bluuebunny/crossref_metadata_2025 huggingface dataset:
Hidden impacts of ocean acidification to live and dead coral framework
Authors: Hennige S. J. , Wicks L. C. , Kamenos N. A. , Perna G. , Findlay H. S. , Roberts J. M.
Published: August 2015

Cold-water corals, such as
Lophelia pertusa
, are key habitat-forming organisms found throughout the world's oceans to 3000 m deep. The complex three-dimensional framework made by these vulnerable marine ecosystems support high biodiversity and commercially important species. Given their importance, a key question is how both the living and the dead framework will fare under projected climate change. Here, we demonstrate that over 12 months
L. pertusa
can physiologically acclimate to increased CO
2
, showing sustained net calcification. However, their new skeletal structure changes and exhibits decreased crystallographic and molecular-scale bonding organization. Although physiological acclimatization was evident, we also demonstrate that there is a negative correlation between increasing CO
2
levels and breaking strength of exposed framework (approx. 20–30% weaker after 12 months), meaning the exposed bases of reefs will be less effective ‘load-bearers’, and will become more susceptible to bioerosion and mechanical damage by 2100.
Hummingbird tongues are elastic micropumps
Authors: Rico-Guevara Alejandro , Fan Tai-Hsi , Rubega Margaret A.
Published: August 2015

Pumping is a vital natural process, imitated by humans for thousands of years. We demonstrate that a hitherto undocumented mechanism of fluid transport pumps nectar onto the hummingbird tongue. Using high-speed cameras, we filmed the tongue–fluid interaction in 18 hummingbird species, from seven of the nine main hummingbird clades. During the offloading of the nectar inside the bill, hummingbirds compress their tongues upon extrusion; the compressed tongue remains flattened until it contacts the nectar. After contact with the nectar surface, the tongue reshapes filling entirely with nectar; we did not observe the formation of menisci required for the operation of capillarity during this process. We show that the tongue works as an elastic micropump; fluid at the tip is driven into the tongue's grooves by forces resulting from re-expansion of a collapsed section. This work falsifies the long-standing idea that capillarity is an important force filling hummingbird tongue grooves during nectar feeding. The expansive filling mechanism we report in this paper recruits elastic recovery properties of the groove walls to load nectar into the tongue an order of magnitude faster than capillarity could. Such fast filling allows hummingbirds to extract nectar at higher rates than predicted by capillarity-based foraging models, in agreement with their fast licking rates.
The ecology of microscopic life in household dust
Authors: Barberán Albert , Dunn Robert R. , Reich Brian J. , Pacifici Krishna , Laber Eric B. , Menninger Holly L. , Morton James M. , Henley Jessica B. , Leff Jonathan W. , Miller Shelly L. , Fierer Noah
Published: August 2015

We spend the majority of our lives indoors; yet, we currently lack a comprehensive understanding of how the microbial communities found in homes vary across broad geographical regions and what factors are most important in shaping the types of microorganisms found inside homes. Here, we investigated the fungal and bacterial communities found in settled dust collected from inside and outside approximately 1200 homes located across the continental US, homes that represent a broad range of home designs and span many climatic zones. Indoor and outdoor dust samples harboured distinct microbial communities, but these differences were larger for bacteria than for fungi with most indoor fungi originating outside the home. Indoor fungal communities and the distribution of potential allergens varied predictably across climate and geographical regions; where you live determines what fungi live with you inside your home. By contrast, bacterial communities in indoor dust were more strongly influenced by the number and types of occupants living in the homes. In particular, the female : male ratio and whether a house had pets had a significant influence on the types of bacteria found inside our homes highlighting that who you live with determines what bacteria are found inside your home.
Selection analysis on the rapid evolution of a secondary sexual trait
Authors: Gordon Swanne P. , Reznick David , Arendt Jeff D. , Roughton Allen , Ontiveros Hernandez Michelle N. , Bentzen Paul , López-Sepulcre Andrés
Published: August 2015

Evolutionary analyses of population translocations (experimental or accidental) have been important in demonstrating speed of evolution because they subject organisms to abrupt environmental changes that create an episode of selection. However, the strength of selection in such studies is rarely measured, limiting our understanding of the evolutionary process. This contrasts with long-term, mark–recapture studies of unmanipulated populations that measure selection directly, yet rarely reveal evolutionary change. Here, we present a study of experimental evolution of male colour in Trinidadian guppies where we tracked both evolutionary change and individual-based measures of selection. Guppies were translocated from a predator-rich to a low-predation environment within the same stream system. We used a combination of common garden experiments and monthly sampling of individuals to measure the phenotypic and genetic divergence of male coloration between ancestral and derived fish. Results show rapid evolutionary increases in orange coloration in both populations (1 year or three generations), replicating the results of previous studies. Unlike previous studies, we linked this evolution to an individual-based analysis of selection. By quantifying individual reproductive success and survival, we show, for the first time, that males with more orange and black pigment have higher reproductive success, but males with more black pigment also have higher risk of mortality. The net effect of selection is thus an advantage of orange but not black coloration, as reflected in the evolutionary response. This highlights the importance of considering all components of fitness when understanding the evolution of sexually selected traits in the wild.
The BM2 protein of influenza B virus is synthesized in the late phase of infection and incorporated into virions as a subviral component
Authors: Odagiri Takato , Hong Jin , Ohara Yoshiro
Published: August 2015

