerns genes involved in immunity. These genes represent 24% of the RABV-upregulated genes and only 4.9% of the HSV-1-upregulated genes. Following RABV infection, the most upregulated genes belong to the immunity cluster and included almost exclusively genes for beta interferon (
IFN
-β) primary and secondary responses as well as genes for chemokines (
CCL-5
,
CXCL-10
) and inflammatory cytokines (interleukin 6 [IL-6], tumor necrosis factor alpha, interleukin 1 alpha). In contrast, HSV-1 infection did not increase
IFN
-β gene transcripts and triggered the production of only
IL-6
and interferon regulatory factor 1 mRNAs. The microarray results were confirmed by real-time PCR, immunocytochemistry, and enzyme-linked immunosorbent assay. Human neurons were found to express Toll-like receptor 3. They produced
IFN
-β after treatment with poly(I:C) but not with lipopolysaccharide. Thus, human neurons can mount an innate immunity response to double-stranded RNA. These observations firmly establish that human neurons, in absence of glia, have the intrinsic machinery to sense virus infection.
Structural Genomics of the Severe Acute Respiratory Syndrome Coronavirus: Nuclear Magnetic Resonance Structure of the Protein nsP7
Authors: Peti Wolfgang , Johnson Margaret A. , Herrmann Torsten , Neuman Benjamin W. , Buchmeier Michael J. , Nelson Mike , Joseph Jeremiah , Page Rebecca , Stevens Raymond C. , Kuhn Peter , Wüthrich Kurt 
Published: September 2005

ABSTRACTHere, we report the three-dimensional structure of severe acute respiratory syndrome coronavirus (SARS-CoV) nsP7, a component of the SARS-CoV replicase polyprotein. The coronavirus replicase carries out regulatory tasks involved in the maintenance, transcription, and replication of the coronavirus genome. nsP7 was found to assume a compact architecture in solution, which is comprised primarily of helical secondary structures. Three helices (α2 to α4) form a flat up-down-up antiparallel α-helix sheet. The N-terminal segment of residues 1 to 22, containing two turns of α-helix and one turn of 310-helix, is packed across the surface of α2 and α3 in the helix sheet, with the α-helical region oriented at a 60° angle relative to α2 and α3. The surface charge distribution is pronouncedly asymmetrical, with the flat surface of the helical sheet showing a large negatively charged region adjacent to a large hydrophobic patch and the opposite side containing a positively charged groove that extends along the helix α1. Each of these three areas is thus implicated as a potential site for protein-protein interactions.
A Short Double-Stranded RNA Motif of
Peach Latent Mosaic Viroid
Contains the Initiation and the Self-Cleavage Sites of Both Polarity Strands
Authors: Delgado Sonia , Martínez de Alba Ángel E. , Hernández Carmen , Flores Ricardo 
Published: September 2005

ABSTRACT

The transcription initiation sites of viroid RNAs, despite their relevance for replication and in vivo folding, are poorly characterized. Here we have examined this question for
Peach latent mosaic viroid
(PLMVd), which belongs to the family of chloroplastic viroids with hammerhead ribozymes (
Avsunviroidae
), by adapting an RNA ligase-mediated rapid amplification of cDNA ends methodology developed for mapping the genuine capped 5′ termini of eukaryotic messenger RNAs. To this aim, the characteristic free 5′-triphosphate group of chloroplastic primary transcripts from PLMVd-infected young fruits was previously capped in vitro with GTP and guanylyltransferase. PLMVd plus and minus initiation sites map at similar double-stranded motifs of 6 to 7 bp that also contain the conserved GUC triplet preceding the self-cleavage site in both polarity strands. Within the branched secondary structures predicted for the two PLMVd strands, this motif is located at the base of a similar long hairpin that presumably contains the promoters for a chloroplastic RNA polymerase. The transcription templates could be the circular viroid RNAs or their most abundant linear counterparts, assuming the involvement of an RNA polymerase able to jump over template discontinuities. Both PLMVd initiation sites were confirmed by applying the same methodology to two purified PLMVd subgenomic RNAs and by primer extension, and they therefore likely reflect the in vivo situation. The location of the PLMVd initiation sites provides a mechanistic view into how the nascent strands may fold and self-cleave during transcription. The approach described here may be extended to other chloroplastic RNA replicons and transcripts accumulating at low levels.
Activation of Innate Defense against a Paramyxovirus Is Mediated by RIG-I and TLR7 and TLR8 in a Cell-Type-Specific Manner
Authors: Melchjorsen Jesper , Jensen Søren B. , Malmgaard Lene , Rasmussen Simon B. , Weber Friedemann , Bowie Andrew G. , Matikainen Sampsa , Paludan Søren R. 
Published: September 2005

