bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of repetitive DNA regions and methylated DNA in ascovirus genomes
Authors: Bigot Yves , Stasiak Karine , Rouleux-Bonnin Florence , Federici Brian A. 
Published: August 2015

The accompanying phylogenetic study of large double-stranded DNA viruses based on their δ DNA polymerase genes suggests that ascoviruses (family Ascoviridae) and iridoviruses (family Iridoviridae) are closely related and may share a common ancestor. This relationship was unexpected because of marked differences between these viruses. Iridoviruses produce icosahedral virions and occur broadly among vertebrates and invertebrates, whereas ascoviruses typically produce reniform or bacilliform virions and are restricted to insect hosts, primarily lepidopterans. Detailed comparisons of these two virus types are not possible because fundamental information on the properties of the virions and their genomes is lacking, especially for ascoviruses. To facilitate further investigation of the putative evolutionary relationship between ascoviruses and iridoviruses, the genomes of representative viruses from each family were compared with respect to physical configuration, presence of DNA repeats and degree of DNA methylation. Genomes from Spodoptera frugiperda (SfAV1), Heliothis virescens (HvAV3) and Diadromus pulchellus (DpAV4) ascoviruses were all found to be circular and partially superhelical and to contain large interspersed repeats of 1–3 kbp. Mosquito (IV type 3), lepidopteran (IV type 6) and isopod (IV type 31) iridovirus genomes were all linear and lacked large regions of repetitive DNA. Ascovirus and iridovirus genomes were methylated and one, DpAV4, had the highest degree of methylation of any reported animal DNA virus. The major differences in the physical and biochemical characteristics of ascoviruses and iridoviruses reported here provide a foundation for further studies of their relatedness while making their possible close relationship and divergence during evolution of even greater interest.
A new ascovirus from Spodoptera exigua and its relatedness to the isolate from Spodoptera frugiperda
Authors: Cheng Xiao-Wen , Carner Gerald R. , Arif Basil M. 
Published: August 2015

A new ascovirus was isolated from Spodoptera exigua in Indonesia and was tentatively assigned as a new species, Spodoptera exigua ascovirus 5a (SeAV-5a) according to the present ICTV ascovirus naming scheme based on DNA restriction fragment length polymorphism (RFLP), hybridization, formation of occlusion body, tissue tropism and host spectrum. SeAV-5a replicated primarily in the fat body of susceptible hosts. SeAV-5a could be transmitted to S. frugiperda, Pseudoplusia includens and Trichoplusia ni, but not to Heliothis virescens. Infection with SeAV-5a arrested growth of the hosts, but prolonged their survival, which continued up to 33 days. Clusters of virions were seen inside the characteristic vesicles. Occasionally, virions were contained within vacuoles (one to five per vacuole) and some virions were embedded in occlusion bodies. The size of the SeAV-5a virion was 347×134 nm; however, aberrant long secondary viral products were also seen. The presence of occlusion body and Southern hybridization and Western immunoblot analyses suggest that SeAV-5a is more closely related to S. frugiperda ascovirus 1a (SfAV-1a) than to Trichoplusia ni ascovirus
2 (TnAV-2). Certain regions of the 182 kb genome of SeAV-5a showed hybridization to that of SfAV-1a. Two fragments in each of the SfAV-1a EcoRI and HindIII digests hybridized to the SeAV-5a genomic DNA probe. Five to eight HindIII and EcoRI fragments in SeAV-5a DNA hybridized to the SfAV-1a genomic probe.
Agnoprotein-1a of avian polyomavirus budgerigar fledgling disease virus: identification of phosphorylation sites and functional importance in the virus life-cycle
Authors: Liu Qiang , Hobom Gerd 
Published: August 2015

The avian polyomavirus budgerigar fledgling disease virus (BFDV) encodes an unusual set of four agnoproteins in its late upstream region. Of the two pairs of these proteins, which overlap each other in two different reading frames, the pL1-promoted agnoprotein-1a (agno-1a) is the dominant species and is able to support virus propagation in the absence of the other three polypeptides. Viral BFDV agno-1a, and also agno-1a expressed via an influenza virus vector, consists of a complex series of electrophoretically separable subspecies that can be reduced by phosphatase action down to a primary unphosphorylated protein with an apparent molecular mass of 31 kDa. Through peptide mass spectrometry and site-directed mutagenesis, the positions of four serine and three threonine residues have been determined as phosphate-accepting groups, which are partially modified by the combined action of three different cellular kinases. Since extensively phosphorylated agno-1a is required for its intracellular function, control over VP protein expression, and unphosphorylated agno-1a is observed as an additional component in the BFDV virion, both extreme subspecies appear to be drawn from that complex mixture, which also includes the intermediate stages of phosphorylation.
Insertion sites for recombinant vaccinia virus construction: effects on expression of a foreign protein
Authors: Coupar Barbara E. H. , Oke Pamela G. , Andrew Marion E. 
Published: August 2015