The influenza B virus genome RNA segment 7 encodes the M1 and BM2 proteins. The BM2 protein is synthesized by a coupled translational termination–reinitiation mechanism at the overlapping stop–start pentanucleotide in a bicistronic mRNA transcribed from RNA segment 7. However, features and functions of this protein remain unclear. In this study the BM2 protein was characterized by using an antiserum raised to the BM2 protein of influenza virus strain B/Yamagata/1/73. In cells infected with B/Yamagata virus the αBM2 antibody specifically detected the BM2 protein with a molecular mass of 12 kDa and also a polypeptide with a molecular mass of 17 kDa. When infected cells were labelled with32Piand immunoprecipitated with the αBM2 antibody, the32P-labelled 17 kDa polypeptide was specifically precipitated. In the presence of casein kinase inhibitor CKI-7 the synthesis of the 17 kDa and BM2 proteins was completely suppressed, although other viral proteins, except for the polymerase protein, were synthesized normally. These results suggest that the 17 kDa species is a phosphorylated form of the BM2 protein. These species were substantially synthesized in the late phase of infection and localized in the cytoplasm throughout infection. Moreover, they were transported to the plasma membrane and thereafter were incorporated into virions. These results therefore suggest that the BM2 and the 17 kDa proteins are necessary for the life-cycle of influenza B virus.
The RNA-dependent RNA polymerases of different members of the family Flaviviridae exhibit similar properties in vitro
Authors: Steffens Sabine , Thiel Heinz-Jürgen , Behrens Sven-Erik
Published: August 2015

The virus-encoded RNA-dependent RNA polymerase (RdRp), which is required for replication of the positive-strand RNA genome, is a key enzyme of members of the virus familyFlaviviridae. By using heterologously expressed proteins, we demonstrate that the 77 kDa NS5B protein of two pestiviruses, bovine viral diarrhoea virus and classical swine fever virus, and the 100 kDa NS5 protein of the West Nile flavivirus possess RdRp activityin vitro. As originally shown for the RdRp of hepatitis C virus, RNA synthesis catalysed by the pestivirus and flavivirus enzymes is strictly primer- dependentin vitro. Accordingly, initiation of RNA polymerization on homopolymeric RNAs and heteropolymeric templates, the latter with a blocked 3′-hydroxyl group, was found to be dependent on the presence of complementary oligonucleotide primer molecules. On unblocked heteropolymeric templates, including authentic viral RNAs, the RdRps were shown to initiate RNA synthesis via intramolecular priming at the 3′-hydroxyl group of the template and ‘copy-back’ transcription, thus yielding RNase- resistant hairpin molecules. Taken together, the RdRps of different members of theFlaviviridaewere demonstrated to exhibit a common reactivity profilein vitro, typical of nucleic acid- polymerizing enzymes.
Two determinants in the capsid of a persistent type 3 poliovirus exert different effects on mutant virus uncoating
Authors: Duncan Gillian , Colbère-Garapin Florence
Published: August 2015

Mutant polioviruses (PV) have been previously found to be capable of establishing persistent infections in HEp-2c cells. Together, two amino acid substitutions in the viral capsid of a type 3 poliovirus (PV-3), at positions VP213 and VP1290, are sufficient to confer the persistent phenotype to a normally lytic virus. When susceptible cells are infected, the double mutant T7L+2L 131N290 undergoes unique conformational changes in the capsid, modifying its sedimentation coefficient from 160S to 147S. In the present study, we have further investigated mutant PV decapsidation and, in particular, the effect of each determinant independently. Our results indicate that the novel 147S form was also generated by a mutant carrying only the determinant 1N290. This form was not produced as a result of inherent capsid instability and it was generated only upon specific PV–host cell interactions. The second viral determinant, 2L13, also modified receptor-induced conformational changes, although differently from 1N290.
Processing and intracellular location of human astrovirusnon-structural proteins
Authors: Willcocks Margaret M. , Boxall Angela S. , Carter Michael J.
Published: August 2015

Human astrovirus (HAst) non-structural polyproteins are encoded in two open reading frames linked in expression by a ribosomal frameshifting event. The first of these (ORF 1a) specifies the serine protease, whilst the second (ORF 1b) encodes the virus RNA-dependent RNA polymerase. The ORF 1a product contains an unusual motif for small RNA viruses which could potentially direct proteins to the cell nucleus. We have expressed part of ORF 1a containing this motif and the whole of ORF 1b separately in recombinant baculovirus and raised specific antisera to each. We now report that expressed proteins from ORF 1a accumulate in the nucleus of both baculovirus-infected insect cells and HAst-infected CaCo-2 cells. In contrast the products of ORF 1b remain predominantly cytoplasmic.
Isolation and phylogeny of endogenous retrovirus sequences belonging to the HERV-W family in primates
Authors: Kim Heui-Soo , Takenaka Osamu , Crow Timothy J.
Published: August 2015

