Identification of Trichosanthes associated rhabdovirus 1, a novel member of the genus Cytorhabdovirus of the family Rhabdoviridae, in the Trichosanthes kirilowii transcriptome.

The genome sequence of a novel RNA virus, Trichosanthes associated rhabdovirus 1 (TrARV1), was identified in a transcriptome dataset isolated from a root sample of Trichosanthes kirilowii, which is a flowering plant belonging to the family Cucurbitaceae. The fruits, seeds, and root tubers of T. kirilowii have been used clinically in traditional Chinese medicine. The TrARV1 genome sequence was predicted to have six open reading frames (ORFs) encoding five canonical structural proteins of the family Rhabdoviridae (N ORF for nucleocapsid, P ORF for phosphoprotein, M ORF for matrix protein, G ORF for glycoprotein, and L ORF for polymerase), and an accessory protein. Sequence comparisons and phylogenetic analyses based on L and N proteins confirmed that TrARV1 is a novel member of the genus Cytorhabdovirus of the family Rhabdoviridae. TrARV1 is most closely related to Wuhan insect virus 5 and persimmon virus A. The putative cis-regulatory elements involved in transcription termination and polyadenylation, commonly found in the gene junction regions of rhabdoviruses, were also identified in the TrARV1 genome having the consensus sequence 3'- ACUAAAUUAUUUUGAUCUUU-5'. The genome sequence of TrARV1 may be useful to study the evolution and molecular biology of cytorhabdoviruses. Keywords: Trichosanthes associated rhabdovirus 1; Cytorhabdovirus; Rhabdoviridae; Trichosanthes kirilowii.

Identification of Pistacia-associated flexivirus 1, a putative mycovirus of the family Gammaflexiviridae, in the mastic tree (Pistacia lentiscus) transcriptome.

In this study, we identified the genome sequence of the novel virus Pistacia-associated flexivirus 1 (PAFV1), a putative member of the mycovirus family Gammaflexiviridae (the order Tymovirales), via analysis of a transcriptome dataset for the mastic tree (Pistacia lentiscus, the family Anacardiaceae). PAFV1 was predicted to have three open reading frames (ORFs): ORF1, encoding a replicase (REP) with RNA-dependent RNA polymerase activity; ORF2, a movement protein (MP); and ORF3, a hypothetical protein. The PAFV1 REP sequence showed high similarity to those of three known members of the family Gammaflexiviridae i.e., Entoleuca gammaflexivirus 1 (EnFV1), Entoleuca gammaflexivirus 2 (EnFV2), and Botrytis virus F (BVF). A genome contig of the fungus Monosporascus cannonballus also contained a sequence of an endogenous virus similar to that of PAFV1. Sequence comparison and phylogenetic analysis indicated that PAFV1, EnFV1, and the endogenous virus of M. cannonballus formed a distinct subgroup (apart from EnFV2 and BVF), and may be the founding members of a novel genus in the family Gammaflexiviridae. Notably, MP sequences of PAFV1/EnFV1 showed similarity to the MP sequences of the mycovirus group called tobamo-like mycoviruses (an unassigned taxon), implying that genomic recombination occurred between members of the family Gammaflexiviridae and tobamo-like mycoviruses. Since PAFV1 is phylogenetically related to mycoviruses, PAFV1 may also be a mycovirus that infected a fungus associated with the mastic tree sample, which is evidenced by the presence of fungal ribosomal RNA sequences in the mastic tree transcriptome. Thus, the PAFV1 genome sequence may be useful in elucidating the genome evolution of Gammaflexiviridae and tobamo-like mycoviruses. Keywords: Pistacia-associated flexivirus 1; Gammaflexiviridae; mycovirus, mastic tree.

A novel Waikavirus (the family Secoviridae) genome sequence identified in rapeseed (Brassica napus).

