Genomes and Genes
Summary: The complete genetic complement contained in a DNA or RNA molecule in a virus.
- Fradet Turcotte A, Moody C, Laimins L, Archambault J. Nuclear export of human papillomavirus type 31 E1 is regulated by Cdk2 phosphorylation and required for viral genome maintenance. J Virol. 2010;84:11747-60 pubmed publisherThe initiator protein E1 from human papillomavirus (HPV) is a helicase essential for replication of the viral genome. E1 contains three functional domains: a C-terminal enzymatic domain that has ATPase/helicase activity, a central DNA-..
- Fox C, Shannon Lowe C, Gothard P, Kishore B, Neilson J, O CONNOR N, et al. Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis in adults characterized by high viral genome load within circulating natural killer cells. Clin Infect Dis. 2010;51:66-9 pubmed publisher..In most analyzed cases, EBV has been found predominantly in T cells. We describe the novel finding of high EBV genome numbers within circulating natural killer cells in adult patients with EBV-HLH...
- Paden C, Forrest J, Moorman N, Speck S. Murine gammaherpesvirus 68 LANA is essential for virus reactivation from splenocytes but not long-term carriage of viral genome. J Virol. 2010;84:7214-24 pubmed publisher..receptor knockout (IFN-alpha/betaR(-/-)) mice via intranasal inoculation and observed the presence of viral genome-positive splenocytes at day 18 postinfection at approximately 10-fold-lower levels than in the genetically ..
- Carroll S, Bird B, Rollin P, Nichol S. Ancient common ancestry of Crimean-Congo hemorrhagic fever virus. Mol Phylogenet Evol. 2010;55:1103-10 pubmed publisher..Changes in agricultural practices and climate occurring near the time of the most recent common ancestor of CCHFV may have contributed to its emergence and spread. ..
- Kalla M, Schmeinck A, Bergbauer M, Pich D, Hammerschmidt W. AP-1 homolog BZLF1 of Epstein-Barr virus has two essential functions dependent on the epigenetic state of the viral genome. Proc Natl Acad Sci U S A. 2010;107:850-5 pubmed publisher..Our data indicate that the viral BZLF1 protein is crucial both to establish latency and to escape from it. Our data also indicate that EBV has evolved to appropriate its host's mode of methylating DNA for its own epigenetic regulation. ..
- Guo L, Xu X, Song J, Wang W, Wang J, Hung T. Molecular characterization of astrovirus infection in children with diarrhea in Beijing, 2005-2007. J Med Virol. 2010;82:415-23 pubmed publisher..No recombination events were observed in HAstVs in this study. The findings of this study will provide baseline data for HAstVs surveillance and control. J. Med. Virol. 82:415-423, 2010. (c) 2010 Wiley-Liss, Inc. ..
- Mori M, Dietrich U, Manetti F, Botta M. Molecular dynamics and DFT study on HIV-1 nucleocapsid protein-7 in complex with viral genome. J Chem Inf Model. 2010;50:638-50 pubmed publisher..Results show that the interaction between the NCp7 and the viral genome is probably based on electrostatic interactions due to a cluster of basic residues, which is reinforced by the ..
- Bar K, Li H, Chamberland A, Tremblay C, Routy J, Grayson T, et al. Wide variation in the multiplicity of HIV-1 infection among injection drug users. J Virol. 2010;84:6241-7 pubmed publisher..14; 95% confidence interval [CI], 1.37 to 31.27; P = 0.008). These findings highlight the diversity in HIV-1 infection risks among different IDU cohorts and the challenges faced by vaccines in protecting against this mode of infection. ..
- Thaa B, Hofmann K, Veit M. Viruses as vesicular carriers of the viral genome: a functional module perspective. Biochim Biophys Acta. 2010;1803:507-19 pubmed publisher..cargo between membranous organelles inside the cell, while enveloped viruses can be seen as carriers of the viral genome delivering their cargo from an infected to an uninfected cell...
- Passaes C, Guimarães M, Bello G, Morgado M. Near full-length genome characterization of HIV type 1 unique BC recombinant forms from Southern Brazil. AIDS Res Hum Retroviruses. 2009;25:1339-44 pubmed publisher..Our data provide the first description of the near full-length genomes of URFs_BC in Brazil and offer important insights about the complexity of HIV-1 recombinant strains currently in circulation in the south of Brazil. ..
- Yutin N, Koonin E. Evolution of DNA ligases of nucleo-cytoplasmic large DNA viruses of eukaryotes: a case of hidden complexity. Biol Direct. 2009;4:51 pubmed publisher..However, the details of the evolution of these genes that bear on the complexity of the putative ancestral NCLDV and on the evolutionary relationships between viruses and their hosts are not well understood...
- Sayers E, Barrett T, Benson D, Bolton E, Bryant S, Canese K, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010;38:D5-16 pubmed publisher..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. ..
- Benson D, Karsch Mizrachi I, Lipman D, Ostell J, Sayers E. GenBank. Nucleic Acids Res. 2010;38:D46-51 pubmed publisher..Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov. ..