An investigation was undertaken of primate pol gene sequences from a novel endogenous retrovirus family, ERV-W, related to a new human endogenous retrovirus family (HERV-W) that includes multiple sclerosis-associated retrovirus (MSRV) sequences identified in particles recovered from monocyte cultures from patients with multiple sclerosis. The pol gene sequences of the ERV-W family were detected in hominoids and Old World monkeys, but not in New World monkeys, whereas ERV-W long terminal repeat-like elements were detected in all primates (hominoids, Old World monkeys and New World monkeys). Thirty-two pol gene sequences from hominoids and Old World monkeys showed a high degree of sequence identity to MSRV and other HERV-W sequences. Phylogenetic analysis indicated close relationships of pol gene sequences across primate species. The analysis suggests that the ERV-W family has evolved independently but in constrained patterns (‘parallel evolution’) in different primate species, including man. The ratio of synonymous to non- synonymous substitutions indicated that negative selective pressure is acting on CHW1-1 from chimpanzee, HBW6-6 from baboon and HWX5 from man, sequences that have no disruption by point mutation or insertions/deletions. Therefore, these pol gene sequences could be associated with an active provirus in primates. The findings indicate that the ERV-W family has continued to evolve in the course of the primate radiation and may include members with a capacity to influence gene function and possibly cause disease.
A novel negative cis-regulatory element on the hepatitis B virus S-(+)-strand
Authors: Wagner Markus , Alt Michael , Hofschneider Peter Hans , Renner Matthias
Published: August 2015

Hepatitis B virus (HBV) has a double-stranded DNA genome. The minus-strand contains coding regions for all known HBV proteins and most of thecis-regulatory elements. Little is known about transcription from the S-(+)-strand and its regulation. Thus, the presence of regulatory elements located on the S-(+)-strand was investigated by inserting nt 1038–1783 of HBV in both orientations between the human cytomegalovirus (HCMV) promoter and a luciferase gene. Transfection experiments revealed that the plasmid containing this HBV DNA fragment in an orientation allowing expression from the S-(+)-strand (antisense) led to inhibition of luciferase gene expression compared to the plasmid containing this sequence in an orientation that allows gene expression from the L-(−)-strand (sense). Deletion analyses delimit the sequence essential for the inhibitory effect to a 150 bp region that also carries part of the enhancerII/core promoter complex. However, the possible influence of this regulatory element has been excluded in various experiments. The repressing HBV sequence acts in an orientation- and position-dependent manner; no inhibition was observed when this DNA element was inserted upstream of the HCMV promoter or downstream of the luciferase gene. Northern blot analyses revealed reduced luciferase mRNA steady-state levels in cells transfected with constructs containing the essential HBV sequence in antisense orientation compared to plasmids containing this sequence in sense orientation. Since nuclear run-on experiments showed similar transcription initiation rates with these plasmids, the diminished luciferase mRNA steady-state levels must be due to altered stabilities, suggesting that nt 1783–1638 of HBV encode an RNA-destabilizing element.
Hepatitis B virus genomes from long-term immunosuppressed virus carriers are modified by specific mutations in several regions
Authors: Preikschat Petra , Meisel Helga , Will Hans , Günther Stephan
Published: August 2015

There is increasing evidence that hepatitis B virus (HBV) infection of an immunosuppressed host is associated with the appearance of virus mutants. To characterize the virus circulating in patients in detail, eleven full-length HBV genomes, isolated from the serum of five highly viraemic renal transplant recipients with liver disease, were cloned and sequenced. The genomes contained deletions in the C gene, deletions in the pre-S1/2 region frequently removing the pre-S2 initiation codon, premature termination codons in the pre-S1 or S region, and/or deletions/insertions in the X gene/core promoter. The mutations occurred at different positions and in various combinations; even mutant genomes circulating within a patient differed strikingly. It is concluded that long-term immunosuppression is associated with the occurrence of heterogeneous populations of partially defective HBV characterized by a specific mutation pattern. Efficient intracellular trans-complementation probably enables high virus replication in vivo.
Mapping T and B lymphocyte epitopes of bovine herpesvirus-1 glycoprotein B
Authors: Gao Yi , Wang Chong , Splitter Gary A.
Published: August 2015

Glycoprotein B (gB) is a major envelope protein of bovine herpesvirus-1 (BHV-1). As a subunit vaccine, the extracellular domain of recombinant gB induces neutralizing antibody and T cell responses that engender protection against virus challenge. Here, lymphocytes from animals of different parentage were analysed for T cell proliferation to the gB extracellular domain for immune recognition. Four truncated overlapping gB gene segments encoding 742 amino acids were expressed from a baculovirus vector to identify antigenic regions. One immunodominant region (amino acids 254–532) was recognized by T cells from immune individuals of different parentage. Serial synthetic peptides spanning this region localized the T cell (amino acids 319–340 and 415–436) and B cell (amino acids 331–352, 475–496 and 487–508) epitopes. Elucidation of gB epitopes indicates the diverse and distinctive recognition by T cells and antibodies of this envelope glycoprotein by cattle, the natural host of BHV-1.
Temporal mapping of transcripts in human herpesvirus-7
Authors: Menegazzi Paola , Galvan Monica , Rotola Antonella , Ravaioli Tullia , Gonelli Arianna , Cassai Enzo , Di Luca Dario
Published: August 2015