The genome sequence of a novel species of the genus Waikavirus (the family Secoviridae), which we named Brassica napus RNA virus 1 (BnRV1), was identified in a rapeseed (Brassica napus) transcriptome dataset. The BnRV1 genome was 12,293 nucleotides long followed by a poly(A) tail. Two open reading frames (ORFs), called ORF1 and ORFX, were predicted. The larger ORF, ORF1, encodes a polyprotein of 3,471 amino acids and the smaller ORF, ORFX, overlaps ORF1 and encodes an 87 aa long protein of unknown function. The BnRV1 ORF1 polyprotein was predicted to undergo proteolytic processing to yield seven mature proteins, including an RNA-dependent RNA polymerase and three distinct coat proteins. The ORF1 and ORFX proteins share sequence similarities with the respective proteins of viruses in the genus Waikavirus, including the bellflower vein chlorosis virus, rice tungro spherical virus, and maize chlorotic dwarf virus. A phylogenetic tree inferred from a conserved segment of the polyproteins of several Secoviridae viruses confirmed that BnRV1 is a novel species of the genus Waikavirus. The BnRV1 genome sequence identified in this study may be useful for the study of waikavirus biology and waikavirus-derived diseases. Keywords: Brassica napus RNA virus 1; Waikavirus; Secoviridae; rapeseed.

Identification of a novel member of the family Betaflexiviridae from the hallucinogenic plant Salvia divinorum.

Betaflexiviridae is a family of plant-infecting RNA viruses with 11 recognized genera, of which genomes have diverse organization with three to six open reading frames (ORFs). A genome sequence of a novel Betaflexiviridae species, named Salvia divinorum RNA virus 1 (SdRV1), was identified in Salvia divinorum, herbal mint plant with hallucinogenic properties. The SdRV1 genome was predicted to have four ORFs encoding a replicase polyprotein (REP), a movement protein (MP), a coat protein (CP), and a putative nucleic acid-binding protein (NBP). Phylogenetic analyses based on the REP, MP, and CP sequences indicated that SdRV1 is most closely related to members of the genus Citrivirus. However, the genome organization of SdRV1 is the same as that of the genus Prunevirus. Moreover, the SdRV1 NBP had greatest sequence similarity with members of the genus Carlavirus. A complex evolutionary history involving ancestors of these three genera might have resulted in the unique phylogenetic position of SdRV1, which could be considered the founding member of a new genus in the family Betaflexiviridae. The genome sequence of SdRV1 might be useful for studies on the evolution of Betaflexiviridae. Keywords: Salvia divinorum RNA virus 1; Betaflexiviridae; Salvia divinorum.

Novel Foveavirus (the family Betaflexiviridae) species identified in ginseng (Panax ginseng).

Ginseng (Panax ginseng) is a valuable herb that is widely cultivated in Korea, China, and Japan because it contains a variety of pharmacologically active substances with a wide range of positive effects on human health. Identification and prevention of disease-causing viral pathogens of ginseng is important for improving the yield and quality of ginseng-derived bioactive molecules. In this study, the genome sequence of the virus Panax ginseng flexivirus 1 (PgFV1) was identified from a ginseng root transcriptome data set. Sequence comparison and phylogenetic analysis showed that PgFV1 is a novel plant RNA virus species of the genus Foveavirus (the family Betaflexiviridae). Foveaviruses have flexuous and filamentous virions with a single-stranded positive-sense mono-segmented RNA genome. Its infection causes diseases with mosaic and ringspot symptoms in the stems and leaves. The PgFV1 genome encodes for 5 open reading frames: a replicase polyprotein for viral genome replication, 3 triple gene block proteins for viral cell-to-cell movement, and coat protein. Phylogenetic trees inferred from replicase polyprotein or coat protein sequences showed that PgFV1 is most closely related to grapevine virus T. PgFV1 is the first foveavirus identified to be associated with ginseng. Given the potential pathogenic features of previously known foveaviruses and importance of ginseng in the health industry, the PgFV1 genome sequence may be highly useful for studying ginseng foveaviruses. Keywords: ginseng; Panax ginseng flexivirus 1; Foveavirus; Betaflexiviridae.

Zostera virus T - a novel virus of the genus Tepovirus identified in the eelgrass, Zostera muelleri.