The expression of antigens or other molecules from recombinant vaccinia viruses requires the insertion of coding sequence at specific sites in the viral genome. Here we investigate the influence of two different sites on the level of protein expressed during a viral infection. The level of immune response in mice to vaccinia virus-expressed murine interleukin 2 (IL-2) or IL-4 varied depending on whether the coding sequence was inserted into the vaccinia virus thymidine kinase (tk) gene or into the HindIII F fragment of the viral genome where herpes simplex virus (HSV) tk was used as a selectable marker. In each case the intensity of the response was greater when the relevant gene was expressed from the HindIII F insertion site. In order to quantify these differences a series of recombinant viruses expressing luciferase was constructed. Luciferase activity from coding sequence inserted into the HindIII F fragment was significantly higher than that from the tk gene insertion, provided HSV tk+ constructs were compared. Insertion of a marker gene (HSV tk) into the HindIII F site with disruption of the F7L open reading frame led to a reduced level of luciferase expressed from the tk insert, despite more than 45 kb of intervening sequence. In mice, luciferase expression was higher from the HindIII F inserted gene than from the tk insert in both lungs and ovaries.
Spread of distinct human immunodeficiency virus type 1 AG recombinant lineages in Africa
Authors: Cornelissen Marion , van den Burg Remco , Zorgdrager Fokla , Goudsmit Jaap 
Published: August 2015

To identify new subtype G human immunodeficiency virus type 1 (HIV-1) strains and AG recombinant forms, we collected 28 serum samples from immigrants to the Netherlands from 12 countries throughout Africa. Based on the gag sequences 22 isolates were identified as subtype A or G. Phylogenetic analysis of discontinuous regions of the gag (726 nt), pol (1176 nt) and env (276 nt) genes revealed 13 AG recombinants with the mosaic structure A
gag
/G
pol
/A
env
, three with A
gag
/G
pol
/G
env
and one other with A
gag
/G
pol
/G
env
, in addition to ‘pure’ subtypes A
gag
/A
pol
/A
env
(n=1) and G
gag
/G
pol
/G
env
(n=4). To analyse the crossover points in more detail, a new RT–PCR was developed resulting in a large contiguous sequence of 2600 nt from the gag region to half the pol region. All the 13 A
gag
/G
pol
/A
env
recombinants appeared to belong to the circulating recombinant form (CRF) AG (IbNG). The three A
gag
/G
pol
/G
env
recombinants differed from the CRF AG (IbNG) subtype, suggesting the identification of a new CRF subtype. The recovery of AG recombinants from African countries a thousand miles apart indicates the active spread of new recombinants.
Properties of a neutralizing antibody that recognizes a conformational form of epitope ERDRD in the gp41 C-terminal tail of human immunodeficiency virus type 1
Authors: Cleveland S. Matthew , Jones Tim D. , Dimmock Nigel J. 
Published: August 2015

The possibility that epitopes from the C-terminal tail of the gp41 transmembrane protein of human immunodeficiency virus type 1 (HIV-1) are exposed the surface of the virion has long been contentious. Resolution of this has been hampered by the absence of any neutralizing monoclonal antibodies, but we have recently epitope-purified a neutralizing polyclonal IgG specific for one of the putative gp41 tail epitopes, 746ERDRD750. This was obtained from mice immunized parenterally with a plant virus chimera expressing residues 731–752 from the gp41 tail. The ERDRD epitope is highly conformational and is conserved in 81% of B clade viruses. Here, it is shown that this polyclonal ERDRD-specific IgG is highly potent, with an affinity of 2·2×108 M−1, and a neutralization rate constant (−K
neut) of 7·8×104 M−1 s−1 that exceeds that of nearly all other known HIV-1-neutralizing antibodies. ERDRD-specific IgG gave 50% neutralization at 0·1–0·2 μg/ml and 90% neutralization at approximately 3 μg/ml. It also neutralized virus that was already attached to target cells, and this and other data suggest that it neutralized by inhibiting a virion event that precedes the fusion–entry process. Consistent with this conclusion was the finding that neutralizing amounts of ERDRD-specific IgG did not inhibit the attachment of free virus to target cells. ERDRD-specific IgG was also cross-reactive and neutralized all but one of six B clade T cell line-adapted strains tested.
Enzymatic properties of hepatitis C virus NS3-associated helicase
Authors: Paolini Chantal , De Francesco Raffaele , Gallinari Paola 
Published: August 2015