Transcription of human herpesvirus-7 (HHV-7) in cultures of productively infected T-cells was studied. Transcription of HHV-7 was regulated by the typical herpesvirus cascade in which α, β and γ genes are sequentially transcribed. Transcripts of U10, U14, U18, U31, U39, U41, U42, U53, U73 and U89/90 were detected 3 h after infection and were not inhibited by the absence of protein synthesis and therefore were α functions. U19 and U18/20 were β genes; their transcription was inhibited by cycloheximide but not by phosphonoacetate, an inhibitor of DNA synthesis. U60/66 and U98/100 were γ genes since their spliced transcripts were not detected in cells treated with phosphonoacetate. HHV-7 transcription was regulated by complex mechanisms, which involve the temporal coordinated activation of specific viral promoters and post-transcriptional processing. Splice mechanisms were also temporally regulated. Transcription of U89/90 pre-mRNA and splice took place simultaneously in the immediate-early phase. On the other hand, U16/17 pre-mRNA was synthesized with typical α kinetics, but the spliced product was regulated as a β function. Likewise, the primary transcripts of U60/66 and U98/100 were α and β, respectively, but both spliced products were synthesized in the late phase of virus replication. Finally, HHV-7 supported a bona fide latent infection in the adult population, since viral transcripts were not detected in peripheral blood mononuclear cells of healthy donors infected with HHV-7.
Kinetic and phenotypic changes in murine lymphocytes infected with murine gammaherpesvirus-68 in vitro
Authors: Dutia Bernadette M. , Stewart James P. , Clayton Robert A. E. , Dyson Heather , Nash Anthony A.
Published: August 2015

Primary infection with murine gammaherpesvirus-68 (MHV-68), as with other members of the gammaherpesvirus subfamily, is characterized by a lymphoproliferative phase. MHV-68 causes acute splenomegaly and an infectious mononucleosis-like syndrome in which there is expansion of the CD8+ T cell subset. In long-term infections, MHV-68 is associated with lymphoma development. In order to elucidate the mechanisms underlying the proliferative processes, the events following infection of murine splenocytes or purified murine B lymphocytes in vitro have been examined. MHV-68 infection prolonged the viability of murine splenocytes and stimulated cellular proliferation. Unlike Epstein–Barr virus and herpesvirus saimiri, MHV-68 did not cause growth transformation. Growth transformation did not occur even when cells with a predisposition to transformation were infected or when culture conditions were selected to enhance the viability of the cells. Following MHV-68 infection, the latency-associated viral tRNAs were transcribed. However, transcription of the other known latency- associated gene, M2, was not observed. In addition, there was no evidence of productive virus replication either by staining with antibodies specific for late virus antigens or by in situ hybridization for early and late mRNAs. In contrast to Epstein–Barr virus- and herpesvirus saimiri-infected lymphocytes, where episomal genomes are seen, Gardella gel analysis indicated that the primary lymphocytes infected by MHV-68 in vitro contained only linear virus DNA. This DNA was nuclease sensitive, indicating that, while MHV-68 was efficiently uncoated, its circularization in vitro was extremely inefficient. These results are discussed in terms of the host–virus interaction.
Analysis of Epstein–Barr virus (EBV) nuclear antigen 1 subtypes in EBV-associated lymphomas from Brazil and the United Kingdom
Authors: MacKenzie Jane , Gray Diane , Pinto-Paes Roberto , Barrezueta Luis F. M. , Armstrong Alison A. , Alexander Freda A. , McGeoch Duncan J. , Jarrett Ruth F.
Published: August 2015

EBNA-1 is the only viral protein consistently expressed in all cells latently infected by Epstein–Barr virus (EBV). There is a high frequency of sequence variation within functionally important domains of EBNA-1, with five subtypes identified. Individuals may be infected with multiple EBV strains (classified according to EBNA-1 subtype), but Burkitt’s lymphoma (BL) tumours carry a single subtype and exhibit some subtype preference. Subtype variation has also been related to geographical location. In the present study EBNA-1 polymorphisms were examined in a series of haematological malignancies from two distinct geographical regions, Brazil and the United Kingdom. Nucleotide sequence analysis of the carboxy-terminal region of EBNA-1 in 34 cases revealed six distinct sequences, some of which are novel. A new subtype, named V-Ala, was identified. EBNA-1 subtype in tumours differed markedly according to geographical location. In contrast to previous studies, we found evidence of EBNA-1 sequence variation within individual BL tumour samples.
Effect of mutations within the Cys-rich region of potyvirus helper component-proteinase on self-interaction
Authors: Urcuqui-Inchima Silvio , Maia Ivan G. , Drugeon Gabrièle , Haenni Anne-Lise , Bernardi Françoise
Published: August 2015

The first ∼60 amino acids of the N-terminal part of the potyvirus helper component-proteinase (HC-Pro) include highly conserved residues comprising a Cys-rich region. In the present study, the domain in Potato virus Y sufficient for self-interaction was mapped using the yeast two-hybrid system to the 83 N-terminal amino acids of HC-Pro. Mutations in the conserved His and two Cys residues within the Cys-rich region have a strong debilitating effect on self-interaction when introduced in the full-length HC-Pro, but not when introduced in the N-terminal fragment.
Induction of immune responses to bovine herpesvirus type 1 gD in passively immune mice after immunization with a DNA-based vaccine
Authors: Lewis P. J. , van Drunen Littel-van den Hurk S. , Babiuk L. A.
Published: August 2015