ABSTRACTRecognition of pathogens by the innate immune system is mediated by pattern recognition receptors (PRRs), which recognize specific molecular structures of the infectious agents and subsequently trigger expression of genes involved in host defense. Toll-like receptors (TLRs) represent a well-characterized class of membrane-bound PRRs, and the RNA helicase retinoic acid inducible gene I (RIG-I) has recently been described as a novel cytoplasmic PRR recognizing double-stranded RNA (dsRNA). Here we show that activation of signal transduction and induction of cytokine expression by the paramyxovirus Sendai virus is dependent on virus replication and involves PRRs in a cell-type-dependent manner. While nonimmune cells relied entirely on recognition of dsRNA through RIG-I for activation of an antiviral response, myeloid cells utilized both the single-stranded RNA sensing TLR7 and TLR8 and dsRNA-dependent mechanisms independent of RIG-I, TLR3, and dsRNA-activated protein kinase R to trigger this response. Therefore, there appears to be a large degree of cell-type specificity in the mechanisms used by the host to recognize infecting viruses.
Cleavage of Human Cytomegalovirus Protease pUL80a at Internal and Cryptic Sites Is Not Essential but Enhances Infectivity
Authors: Loveland Amy N. , Chan Chee-Kai , Brignole Edward J. , Gibson Wade 
Published: September 2005

ABSTRACT

The cytomegalovirus (CMV) maturational protease, assemblin, contains an “internal” (I) cleavage site absent from its homologs in other herpesviruses. Blocking this site for cleavage did not prevent replication of the resulting I
−
mutant virus. However, cells infected with the I
−
virus showed increased amounts of a fragment produced by cleavage at the nearby “cryptic” (C) site, suggesting that its replication may bypass the I-site block by using the C site as an alternate cleavage pathway. To test this and further examine the biological importance of these cleavages, we constructed two additional virus mutants—one blocked for C-site cleavage and another blocked for both I- and C-site cleavage. Infectivity comparisons with the parental wild-type virus showed that the I
−
mutant was the least affected for virus production, whereas infectivity of the C
−
mutant was reduced by ≈40% and when both sites were blocked virus infectivity was reduced by nearly 90%, providing the first evidence that these cleavages have biological significance. We also present and discuss evidence suggesting that I-site cleavage destabilizes assemblin and its fragments, whereas C-site cleavage does not.
Induction and Utilization of an ATM Signaling Pathway by Polyomavirus
Authors: Dahl Jean , You John , Benjamin Thomas L. 
Published: September 2005

ABSTRACTProgression from G1to S is essential for polyomavirus DNA replication and depends on the interaction of large T with the retinoblastoma gene product pRb. This virus-induced replication pathway is accompanied by p53 activation resembling a DNA damage response (12). We sought to determine whether this pathway depends in part on activation of the ATM (ataxiatelangiectasiamutated) kinase and whether the virus gains advantages from this pathway beyond that of entry into S. We show that polyomavirus infection activates the S- and G2-phase checkpoints in primary as well as established mouse cells. Infected cells undergo a prolonged S phase compared to uninfected serum-stimulated cells and show no evidence of a G2→M transition before lytic death ensues. Infection is accompanied by increases in ATM activity in vitro and in the level of ATM-S1981-P in vivo. The incubation of infected cells with caffeine, a known ATM inhibitor, did not block entry into S but reduced the rate of viral compared to cellular DNA synthesis. Importantly, caffeine lowered the yields of viral DNA an average of 3- to 6-fold and those of infectious virus by as much as 10-fold. Virus yields were 10-fold lower in ATM−/−p53−/−than in ATM+/+p53−/−mouse embryo fibroblasts, indicating a p53-independent role of ATM in productive infection. Replacement of the normal SMC1 (structuralmaintenance ofchromosomes, or cohesin) protein, a critical ATM substrate in the DNA repair pathway, with its phosphorylation mutant SMC1S957AS966Aalso lowered virus yields by roughly 90%. We suggest that polyomavirus activates and utilizes a component(s) of an ATM pathway of DNA repair to prolong S phase and aid its own replication.
Oxadiazols: a New Class of Rationally Designed Anti-Human Immunodeficiency Virus Compounds Targeting the Nuclear Localization Signal of the Viral Matrix Protein
Authors: Haffar Omar , Dubrovsky Larisa , Lowe Richard , Berro Reem , Kashanchi Fatah , Godden Jeffrey , Vanpouille Christophe , Bajorath Jürgen , Bukrinsky Michael 
Published: September 2005