The hepatitis C virus non-structural protein 3 (NS3) possesses a serine protease activity in the N-terminal one-third, whereas RNA-stimulated NTPase and helicase activities reside in the C-terminal portion. In this study, an N-terminal hexahistidine-tagged full-length NS3 polypeptide was expressed inEscherichia coliand purified to homogeneity by conventional chromatography. Detailed characterization of the helicase activity of NS3 is presented with regard to its binding and strand release activities on different RNA substrates. On RNA double-hybrid substrates, the enzyme was shown to perform unwinding activity starting from an internal ssRNA region of at least 3 nt and moving along the duplex in a 3′ to 5′ direction. In addition, data are presented suggesting that binding to ATP reduces the affinity of NS3 for ssRNA and increases its affinity for duplex RNA. Furthermore, we have ascertained the capacity of NS3 to specifically interact with and resolve the stem–loop RNA structure (SL I) within the 3′-terminal 46 bases of the viral genome. Finally, our analysis of NS3 processive unwinding under single cycle conditions by addition of heparin in both helicase and RNA-stimulated ATPase assays led to two conclusions: (i) NS3-associated helicase acts processively; (ii) most of the NS3 RNA-stimulated ATPase activity may not be directly coupled to translocation of the enzyme along the substrate RNA molecule.
Inhibition of cap-dependent gene expression induced by protein 2A of hepatitis A virus
Authors: Maltese Elisabetta , Bucci Mauro , Macchia Stefania , Latorre Patrizia , Pagnotti Paolo , Pierangeli Alessandra , Bercoff Raoul Pérez 
Published: August 2015

The viral protein 2A of hepatitis A virus (HAV) lacks the conserved 18 aa sequence found in other picornavirus proteases; hence, it is unclear whether the induction of CPE by culture-adapted HAV strains is due to 2A-mediated activity. Moreover, the cleavage sites and actual borders of HAV 2A are not known. Accordingly, a nested series of cDNA sequences encoding the segment of the HAV polyprotein (aa 760–1087) were linked to the 5′-UTR of poliovirus type 2 (Lansing strain) and inserted downstream of the gene encoding human growth hormone (GH). Following transfection of COS-1 cells, levels of GH (translation of which was entirely cap dependent) were determined in culture supernatants. Expression of HAV peptides extending from aa 764, 776 or 791 to 981 strongly inhibited cap-dependent translation of GH, whereas cap-independent expression of a reporter gene (CAT) directed by the poliovirus RNA 5′-UTR was unaffected. The inhibitory effect was absent in constructs expressing either the short peptide encompassing aa 760–836 or proteins initiated downstream of the putative cleavage site 836–837, suggesting that the boundaries of a functional HAV 2A may extend from the Gln/Ser junction 791–792 to residue 981, while peptides initiated at the Gln/Ala pair 836–837 may result from alternative cleavage. Point mutations that substituted members of the triad Ser916, His927 and Asp931 abolished the inhibitory effect on cap-dependent translation, suggesting that the HAV-induced CPE may be mediated by 2A protein.
The strong positive correlation between effective affinity and infectivity neutralization of highly cross-reactive monoclonal antibody IIB4, which recognizes antigenic site B on influenza A virus haemagglutinin
Authors: Kostolanský F. , Varečková E. , Betáková T. , Mucha V. , Russ G. , Wharton S. A. 
Published: August 2015

Monoclonal antibody (MAb) IIB4 displays a rare combination of virus neutralization (VN) activity and broad cross-reactivity with influenza A virus strains of the H3 subtype isolated in a period from 1973 to 1988. The epitope of this antibody has been identified as around HA1 residues 198, 199 and 201. Here we report that residues 155, 159, 188, 189 and 193 also influence the binding of this antibody. We have used this antibody to study the relationship between antibody affinity and VN activity. Using one MAb and a single epitope on the haemagglutinin (HA) of different influenza viruses we found a strong positive correlation between effective affinity and VN activity of MAb IIB4. A 10-fold increase in effective affinity corresponded to the 2000-fold increase in VN titre. It follows from the law of mass action that for an effective affinityK=9×108 l/mol, 50% VN was achieved at approx. 10% occupation of HA spikes with antibody. In contrast, for an effective affinityK=6×107 l/mol, to achieve 50% VN, occupation of up to 98% of HA spikes was required. An effective affinity aboutK=6×107l/mol thus represents the limiting value for VN because a further decrease in the affinity cannot be compensated by a higher concentration of antibody.
Expression of a Tranosema rostrale polydnavirus gene in the spruce budworm, Choristoneura fumiferana
Authors: Béliveau Catherine , Laforge Marlène , Cusson Michel , Bellemare Guy 
Published: August 2015