The potential for plasmids encoding a secreted form of bovine herpesvirus type 1 (BHV-1) glycoprotein D (gD) to elicit immune responses in passively immune mice following intramuscular immunization was investigated. In these experiments, 6- to 8-week-old female C3H/HeN or C57BL/6 mice were passively immunized with hyperimmune antisera raised against BHV-1 recombinant, truncated (secreted) gD immediately prior to immunization with plasmids. A single immunization of passively immune mice with plasmid encoding the secreted form of BHV-1 gD resulted in rapid development of both cell-mediated immunity and antibody responses. Furthermore, 50% of mice immunized with a suboptimal dose of recombinant gD formulated into an adjuvant developed significant levels of serum antibodies if mice were pre-treated with hyperimmune antisera. The apparent failure of passive polyclonal antisera to suppress the induction of immune responses to pSLRSV may be related to the immunoglobulin subtypes present in the hyperimmune sera.
Identification and characterization of bovine herpesvirus type 5 glycoprotein H gene and gene products
Authors: Meyer G. , Bare O. , Thiry E.
Published: August 2015

Bovine herpesvirus type 5 (BHV-5) is the causative agent of a fatal meningo-encephalitis in calves and is closely related to BHV-1 which causes infectious bovine rhinotracheitis. The gene encoding BHV-5 glycoprotein gH was sequenced. A high degree of conservation was found between BHV-1 and BHV-5 deduced gH amino acid sequences (86·4%), which is also observed for all alphaherpesvirus gH sequences. Transcriptional analysis revealed a 3·1 kb mRNA as the specific gH transcript which was detected 2 h post-infection (p.i.). Twelve out of twenty-one MAbs directed against BHV-1 gH immunoprecipitated a 108–110 kDa glycoprotein, which was then designated BHV-5 gH. Synthesis and intracellular processing of BHV- 5 gH was analysed in infected MDBK cells using gH cross-reacting MAbs. Glycoprotein gH was expressed as a beta-gamma protein, detected by radioimmunoprecipitation as early as 3 h p.i. Glycosylation studies indicated that BHV-5 gH contains N-linked carbohydrates which are essential for the recognition of the protein by the MAbs. This suggests that N-linked glycans are involved in protein folding or are targets for the gH cross-reacting MAbs. Plaque- reduction neutralization assays showed that at least one BHV-1 gH antigenic domain is lacking in BHV-5 which may possibly relate to in vivo differences in virus tropism.
Polyomavirus large- and small-T relieve middle-T-induced cell cycle arrest in normal fibroblasts
Authors: Marti Alain , Ballmer-Hofer Kurt
Published: August 2015

Papovavirus tumour antigens have been widely used to study cell growth regulation in cultured cells. We investigated the role of mouse polyomavirus T antigens, small-, middle- and large-T, in stimulating growth-arrested REF52 fibroblasts to enter the S phase. Microinjecting cells with cDNAs encoding the various T antigens showed: first, that middle-T expression blocked cell cycle stimulation by serum; second, that middle-T-arrested cells were released into the S phase upon coexpression of small-T; third, that expression of middle-T together with large-T committed resting cells to enter the cell cycle even in the absence of serum. Our data indicate that extensive cooperation among polyomavirus T antigens is essential for T antigen-mediated cell cycle stimulation in growth-arrested cells. In addition, the data suggest a new role for small-T in signalling to mitogenic pathways.
Complete nucleotide sequence, genomic organization and phylogenetic analysis of a novel genital human papillomavirus type, HLT7474-S
Authors: Chow Vincent T. K. , Leong Peter W. F.
Published: August 2015

A novel human papillomavirus (HPV) type, HLT7474-S, was isolated from a cervical scraping of a female sex worker with a wart virus infection. The complete DNA sequence of 7812 bp was derived from four overlapping PCR products and authenticated by RFLP analysis. The L1 gene exhibited 78% identity to those of its most closely related known HPV types in group A7, comprising HPV types 18, 39, 45, 59, 68 and 70. The genomic organization and phylogenetic analysis of HLT7474-S and group A7 HPVs reiterated their relatedness. Of significance were the strong sequence similarity, phylogenetic relationship and conservation of critical motifs between the transforming E6 and E7 of HLT7474-S and E6 of HPV-18 and E7 of HPV-59, respectively. These features clearly suggest that HLT7474-S is a high-risk genital HPV isolate, closely related to HPV-18 and other members of the A7 group of genital HPVs.
Dynamic analysis of hepatitis C virus replication and quasispecies selection in long-term cultures of adult human hepatocytes infected in vitro
Authors: Rumin Sylvie , Berthillon Pascale , Tanaka Eiji , Kiyosawa Kendo , Trabaud Mary-Anne , Bizollon Thierry , Gouillat Christian , Gripon Philippe , Guguen-Guillouzo Christiane , Inchauspé Geneviève , Trépo Christian
Published: August 2015

Primary human hepatocytes were used to develop a culture model for in vitro propagation of hepatitis C virus (HCV). Production of positive- strand full-length viral RNA in cells and culture supernatants was monitored by PCR methods targeting three regions of the viral genome: the 5′ NCR, the 3′ X-tail and the envelope glycoprotein E2. De novo synthesis of negative-strand RNA was also demonstrated. Evidence for a gradual increase in viral components over a 3 month period was obtained by two quantitative assays: one for evaluation of genomic titre (quantitative PCR) and one for detection of the core antigen. Production of infectious viral particles was indicated by passage of infection to naive hepatocyte cultures. Reproducibility of the experiments was assessed using cultures from three liver donors and eleven sera. Neither the genotype, nor the genomic titre, nor the anti-HCV antibody content, were reliable predictive factors of serum infectivity, while the liver donor appeared to play a role in the establishment of HCV replication. Quasispecies present in hepatocyte cultures established from three different liver donors were analysed by sequencing hypervariable region 1 of the E2 protein. In all three cases, the complexity of viral quasispecies decreased after in vitro infection, but the major sequences recovered were different. These data strongly suggest that human primary hepatocytes are a valuable model for study of persistent and complete HCV replication in vitro and for identification of the factors (viral and/or cellular) associated with successful infection.
Mapping a neutralizing epitope on the coat protein of striped jack nervous necrosis virus
Authors: Nishizawa Toyohiko , Takano Ryoko , Muroga Kiyokuni
Published: August 2015