ABSTRACTDespite recent progress in anti-human immunodeficiency virus (HIV) therapy, drug toxicity and emergence of drug-resistant isolates during long-term treatment of HIV-infected patients necessitate the search for new targets that can be used to develop novel antiviral agents. One such target is the process of nuclear translocation of the HIV preintegration complex. Previously we described a class of arylene bis(methylketone) compounds that inhibit HIV-1 nuclear import by targeting the nuclear localization signal (NLS) in the matrix protein (MA). Here we report a different class of MA NLS-targeting compounds that was selected using computer-assisted drug design. The leading compound from this group, ITI-367, showed potent anti-HIV activity in cultures of T lymphocytes and macrophages and also inhibited HIV-1 replication in ex vivo cultured lymphoid tissue. The virus carrying inactivating mutations in MA NLS was resistant to ITI-367. Analysis by real-time PCR demonstrated that the compound specifically inhibited nuclear import of viral DNA, measured by two-long terminal repeat circle formation. Evidence of the existence of this mechanism was provided by immunofluorescent microscopy, using fluorescently labeled HIV-1, which demonstrated retention of the viral DNA in the cytoplasm of drug-treated macrophages. Compounds inhibiting HIV-1 nuclear import may be attractive candidates for further development.
Human Herpesvirus 6 Open Reading Frame U14 Protein and Cellular p53 Interact with Each Other and Are Contained in the Virion
Authors: Takemoto Masaya , Koike Masato , Mori Yasuko , Yonemoto Sayoko , Sasamoto Yumi , Kondo Kazuhiro , Uchiyama Yasuo , Yamanishi Koichi 
Published: September 2005

ABSTRACTA mass spectroscopic analysis of proteins from human herpesvirus 6 (HHV-6)-infected cells showed that the HHV-6 U14 protein coimmunoprecipitated with the tumor suppressor p53. The binding of U14 to p53 was verified by coimmunoprecipitation experiments in both Molt-3 cells infected with HHV-6 and 293 cells cotransfected with U14 and p53 expression vectors. Indirect immunofluorescence assays (IFAs) showed that by 18 h postinfection (hpi) U14 localized to the dot-like structures observed in both the nucleus and cytoplasm where p53 was partly accumulated. Despite Northern blotting evidence that U14 follows late kinetics, the U14 protein was detected immediately after infection (at 3 hpi) by IFA. In addition, by Western blotting, U14 was detected at 0 hpi or in the presence of cycloheximide which completely abolished the expression of IE1 protein. In addition to U14, p53 was detected at 0 hpi although it was not detected in mock-infected cells. Furthermore, both U14 and p53 were clearly detected in the viral particles by Western blotting and immunoelectron microscopy, supporting the idea that U14 and p53 are incorporated into virions. Our study provides the first evidence of the incorporation of cellular p53 into viral particles and suggests that p53 may play an important role in viral infection.
Complete Nucleotide Sequence of Polyomavirus SA12
Authors: Cantalupo Paul , Doering Adrienne , Sullivan Christopher S. , Pal Achintya , Peden K. W. C. , Lewis Andrew M. , Pipas James M. 
Published: September 2005

ABSTRACT

The
Polyomaviridae
have small icosahedral virions that contain a genome of approximately 5,000 bp of circular double-stranded DNA. Polyomaviruses infect hosts ranging from humans to birds, and some members of this family induce tumors in test animals or in their natural hosts. We report the complete nucleotide sequence of simian agent 12 (SA12), whose natural host is thought to be
Papio ursinus
, the chacma baboon. The 5,230-bp genome has a genetic organization typical of polyomaviruses. Sequences encoding large T antigen, small t antigen, agnoprotein, and the viral capsid proteins VP1, VP2, and VP3 are present in the expected locations. We show that, like its close relative simian virus 40 (SV40), SA12 expresses microRNAs that are encoded by the late DNA strand overlapping the 3′ end of large T antigen coding sequences. Based on sequence comparisons, SA12 is most closely related to BK virus (BKV), a human polyomavirus. We have developed a real-time PCR test that distinguishes SA12 from BKV and the other closely related polyomaviruses JC virus and SV40. The close relationship between SA12 and BKV raises the possibility that these viruses circulate between human and baboon hosts.
A practical approach to the clinical diagnosis of Ewing’s sarcoma/primitive neuroectodermal tumour and other small round cell tumours sharing EWS rearrangement using new fluorescence in situ hybridisation probes for EWSR1 on formalin fixed, paraffin wax embedded tissue
Authors: Yamaguchi U , Hasegawa T , Morimoto Y , Tateishi U , Endo M , Nakatani F , Kawai A , Chuman H , Beppu Y , Endo M , Kurotaki H , Furuta K 
Published: September 2005