The endoparasitic wasp Tranosema rostrale (Ichneumonidae) transmits a polydnavirus (PDV) to its host, Choristoneura fumiferana, during oviposition. Unlike most other PDVs examined, the virus of T. rostrale (TrPDV) does not appear to play an important role in suppressing the host cellular immune response. However, it inhibits host metamorphosis. In the present study, TrPDV gene expression was examined in parasitized and virus-injected last-instar caterpillars. Northern analysis with viral DNA as a probe revealed only one detectable mRNA, of about 650 bp. The corresponding cDNA, termed TrV1, was cloned and sequenced and found to encode a protein of 103 amino acids which, following cleavage of the putative signal peptide, has a predicted molecular mass of 9·3 kDa. This protein displays limited similarity to the VHv1.4 cysteine-rich protein from the PDV of Campoletis sonorensis, mostly within the signal peptide region. By using a TrV1-specific probe, the TrV1 gene was localized to segment G of the TrPDV genome. The cuticle and fat body were identified as the principal sites of TrV1 transcription, with little transcription observed in haemocytes and midgut. Western analysis of proteins extracted from selected tissues of parasitized insects suggested that the TrV1 protein is secreted in the haemolymph. As observed for other PDVs, injection of TrPDV did not suppress transcription of the gene that encodes juvenile hormone esterase, the activity of which is inhibited by the virus. We speculate that the TrV1 protein may play a role in the inhibition of C. fumiferana metamorphosis.
Phylogenetic analysis of influenza C virus nonstructural (NS) protein genes and identification of the NS2 protein
Authors: Alamgir A. S. M. , Matsuzaki Yoko , Hongo Seiji , Tsuchiya Emi , Sugawara Kanetsu , Muraki Yasushi , Nakamura Kiyoto 
Published: August 2015

The nucleotide sequences of RNA segment 7 (nonstructural protein gene; NS) were compared among 34 influenza C virus strains isolated between 1947 and 1992. The results showed that all the NS genes analysed had the potential to encode NS1 and NS2 proteins of 246 and 182 amino acids, respectively. The deduced amino acid sequence of the previously unidentified NS2 was fairly well conserved, although it was more divergent than the NS1 protein sequence. Moreover, immunoprecipitation experiments with rabbit immune serum against a glutathione S-transferase fusion protein containing the C-terminal region of the 182 amino acid NS2 protein revealed synthesis of a protein with an apparent molecular mass of ∼22 kDa in infected cells. A phylogenetic analysis showed that the 34 NS genes were split into two distinct groups, A and B. Comparison of the phylogenetic positions of the individual isolates in the NS gene tree with those in the haemagglutinin–esterase (HE) gene tree suggested that most of the influenza C viruses currently circulating in Japan, irrespective of their HE gene lineage, had acquired group B NS genes through reassortment events that presumably occurred either in the 1970s or in the early 1980s.
Distinct patterns of alteration of myc genes associated with integration of human papillomavirus type 16 or type 45 DNA in two genital tumours
Authors: Sastre-Garau Xavier , Favre Michel , Couturier Jérôme , Orth Gérard 
Published: August 2015