Analysis of a transcriptome dataset obtained from tissue samples of the eelgrass Zostera muelleri, an aquatic flowering plant species of the family Zosteraceae, yielded three genome sequence contigs of a novel RNA virus. Sequence comparison and phylogenetic analysis revealed that the novel RNA virus, named Zostera virus T (ZoVT), belongs to the genus Tepovirus of the family Betaflexiviridae. The three genome contigs of ZoVT showed 88.2‒97.2% nucleotide sequence identity to each other, indicating that they descended from a common ancestor. The ZoVT genome contains three open reading frames (ORFs): ORF1 encodes a 1816 amino acid (aa) replicase (REP) with RNA-dependent RNA polymerase (RdRp) activity; ORF2, a 398 aa movement protein (MP); and ORF3, a 240 aa coat protein (CP). The phylogenetic analysis using REP sequences of ZoVT and other Betaflexiviridae viruses showed that Prunus virus T is the closest known virus to ZoVT, whereas potato virus T, the type species of the genus Tepovirus, is the second closest virus. Genome sequences of ZoVT, which is the third tepovirus species identified to date, may be useful for investigating the evolution and molecular biology of tepoviruses. Keywords: Zostera virus T; Tepovirus; Betaflexiviridae; eelgrass; Zostera muelleri.

Novel Divavirus (the family Betaflexiviridae) and Mitovirus (the family Narnaviridae) species identified in basil (Ocimum basilicum).

Transcriptome data obtained from a plant sample often contain a large number of reads that are derived from associated RNA virus genomes that were co-isolated during RNA preparation. These virus-derived reads can be assembled into a novel plant RNA genome sequence. Here, a basil (Ocimum basilicum) transcriptome dataset was analyzed to identify two new RNA viruses, which were named Ocimum basilicum RNA virus 1 (ObRV1) and Ocimum basilicum RNA virus 2 (ObRV2). A phylogenetic analysis of the ObRV1 RNA-dependent RNA polymerase (RdRp) motif indicated that ObRV1 is a novel species of the genus Divavirus of the family Betaflexiviridae. ObRV1 is the fourth divavirus species to be identified. The ObRV2 RdRp motif showed sequence similarity to viruses of the genus Mitovirus of the family Narnaviridae, which infect fungal mitochondria. Although most of the known mitoviruses do not produce a functional RdRp using the plant mitochondrial genetic code, the ObRV2 encodes a full-length RdRp using both the fungal and plant mitochondrial genetic codes.

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus.

Amalgaviridae is a family of double-stranded, monosegmented RNA viruses that are associated with plants, fungi, microsporidians, and animals. A sequence contig derived from the transcriptome of a eudicot, Cistus incanus (the family Cistaceae; commonly known as hoary rockrose), was identified as the genome sequence of a novel plant RNA virus and named Cistus incanus RNA virus 1 (CiRV1). Sequence comparison and phylogenetic analysis indicated that CiRV1 is a novel species of the genus Amalgavirus in the family Amalgaviridae. The CiRV1 genome contig has two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. An ORF1+2 fusion protein, which functions in viral RNA replication, is produced by a +1 programmed ribosomal frameshifting (PRF) mechanism. A +1 PRF motif UUU_CGU, which matches the conserved amalgavirus +1 PRF consensus sequence UUU_CGN, was found at the boundary of CiRV1 ORF1 and ORF2. Comparison of 25 amalgavirus ORF1+2 fusion proteins revealed that only three different positions within a 13-amino acid segment were recurrently used at the boundary, possibly being selected so as not to interfere with correct folding and function of the fusion protein. CiRV1 is the first virus found to be associated with the Cistus species and may be useful for studying amalgaviruses.

Genome sequence of a distinct watermelon mosaic virus identified from ginseng (Panax ginseng) transcriptome.

Watermelon mosaic virus (WMV) is a member of the genus Potyvirus, which is the largest genus of plant viruses. WMV is a significant pathogen of crop plants, including Cucurbitaceae species. A WMV strain, designated as WMV-Pg, was identified in transcriptome data collected from ginseng (Panax ginseng) root. WMV-Pg showed 84% nucleotide sequence identity and 91% amino acid sequence identity with its closest related virus, WMV-Fr. A phylogenetic analysis of WMV-Pg with other WMVs and soybean mosaic viruses (SMVs) indicated that WMV-Pg is a distinct subtype of the WMV/SMV group of the genus Potyvirus in the family Potyviridae.

Apoptosis induced by copper oxide quantum dots in cultured C2C12 cells via caspase 3 and caspase 7: a study on cytotoxicity assessment.