Background:Over 90% of Ewing’s sarcoma/primitive neuroectodermal tumour (ES/PNET) cases have the t(11;22) chromosomal rearrangement, which is also found in other small round cell tumours, including desmoplastic small round cell tumour (DSRCT) and clear cell sarcoma (CCS). Although this rearrangement can be analysed by fluorescence in situ hybridisation (FISH) using routinely formalin fixed, paraffin wax embedded (FFPE) tissues when fresh or frozen tissues are not available, a sensitive and convenient detection method is needed for routine clinical diagnosis.Aims:To investigate the usefulness of newly developed probes for detecting EWS rearrangement resulting from chromosomal translocations using FISH and FFPE tissue in the clinical diagnosis of ES/PNET, DSRCT, and CCS.Methods:Sixteen ES/PNETs, six DSRCTs, and six CCSs were studied. Three poorly differentiated synovial sarcomas, three alveolar rhabdomyosarcomas, and three neuroblastomas served as negative controls. Interphase FISH analysis was performed on FFPE tissue sections with a commercially available EWSR1 (22q12) dual colour, breakapart rearrangement probe.Results:One fused signal and one split signal of orange and green, demonstrating rearrangement of the EWS gene, was detected in 14 of 16 ES/PNETs, all six DRSCTs, and five of six CCSs, but not in the negative controls.Conclusions:Interphase FISH using this newly developed probe is sensitive and specific for detecting the EWS gene on FFPE tissues and is of value in the routine clinical diagnosis of ES/PNET, DSRCT, and CCS.
Melanoma inhibitor of apoptosis protein is expressed differentially in melanoma and melanocytic naevus, but similarly in primary and metastatic melanomas
Authors: Gong J , Chen N , Zhou Q , Yang B , Wang Y , Wang X 
Published: September 2005

Background:Malignant melanoma is highly resistant to current treatments. The inhibitor of apoptosis protein (IAP) family member, melanoma IAP (ML-IAP), is overexpressed in some melanoma cell lines, rendering them resistant to apoptotic signals. Targeting ML-IAP is a promising approach to treating melanoma. However, the status of ML-IAP expression in human melanoma tissues and the difference in expression between melanoma and melanocytic naevus are not known.Aims:To investigate these issues.Methods:ML-IAP expression in 48 archived patient samples (34 melanomas and 14 dermal naevi) was assessed by immunohistochemistry and by in situ hybridisation and reverse transcription polymerase chain reaction (RT-PCR) assays developed for the study.Results:Expression of ML-IAP was detected in 47.6–70.6% (10 of 21 to 24 of 34) of the melanomas, varying with detection methods. The expression rate in melanoma was much higher than that in melanocytic naevus (10.0–21.4%; one of 10 to three of 14). No significant difference was seen between primary and secondary melanomas. ML-IAP expression rates assessed by the three methods were in agreement.Conclusions:The ML-IAP expression rate in archived melanoma tissues is around 50–70%, with no difference between primary and secondary melanomas. A small number of dermal naevi (∼ 20%) also expressed ML-IAP.
STRAD in Peutz-Jeghers syndrome and sporadic cancers
Authors: de Leng W W J , Keller J J , Luiten S , Musler A R , Jansen M , Baas A F , de Rooij F W M , Gille J J P , Menko F H , Offerhaus G J A , Weterman M A J 
Published: September 2005