Striped jack nervous necrosis virus (SJNNV), a fish nodavirus, is the causative agent of viral nervous necrosis in marine fishes. The fish nodaviruses are divided into four different genotypes based on the nucleotide sequence of the coat protein gene. In the present study, partial coat protein genes of fish nodaviruses were expressed. This allowed the serological relationship among the different virus genotypes to be analysed and neutralizing epitopes on the coat protein to be mapped. Western blot analysis revealed that SJNNV and other fish nodavirus genotypes shared a significant number of common antigenic determinants, although SJNNV was serologically distinguishable. The results suggested that the SJNNV determinant for neutralizing MAbs was a linear epitope, which consisted of a repeated amino acid sequence within the coat protein. One of the neutralizing epitopes of SJNNV was deduced to be PAN at aa 254–256 in the coat protein.
Transcriptional activation of human TR3/nur77 gene expression by human T-lymphotropic virus type I Tax protein through two AP-1-like elements
Authors: Liu Xiangdong , Chen Xiaolin , Zachar Vladimir , Chang Chawnshang , Ebbesen Peter
Published: August 2015

The Tax transactivator of human T-lymphotropic virus type I (HTLV-I) is capable of inducing expression of the human immediate-earlyTR3/nur77gene. Deletion and mutation analyses of theTR3/nur77promoter demonstrated that multiple transcription elements in the 121 bp sequence proximal to the transcription start site are required for full Tax transactivation. Mutations of CArG-like, Ets and RCE motifs in this region severely decreased Tax transactivation. Mutation of either of the two identical AP-1-like elements (NAP 1 and 2) immediately upstream of the TATA box caused around 80% reduction of Tax transactivation. Mutation of both NAP elements blocked Tax-mediated activation totally. These two NAP elements could confer Tax-responsiveness on a heterologous basal promoter. Furthermore, the specific NAP-binding complex was only observed in HTLV-I-infected cells. Formation of this specific NAP-binding complex was correlated directly with Tax expression, as demonstrated in JPX-9 cells upon induction of Tax expression. The specific NAP binding could be competed for by consensus AP-1 and CREB elements, indicating that the NAP-binding proteins probably belong to the AP-1 and CREB/ATF transcription factor families. Supershift analysis with antibodies to both the AP-1 and CREB/ATF transcription factor families revealed that only anti-JunD antibody could partially shift this NAP-binding complex, indicating that JunD is a component of the NAP complex. This work suggests that JunD is involved in Tax-regulated TR3/nur77 expression.
Specific passage of simian immunodeficiency virus fromend-stage disease results in accelerated progression to AIDS in rhesus macaques
Authors: Holterman Lennart , Niphuis Henk , ten Haaft Peter J. F. , Goudsmit Jaap , Baskin Gary , Heeney Jonathan L.
Published: August 2015

To determine whether passage of late-stage variants of simian immunodeficiency virus (SIV) would lead to a more virulent infection and rapid disease progression, a study was designed to examine the effects of selective transmission of SIV from late-stage cases of AIDS in Macaca mulatta. In a uniform group of 10 age-matched animals from the same genetic breeding stock infected with SIVB670, it took 7 months before one of the ten animals developed AIDS. Passage of virus taken from this animal immediately prior to death resulted in death of the recipient due to AIDS within 4 months. Again, subsequent passage of virus taken late in disease resulted in an accelerated disease course, with AIDS developing within 2·5 and 1·8 months in two recipients. The fourth passage of virus taken late in disease from the most rapid progressor (1·8 months) resulted in AIDS developing in this recipient within 1 month of infection. During each consecutive passage in vivo, the loss of memory T cells became more acute. Evidence that the virus became more virulent with selective passage of late-stage variants was provided by the markedly increased levels of both plasma antigen and viral RNA. Subsequent in vivo passage from end-stage AIDS selected for a strain of SIV capable of causing the acute development of AIDS as rapidly as 1 month post-infection. The pathology of acute AIDS in these cases closely resembled that seen after a chronic disease course.
The human herpesvirus-8 ORF 57 gene and its properties
Authors: Bello Leonard J. , Davison Andrew J. , Glenn Mark A. , Whitehouse Adrian , Rethmeier Nikki , Schulz Thomas F. , Barklie Clements J.
Published: August 2015