We report herein the synthesis and characterization of copper oxide quantum dots and their cytotoxic impact on mouse C2C12 cells. The utilized CuO quantum dots were prepared by the one-pot wet chemical method using copper acetate and hexamethylenetetramine as precursors. The physicochemical characterization of the synthesized CuO quantum dots was carried out using X-ray diffraction, energy-dispersive X-ray analysis, and transmission electron microscopy. To examine the in vitro cytotoxicity, C2C12 cell lines were treated with different concentrations of as-prepared quantum dots and the viability of cells was analyzed using Cell Counting Kit-8 assay at regular time intervals. The morphology of the treated C2C12 cells was observed under a phase-contrast microscope, whereas the quantification of cell viability was carried out via confocal laser scanning microscopy. To gain insight into the mechanism of cell death, we examined the effect of CuO quantum dots on the candidate genes such as caspases 3 and 7, which are key mediators of apoptotic events. In vitro investigations of the biological effect of CuO quantum dots have shown that it binds genomic DNA, decreases significantly the viability of cells in culture in a concentration (10-20 µg/mL) dependent manner, and inhibits mitochondrial caspases 3 and 7. To sum up, the elucidation of the pathways is to help in understanding CuO quantum dot-induced effects and evaluating CuO quantum dot-related hazards to human health.

Presentation of viral antigen to class I major histocompatibility complex-restricted cytotoxic T lymphocyte. Recognition of an immunodominant influenza hemagglutinin site by cytotoxic T lymphocyte is independent of the position of the site in the hemagglutinin translation product.

Class I major histocompatibility complex (MHC) restricted T lymphocytes preferentially recognize fragments of polypeptides processed through a nonendosomal presentation pathway. At present the intracellular compartment(s) in which polypeptide fragmentation occurs and factors which influence the formation of an antigenic epitope are not well understood. To assess the role of residues flanking an antigenic site in the generation of the antigenic moiety recognized by class I MHC restricted T lymphocytes we have moved the coding sequence for an immunodominant H-2Kd restricted site on the influenza A/JAPAN/57 hemagglutinin (residues 202-221) by site-directed mutagenesis to six different positions along the coding sequence of the hemagglutinin gene. We have found that all six classes of mutants are recognized by MHC class I restricted T cells as efficiently as the wild type hemagglutinin gene product. Thus neither N-terminal to C-terminal position within the translation product nor sequences flanking the antigenic site influence processing.

The requirement for proteasome activity class I major histocompatibility complex antigen presentation is dictated by the length of preprocessed antigen.

Accumulating evidence has implicated the proteasome in the processing of protein along the major histocompatibility complex (MHC) class I presentation pathway. The availability of potent proteasome inhibitors provides an opportunity to examine the role of proteasome function in antigen presentation by MHC class I molecules to CD8+ cytotoxic T lymphocytes (CTLs). We have investigated the processing and presenting of antigenic epitopes from influenza hemagglutinin in target cells treated with the inhibitor of proteasome activity MG132. In the absence of proteasome activity, the processing and presentation of the full-length hemagglutinin was abolished, suggesting the requirement for proteasome function in the processing and presentation of the hemagglutinin glycoprotein. Epitope-containing translation products as short as 21 amino acids when expressed in target cells required proteasome activity for processing and presentation of the hemagglutin epitope to CTLs. However, when endogenous peptides of 17 amino acids or shorter were expressed in target cells, the processing and presentation of epitopes contained in these peptides were insensitive to the proteasome inhibitor. Our results support the hypothesis that proteasome activity is required for the generation of peptides presented by MHC class I molecules and that the requirement for proteasome activity is dependent on the size of the translation product expressed in the target cell. The implications of these findings are discussed.

CD8+ T cell recognition of an endogenously processed epitope is regulated primarily by residues within the epitope.