Background/Aims:LKB1is a tumour suppressor gene that is associated with Peutz-Jeghers syndrome (PJS), a rare autosomal dominant cancer predisposition syndrome. However, germline mutations in theLKB1gene are found in only about 60% of patients with PJS, suggesting the existence of a second PJS gene. TheSTRADgene, encoding an LKB1 interacting protein that activates LKB1, which subsequently leads to polarisation of cells, is an interesting candidate for a second PJS gene and a potential tumour suppressor gene in sporadic carcinomas.Methods:The involvement of STRAD in 42 PJS associated tumours (sporadic lung, colon, gastric, and ovarian adenocarcinomas) was studied using loss of heterozygosity (LOH) analysis of eight microsatellite markers on chromosome 17, includingTP53,BRCA1, andSTRADmarkers.Results:Loss of the marker near theSTRADlocus was seen in 13 of 29 informative cases, including all gastric adenocarcinomas. Specific LOH of theSTRADmarker was found in four of 29 informative cases. For these patients all exons and exon–intron boundaries of theSTRADgene were sequenced, but no somatic mutations were identified. Furthermore, no germlineSTRADmutations were found in 10 patients with PJS and family members withoutLKB1germline mutation.Conclusions:Despite the frequent occurrence of LOH in theSTRADregion, these results indicate that inactivation of theSTRADgene is not essential in the sporadic adenocarcinomas studied, although it is possible thatSTRADmay be inactivated in different ways. In addition, no evidence was found for the hypothesis that STRAD is a second PJS susceptibility gene.
The roles of Bcl-xL in modulating apoptosis during development of Xenopus laevis
Authors: Johnston Jillian , Chan Robert , Calderon-Segura Maria , McFarlane Sarah , Browder Leon W 
Published: September 2005

Abstract

Background
Apoptosis is a common and essential aspect of development. It is particularly prevalent in the central nervous system and during remodelling processes such as formation of the digits and in amphibian metamorphosis. Apoptosis, which is dependent upon a balance between pro- and anti-apoptotic factors, also enables the embryo to rid itself of cells damaged by gamma irradiation. In this study, the roles of the anti-apoptotic factor Bcl-xL in protecting cells from apoptosis were examined in Xenopus laevis embryos using transgenesis to overexpress the XR11 gene, which encodes Bcl-xL. The effects on developmental, thyroid hormone-induced and γ-radiation-induced apoptosis in embryos were examined in these transgenic animals.

Results
Apoptosis was abrogated in XR11 transgenic embryos. However, the transgene did not prevent the apoptotic response of tadpoles to thyroid hormone during metamorphosis. Post-metamorphic XR11 frogs were reared to sexual maturity, thus allowing us to produce second-generation embryos and enabling us to distinguish between the maternal and zygotic contributions of Bcl-xL to the γ-radiation apoptotic response. Wild-type embryos irradiated before the mid-blastula transition (MBT) underwent normal cell division until reaching the MBT, after which they underwent massive, catastrophic apoptosis. Over-expression of Bcl-xL derived from XR11 females, but not males, provided partial protection from apoptosis. Maternal expression of XR11 was also sufficient to abrogate apoptosis triggered by post-MBT γ-radiation. Tolerance to post-MBT γ-radiation from zygotically-derived XR11 was acquired gradually after the MBT in spite of abundant XR11 protein synthesis.

Conclusion
Our data suggest that Bcl-xL is an effective counterbalance to proapoptotic factors during embryonic development but has no apparent effect on the thyroid hormone-induced apoptosis that occurs during metamorphosis. Furthermore, post-MBT apoptosis triggered by irradiation before the MBT could only be restrained by maternal expression of Bcl-x

L
. Although maternal expression of XR11 was sufficient to abrogate apoptosis triggered by post-MBT γ-radiation, radiation tolerance from zygotically-derived XR11 was acquired gradually, indicating that synthesis of XR11 protein is not sufficient to prevent apoptosis. Thus, repression of radiation-induced apoptosis by overexpression of Bcl-xL during embryonic development depends upon the timing of its expression and post-translational events that enable the protein to become effective.
Synthesis of Cubic Ia3d-like Mesostructured Silica at Low Temperature Using an Oligomeric Nonionic Surfactant
Authors: Lim SungHyun , Yoshitake Hideaki , Tatsumi Takashi 
Published: September 2005

Abstract
A mesoporous silica having the cubic structure similar to MCM-48 has been synthesized at low temperature using Brij 56 as surfactant in acidic media free of additives as evidenced by showing (211) and (220) reflection peaks in the XRD patterns and the same TEM images as MCM-48.
Highly Effective Synthesis of Cyclohexanone Oxime over a Novel Titanosilicate Ti-MWW
Authors: Song Fen , Liu Yueming , Wu Haihong , He Mingyuan , Wu Peng , Tatsumi Takashi 
Published: September 2005

Abstract
Liquid-phase ammoximation of cyclohexanone proceeds extremely efficiently, selectively, and stablely over a novel titanosilicate Ti-MWW in a clean solvent of water, which would lead to a potential process more environmentally benign for synthesizing cyclohexanone oxime.