Human herpesvirus-8 (HHV-8) is a γ2 lymphotropic herpesvirus associated with Kaposi’s sarcoma, a major neoplasm of AIDS patients, and with other AIDS-related neoplasms. The HHV-8 ORF 57 gene is conserved throughout the herpesvirus family and has a herpes simplex virus type 1 homologue, IE63 (also termed ICP27), which is an essential regulatory protein and acts at both transcriptional and post-transcriptional levels. We show that, contrary to the published HHV-8 sequence, which predicts a protein of 275 amino acids, the ORF 57 gene is spliced, contains a single intron and encodes a protein of 455 amino acids. For several gammaherpesviruses examined, the upstream coding exon is 16–17 amino acids in length and is rich in methionine residues. When ORF 57 was fused to the gene for enhanced green fluorescent protein (EGFP), the fusion protein exhibited a punctate nuclear distribution that co-localized with the cellular splicing factor SC-35. Unlike the IE63–EGFP fusion protein, ORF 57–EGFP did not shuttle from the nucleus to the cytoplasm in the presence of actinomycin D. However, ORF 57–EGFP was capable of shuttling from a transfected monkey nucleus to a recipient mouse nucleus in an interspecies heterokaryon assay. These data indicate that HHV-8 ORF 57 and IE63 possess certain common properties.
Site-saturation mutagenesis of the PALTAVETG motif in coxsackievirus A9 capsid protein VP1 reveals evidence of conservation of a periodic hydrophobicity profile
Authors: Airaksinen Antero , Roivainen Merja , Stanway Glyn , Hovi Tapani
Published: August 2015

Enteroviruses possess a highly conserved 9 amino acid stretch of mainly hydrophobic character in the capsid protein VP1. A novel strategy, combining site-saturation mutagenesis and a single-tube cloning and transfection procedure, has been developed for the analysis of this motif in coxsackievirus A9 (CAV-9). Four individual amino acids were separately mutated. Mutagenesis of three of the four positions in CAV-9 resulted in a number of viable but impaired mutant strains, each containing a single amino acid substitution. In contrast, no mutants with amino acid substitutions at leucine 31 were isolated, although three different leucine codons were found among the viruses recovered. Small plaque size was regularly associated with reduced yields of infectious virus and an amino acid substitution at the target site in the viruses isolated from the site-saturated virus pools. From the range of amino acids observed in viable mutants, it was possible to estimate the characteristics that are required at individual amino acid positions. It seems that in the motif studied here, a periodic hydrophobicity profile needs to be conserved. The constraints observed on the ranges of acceptable amino acids presumably reflect the structural–functional requirements that have resulted in the conservation of the motif.
The C-terminal region of the hepatitis C virus E1 glycoprotein confers localization within the endoplasmic reticulum
Authors: Flint Mike , McKeating Jane A.
Published: August 2015

Expression of the hepatitis C virus glycoprotein E1 in cultured cells localizes it to the endoplasmic reticulum, suggesting that E1 contains a signal mediating retention. Fusion of the C-terminal region of E1 to the ectodomain of CD4 prevented it from being transported to the cell surface. Fusion of this region of E1 resulted in localization of CD4 and influenza virus haemagglutinin chimeric molecules to a pre-medial Golgi compartment. This signal was present within E1 residues 311–383. Retention was not due to misfolding since the chimeric molecules did not form disulphide-linked aggregates indicative of misfolded proteins, and could be recognized by MAbs specific for conformational epitopes.
Genetic stability of equine arteritis virus during horizontal and vertical transmission in an outbreak of equine viral arteritis
Authors: Balasuriya Udeni B. R. , Hedges Jodi F. , Nadler Steven A. , McCollum William H. , Timoney Peter J. , MacLachlan N. James
Published: August 2015

An imported carrier stallion (A) from Europe was implicated in causing an extensive outbreak of equine viral arteritis (EVA) on a Warmblood breeding farm in Pennsylvania, USA. Strains of equine arteritis virus (EAV) present in the semen of two carrier stallions (A and G) on the farm were compared to those in tissues of foals born during the outbreak, as well as viruses present in the semen of two other stallions that became persistently infected carriers of EAV following infection during the outbreak. The 2822 bp segment encompassing ORFs 2–7 (nt 9807–12628; which encode the GS, GP3, GP4, GL, M and N proteins, respectively) was directly amplified by RT–PCR from semen samples and foal tissues. Nucleotide and phylogenetic analyses confirmed that virus present in the semen of stallion A initiated the outbreak. The genomes of viruses present in most foal tissues (10/11) and serum from an acutely infected mare collected during the outbreak were identical to that of virus present in the lung of the first foal that died of EVA. Virus in the placenta of one foal differed by one nucleotide (99·9% identity) from the predominant outbreak virus. The relative genetic stability of viruses that circulated during the outbreak contrasts markedly with the heterogeneous virus populations variously present in the semen of persistently infected stallions on the farm. These findings are consistent with the hypothesis that the carrier stallion can be a source of genetic diversity of EAV, and that outbreaks of EVA can be initiated by the horizontal aerosol transmission of specific viral variants that occur in the semen of particular carrier stallions.
Mutations in the env gene of human immunodeficiency virus type 1 NDK isolates and the use of African green monkey CXCR4 as a co-receptor in COS-7 cells
Authors: Dumonceaux Julie , Chanel Chantal , Valente Susana , Quivet Laurence , Briand Pascale , Hazan Uriel
Published: August 2015