Cytotoxic T lymphocytes (CTL) recognize short antigenic peptides associated with cell surface class I major histocompatibility complex (MHC) molecules. This association presumably occurs between newly synthesized class I MHC molecules and peptide fragments in a pre-Golgi compartment. Little is known about the factors that regulate the formation of these antigenic peptide fragments within the cell. To examine the role of residues within a core epitope and in the flanking sequences for the generation and presentation of the newly synthesized peptide fragment recognized by CD8+ CTL, we have mutagenized the coding sequence for the CTL epitope spanning residues 202-221 in the influenza A/Japan/57 hemagglutinin (HA). In this study over 60 substitution mutations in the epitope were tested for their effects on target cell sensitization using a cytoplasmic viral expression system. The HA202-221 site contains two overlapping subsites defined by CTL clones 11-1 and 40-2. Mutations in HA residues 204-213 or residues 210-219 often abolished target cell lysis by CTL clones 11-1 and 40-2, respectively. Although residues outside the core epitope did not usually affect the ability to be lysed by CTL clones, substitution of a Gly residue for Val-214 abolished lysis by clone 11-1. These data suggest that residues within a site that affect MHC binding and T cell receptor recognition appear to play the predominant role in dictating the formation of the antigenic complex recognized by CD8+ CTL, and therefore the antigenicity of the protein antigen presented to CD8+ T cells. Most alterations in residues flanking the endogenously expressed epitope do not appreciably affect the generation and recognition of the site.

Immobilization of angiotensin II and bovine serum albumin on strip-patterned ZnO nanorod arrays.

For an effective protein immobilization for highly sensitive biosensors, we determined the binding properties and characteristics of angiotensin II and bovine serum albumin on the surface of patterned ZnO nanorod arrays (NRAs) which were selectively grown on desired areas of Si substrates. The surfaces of ZnO NRAs were modified by 3-aminopropyltriethoxysilane and gluteraldehyde, and the activated NRAs were then conjugated with angiotensin II protein and bovine serum albumin. The silanization process and conjugation of protein were verified by secondary ion mass spectroscopy (SIMS) and X-ray photoelectron spectroscopy (XPS) techniques. The immobilizing densities of proteins determined by Coomassie protein assay were 4.5 microg/cm2 for angiotensin II and 5.3 microg/cm2 for bovine serum albumin.

High aspect-ratio ZnO nanowires based nanoscale field effect transistors.

High aspect-ratio ZnO nanowires were grown onto the copper foil, in a large-quantity, by non-catalytic thermal evaporation method. The detailed morphological observations revealed that the diameters and lengths of as-grown nanowires are in the range of 60-100 nm and 10-30 microm, respectively exhibiting a very high-aspect ratio. Detailed structural characterizations confirmed that the as-grown nanowires are well crystalline and possess a wurtzite hexagonal phase, grown along the c-axis direction in preference. The presence of a sharp and strong UV emission at 381 nm in the room temperature photoluminescence (PL) spectrum affirmed that the obtained nanowires have good optical properties. The electrical transport properties of the as-grown nanowires was explored by fabricating the field effect transistors (FETs) using a single ZnO nanowire. From the fabricated single ZnO nanowire based FET, the electron carrier density and field effect mobility were estimated to be approximately 6.7 x 10(13) cm(-3) and approximately 3.8 cm2/Vs, respectively.

ZnO nanonails: synthesis and their application as glucose biosensor.

Well-crystallized zinc oxide nanonails were grown in a high density by thermal evaporation process and were used as supporting matrixes for glucose oxidase (GOx) immobilization to construct efficient glucose biosensor. The GOx attached to the surfaces of ZnO nanonails had more spatial freedom in its orientation, which facilitated the direct electron transfer between the active sites of immobilized GOx and electrode surface. The fabricated biosensor showed a high sensitivity of 24.613 microA cm(-2) mM(-1) with a response time less than 10 s. Moreover, it shows a linear range from 0.1 to 7.1 mM with a correlation coefficient of R = 0.9937 and detection limit of 5 microM.

Hierarchical ZnO nanostructures: growth and optical properties.

Growth of hierarchical ZnO nanostructures composed of ZnO nanoneedles have been achieved via simple thermal evaporation process by using metallic zinc powder in the presence of oxygen at low temperature of 460 degrees C on silicon substrate without the use of any kind of metal catalysts or additives. It is confirmed by detailed structural studies that the as-grown hierarchical nanostructures are single crystalline with a wurtzite hexagonal phase and nanoneedles of these structures are grown along the c-axis in the [0001] direction. The Raman-scattering analysis substantiates a wurtzite hexagonal phase with a good crystal quality for the as-grown products. Room-temperature photoluminescence (PL) exhibits a strong UV emission at 380 nm confirming the excellent optical properties of as-synthesized hierarchical structures. A plausible growth mechanism is also proposed to clearly understand the growth process of the synthesized structures.