We previously described two genital carcinomas (IC2, IC4) containing human papillomavirus type 16 (HPV-16)- or HPV-18-related sequences integrated in chromosomal bands containing the c-myc (8q24) or N-myc (2p24) gene, respectively. The c-myc gene was rearranged and amplified in IC2 cells without evidence of overexpression. The N-myc gene was amplified and highly transcribed in IC4 cells. Here, the sequence of an 8039 bp IC4 DNA fragment containing the integrated viral sequences and the cellular junctions is reported. A 3948 bp segment of the genome of HPV-45 encompassing the upstream regulatory region and the E6 and E7 ORFs was integrated into the untranslated part of N-myc exon 3, upstream of the N-myc polyadenylation signal. Both N-myc and HPV-45 sequences were amplified 10- to 20-fold. The 3′ ends of the major N-myc transcript were mapped upstream of the 5′ junction. A minor N-myc/HPV-45 fusion transcript was also identified, as well as two abundant transcripts from the HPV-45 E6–E7 region. Large amounts of N-myc protein were detected in IC4 cells. A major alteration of c-myc sequences in IC2 cells involved the insertion of a non-coding sequence into the second intron and their co-amplification with the third exon, without any evidence for the integration of HPV-16 sequences within or close to the gene. Different patterns of myc gene alterations may thus be associated with integration of HPV DNA in genital tumours, including the activation of the protooncogene via a mechanism of insertional mutagenesis and/or gene amplification.
Intracellular distribution, cell-to-cell trafficking and tubule-inducing activity of the 50 kDa movement protein of Apple chlorotic leaf spot virus fused to green fluorescent protein
Authors: Satoh Hiroshi , Matsuda Hironori , Kawamura Takehiro , Isogai Masamichi , Yoshikawa Nobuyuki , Takahashi Tsuyoshi 
Published: August 2015

The 50 kDa protein (50KP) encoded by ORF2 of Apple chlorotic leaf spot virus (ACLSV) fused to green fluorescent protein (GFP) was expressed transiently in cells of Nicotiana occidentalis and Chenopodium quinoa leaves. Its intracellular distribution, cell-to-cell trafficking in leaf epidermis and tubule formation on the surface of protoplasts were analysed. The 50KP–GFP fluorescence was distributed as small irregular spots or a fibrous network structure on the periphery of epidermal cells and protoplasts of both plant species. In leaf epidermis of N. occidentalis, the protein spread from the cells that produced it into neighbouring cells in both young and mature leaves and targetted plasmodesmata in these cells. In contrast, GFP was restricted to single cells in most cases in mature leaves. When 50KP and GFP were co-expressed in leaf epidermis of N. occidentalis, GFP spread more widely from the initial cells that produced it than when GFP was expressed alone, suggesting that 50KP facilitated the cell-to-cell trafficking of GFP. 50KP–GFP was able to complement local spread of 50KP-deficient virus when expressed transiently in leaf epidermis of C. quinoa. Expression of 50KP–GFP in protoplasts resulted in the production of tubular structures protruding from the surface. Mutational analyses showed that the C-terminal region (aa 287–457) was not essential for localization to plasmodesmata, cell-to-cell trafficking, complementation of movement of 50KP-deficient virus or tubule formation on protoplasts. In contrast, deletions in the N-terminal region resulted in the complete disruption of all these activities.
Growth of rotaviruses in continuous human and monkey cell lines that vary in their expression of integrins
Authors: Londrigan Sarah L. , Hewish Marilyn J. , Thomson Melanie J. , Sanders Georgina M. , Mustafa Huseyin , Coulson Barbara S. 
Published: August 2015

Rotavirus replication occursin vivoin intestinal epithelial cells. Cell lines fully permissive to rotavirus include kidney epithelial (MA104), colonic (Caco-2) and hepatic (HepG2) types. Previously, it has been shown that cellular integrins α2β1, α4β1 and αXβ2 are involved in rotavirus cell entry. As receptor usage is a major determinant of virus tropism, the levels of cell surface expression of these integrins have now been investigated by flow cytometry on cell lines of human (Caco-2, HepG2, RD, K562) and monkey (MA104, COS-7) origin in relation to cellular susceptibility to infection with monkey and human rotaviruses. Cells supporting any replication of human rotaviruses (RD, HepG2, Caco-2, COS-7 and MA104) expressed α2β1 and (when tested) αXβ2, whereas the non-permissive K562 cells did not express α2β1, α4β1 or αXβ2. Only RD cells expressed α4β1. Although SA11 grew to higher titres in RD, HepG2, Caco-2, COS-7 and MA104 cells, this virus still replicated at a low level in K562 cells. In all cell lines tested, SA11 replicated to higher titres than did human strains, consistent with the ability of SA11 to use sialic acids as alternative receptors. Levels of cell surface α2 integrin correlated with levels of rotavirus growth. The α2 integrin relative linear median fluorescence intensity on K562, RD, COS-7, MA104 and Caco-2 cells correlated linearly with the titre of SA11 produced in these cells at 20 h after infection at a multiplicity of 0·1, and the data best fitted a sigmoidal dose–response curve (r2=1·00,P=0·005). Thus, growth of rotaviruses in these cell lines correlates with their surface expression of α2β1 integrin and is consistent with their expression of αXβ2 and α4β1 integrins.