A previous report from this laboratory described the isolation of the first CD4-independent human immunodeficiency virus type 1 isolate, m7NDK. This independence of CD4 is due to seven mutations located in the C2, V3 and C3 regions of the gp120 protein. The present report describes the entry features of the m5NDK virus, which contains five of the seven m7NDK mutations, located in the V3 loop and C3 region. The entry of this virus is strictly CD4-dependent but it can fuse with African green monkey (agm) COS-7 cells bearing human CD4 (h-CD4). This fusion is directly due to the five mutations in theenvgene. It has also been shown that entry of m7NDK is CD4-independent in COS-7 cells. Since the wild-type NDK and m7NDK viruses use the human CXCR4 protein as co-receptor, agm-CXCR4 was cloned and used in transfection and fusion inhibition experiments to show that this receptor can be used by the m5 and m7NDK viruses. The wild-type NDK virus, which does not enter COS-7 cells, can use agm-CXCR4, but only when the receptor is transfected into target cells. Although co-receptor nature and expression levels are still major determinants of virus entry, this is the first case where a few mutations in theenvgene can overcome this restriction.
Effect of population patchiness and migration rates on the adaptation and divergence of vesicular stomatitis virus quasispecies populations
Authors: Miralles Rosario , Moya Andrés , Elena Santiago F.
Published: August 2015

The effect of migration among different isolated virus quasispecies populations on their adaptation and diversity was analysed through experimental evolution. Anin vitrocell system was employed to simulate migration of vesicular stomatitis virus between isolated homogeneous host cell populations. The results clearly demonstrated a positive correlation between the migration rate and the magnitude of the mean fitness reached by the virus quasispecies populations. The results also showed, although less clearly, that fitness differences among quasispecies decreased with the magnitude of migration. These results are in close agreement with predictions of standard population genetics theory. These results can be explained in terms of the spread of beneficial mutations, originating in a single isolated quasispecies, through the entire system formed by the different quasispecies populations contained in different host cell populations.
Localization of a unique hepatitis B virus epitope sheds new light on the structure of hepatitis B virus surface antigen
Authors: Paulij W. P. , de Wit P. L. M. , Sünnen C. M. G. , van Roosmalen M. H. , Petersen-van Ettekoven A. , Cooreman M. P. , Heijtink R. A.
Published: August 2015

In a search for monoclonal antibodies (MAbs) that can bind hepatitis B virus surface antigen (HBsAg) with amino acid substitutions in the immune dominant ‘a’ region (escape mutants) we investigated the epitope recognition site of the human MAb 4-7B. Pepscan analysis and experiments with alanine substitution as well as substitutions known from nature pointed to residues 178–186 in the small S protein with the amino acid sequence PFVQWFVGL (key amino acids in bold) as the minimal epitope. Single amino acid substitutions at positions 122(R/K)(d/y), 134(Y/F), 145(G/R), 148(T/A) and 160(K/R)(w/r), representing ‘a’ region variants in recombinant HBsAg COS-I cells, did not influence binding of MAb 4-7B. Synthetic peptides (residues 175–189) including the 4-7B epitope sequence were able to evoke an anti-HBs response in rabbits. According to established polypeptide models, the 4-7B epitope region is located in the lipid layer of 20 nm HBsAg particles. The present results, however, suggest that residues 178–186 are exposed on the surface of the 20 nm particle. This may change our view of the structure of HBsAg.
Kinetics of early molecular events in duck hepatitis B virus replication in primary duck hepatocytes
Authors: Qiao M. , Scougall C. A. , Duszynski A. , Burrell C. J.
Published: August 2015

This paper describes the use of one-step growth conditions to study the kinetics of duck hepatitis B virus (DHBV) replication in primary duck hepatocytes. Synchronized infection was achieved using partially purified DHBV virions at an m.o.i. of 640 DHBV DNA-containing virions per cell, and these conditions were shown to produce a single cycle of infection. In this model, input purified DHBV DNA was rapidly internalized by cells at ⩾0·5 h, and localized to the nucleus by 4 h, but both covalently closed circular (CCC) DNA and single-stranded DNA were not detected until 48 h post-inoculation (p.i.), suggesting that there was a ⩾40 h delay between DHBV localization to the nucleus and formation of CCC DNA. In contrast, CCC DNA can be first detected in hepatocytes at 6 h p.i. in in vivo infection of ducks with the same DHBV strain. In an analysis of the nuclear transport of the DHBV genome, release of nuclear viral DNA from a particulate form to a soluble nucleoplasmic form was only 50% complete by 48 h p.i. However, this process occurred simultaneously with genome uncoating since all soluble nucleoplasmic DHBV DNA was free of nucleocapsid material; this suggests that nucleocapsid disassembly and genome uncoating may occur at the nuclear membrane and not within the nucleus. Quantitative analysis demonstrated inefficiency in a number of steps including virus uptake and internalization, translocation of nucleocapsid across the nuclear membrane and antigen expression from intranuclear viral DNA.
The 5′ untranslated region of GB virus B shows functional similarity to the internal ribosome entry site of hepatitis C virus
Authors: Grace Ken , Gartland Margaret , Karayiannis Peter , McGarvey Michael J. , Clarke Berwyn
Published: August 2015

Since its characterization in 1995, there has been increasing interest in the significance of GB virus B (GBV-B) due to its close phylogenetic relationship to hepatitis C virus (HCV). The genome of GBV-B is similar in length and organization to that of HCV and the two viruses share sequence similarity in their 5′ untranslated regions (5′UTR). A secondary structure model of the GBV-B 5′UTR has been proposed by comparative sequence analysis with HCV. The highly conserved secondary structure, present in HCV and the pestiviruses, is also present in the 5′UTR of GBV-B. Translation of the HCV polyprotein initiates via an internal ribosome entry site (IRES) and it is proposed that the GBV-B UTR may function in a similar manner. Dicistronic reporter constructs were made to investigate the function of the GBV-B 5′UTR. Mutational analysis and in vitro translation experiments demonstrate that GBV-B initiates translation via an IRES.