Comparison between the electrical properties of ZnO nanowires based field effect transistors fabricated by back- and top-gate approaches.

Large-quality, well-crystallized growth of ZnO nanowires was done via non-catalytic thermal evaporation process on silicon substrate only by using metallic zinc powder and oxygen as source materials for zinc and oxygen, respectively. The electrical properties of the as-grown ZnO nanowires were examined by fabricating a single nanowire based FETs which were fabricated via two approaches, i.e., back- and top-gate approaches by using electron beam lithography (EBL) and photolithography processes. ZnO FETs electrical properties were characterized by I(DS)-V(DS) and I(DS)-V(GS) measurement. The fabricated single ZnO nanowire based FETs by back- and top-gate approaches exhibited field effect mobilities of approximately 4.25 and approximately 12.76 cm2/Vs, respectively. Moreover, the carrier concentrations for the fabricated back- and top-gate FETs were approximately 1.6 x 10(17) and approximately 1.37 x 10(18) cm(-3), respectively. From our studies it was observed that the fabricated top-gate FETs exhibited higher and good electrical properties as compared to ZnO nanowire FETs fabricated using back-gate approaches.

Structural identity of human histocompatibility leukocyte antigen-B27 molecules from patients with ankylosing spondylitis and normal individuals.

Although the association between human histocompatibility leukocyte antigen (HLA) B27 and ankylosing spondylitis is the prototype of HLA-disease association, the mechanism underlying these associations has not been determined. We have investigated the possibility that the B27 molecules from patients with ankylosing spondylitis are different from those of normals, and only the "different" molecules predispose the individual to disease. Biosynthetically radiolabeled HLA-B27 molecules from patients with ankylosing spondylitis and normal individuals were compared by two-dimensional gel electrophoresis and tryptic peptide mapping with high pressure liquid chromatography. Extensive charge heterogeneity in the 45,000-dalton heavy chain was detected when B27 molecules were analyzed by two-dimensional gel electrophoresis; the charge heterogeneity was reduced, but not eliminated, when the B27 molecules were treated with neuraminidase to remove sialic acid residues before analysis. No structural difference in the B27 molecules from an ankylosing spondylitis patient and a normal individual were detected by two-dimensional gel electrophoresis. Analysis of [(3)H]leucine-labeled and [(3)H]arginine-labeled tryptic peptides and chymotryptic peptides of the trypsin insoluble material by reverse-phase high pressure liquid chromatography revealed identity of the B27 molecules from ankylosing spondylitis patients and normal individuals. These studies indicate that development of akylosing spondylitis in only some B27 positive individuals is not attributable to those individuals possessing variant B27 molecules.

Alveolar epithelial cell chemokine expression triggered by antigen-specific cytolytic CD8(+) T cell recognition.

CD8(+) T lymphocyte responses are a critical arm of the immune response to respiratory virus infection and may play a role in the pathogenesis of interstitial lung disease. We have shown that CD8(+) T cells induce significant lung injury in the absence of virus infection by adoptive transfer into mice with alveolar expression of a viral transgene. The injury is characterized by the parenchymal infiltration of host cells, primarily macrophages, which correlates with physiologic deficits in transgenic animals. CD8(+) T cell-mediated lung injury can occur in the absence of perforin and Fas expression as long as TNF-alpha is available. Here, we show that the effect of TNF-alpha expressed by CD8(+) T cells is mediated not exclusively by cytotoxicity, but also through the activation of alveolar target cells and their expression of inflammatory mediators. CD8(+) T cell recognition of alveolar cells in vitro triggered monocyte chemoattractant protein-1 (MCP-1) and macrophage inflammatory protein-2 (MIP-2) expression in the targets, which was mediated by TNF-alpha. Antigen-dependent alveolar MCP-1 expression was observed in vivo as early as 3 hours after CD8(+) T cell transfer and depended upon TNF-R1 expression in transgenic recipients. MCP-1 neutralization significantly reduced parenchymal infiltration after T cell transfer. We conclude that alveolar epithelial cells actively participate in the inflammation and lung injury associated with CD8(+) T cell recognition of alveolar antigens.