- Kristensen D, Mushegian A, Dolja V, Koonin E. New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 2010;18:11-9 pubmed publisher..Unexpectedly, metagenomics of marine RNA viruses showed that representatives of only one superfamily of eukaryotic viruses, the picorna-like viruses, dominate the RNA virome. ..
- Lai Y, Yue Y, Duan D. Evidence for the failure of adeno-associated virus serotype 5 to package a viral genome > or = 8.2 kb. Mol Ther. 2010;18:75-9 pubmed publisher..Surprisingly, we did not find the full-length single-stranded viral genome by alkaline gel electrophoresis...
- Mueller S, Gausson V, Vodovar N, Deddouche S, Troxler L, Perot J, et al. RNAi-mediated immunity provides strong protection against the negative-strand RNA vesicular stomatitis virus in Drosophila. Proc Natl Acad Sci U S A. 2010;107:19390-5 pubmed publisher..VSV-derived small RNAs produced in infected cells or flies uniformly cover the viral genome, and equally map the genome and antigenome RNAs, indicating that they derive from dsRNA...
- Kamihira S, Yamano Y, Iwanaga M, Sasaki D, Satake M, Okayama A, et al. Intra- and inter-laboratory variability in human T-cell leukemia virus type-1 proviral load quantification using real-time polymerase chain reaction assays: a multi-center study. Cancer Sci. 2010;101:2361-7 pubmed publisher..The relevant choice of not only RM, but also internal control genes for data normalization is expected to be realistic to standardize HTLV-1 VL measurement. ..
- Cataldi M, McCarty D. Differential effects of DNA double-strand break repair pathways on single-strand and self-complementary adeno-associated virus vector genomes. J Virol. 2010;84:8673-82 pubmed publisher..Taken together, the results suggest that productive rAAV genome circularization is mediated primarily by nonhomologous end joining. ..
- Cho N, Dvory Sobol H, Lee C, Cho S, Bryson P, Masek M, et al. Identification of a class of HCV inhibitors directed against the nonstructural protein NS4B. Sci Transl Med. 2010;2:15ra6 pubmed publisher..4BAH2 inhibitors represent an additional class of compounds with potential to effectively treat HCV. ..
- Walsh S, Linnerth Petrik N, Laporte A, Menzies P, Foster R, Wootton S. Full-length genome sequence analysis of enzootic nasal tumor virus reveals an unusually high degree of genetic stability. Virus Res. 2010;151:74-87 pubmed publisher..This work represents an important step in the study of ENTV and sets the foundation for the construction of an infectious molecular clone of ENTV-1...
- Varsani A, de Villiers G, Regnard G, Bragg R, Kondiah K, Hitzeroth I, et al. A unique isolate of beak and feather disease virus isolated from budgerigars (Melopsittacus undulatus) in South Africa. Arch Virol. 2010;155:435-9 pubmed publisher..Maximum-likelihood analysis and recombination analysis suggest that the South African budgerigar BFDV isolates are unique to budgerigars, are non-recombinant in origin, and represent a new genotype of BFDV. ..
- Nakahara K, Shimada R, Choi S, Yamamoto H, Shao J, Uyeda I. Involvement of the P1 cistron in overcoming eIF4E-mediated recessive resistance against Clover yellow vein virus in pea. Mol Plant Microbe Interact. 2010;23:1460-9 pubmed publisher..ClYVV with the point mutation was able to break the resistance. This is a first report demonstrating that P1 is involved in eIF4E-mediated recessive resistance. ..
- Mayer M, Payne J, Gasson M, Narbad A. Genomic sequence and characterization of the virulent bacteriophage phiCTP1 from Clostridium tyrobutyricum and heterologous expression of its endolysin. Appl Environ Microbiol. 2010;76:5415-22 pubmed publisher..The endolysin was inactive against a range of clostridial species but did show lysis of Clostridium sporogenes, another potential spoilage organism. Removal of the C-terminal portion of the endolysin completely abolished lytic activity...
- Krawczyk M, Stankiewicz Drogon A, Haenni A, Boguszewska Chachulska A. Fluorometric assay of hepatitis C virus NS3 helicase activity. Methods Mol Biol. 2010;587:211-21 pubmed publisher..After a few modifications of buffers and assay conditions this method can be applied to various variants of HCV helicase and other proteins with helicase activities. ..
- Yu J, Sun X. Reannotation of protein-coding genes based on an improved graphical representation of DNA sequence. J Comput Chem. 2010;31:2126-35 pubmed publisher..The present method could also be extended to other genomes with or without adaptation of training sets with high accuracy...
- van der Meijden E, Janssens R, Lauber C, Bouwes Bavinck J, Gorbalenya A, Feltkamp M. Discovery of a new human polyomavirus associated with trichodysplasia spinulosa in an immunocompromized patient. PLoS Pathog. 2010;6:e1001024 pubmed publisher..Further studies have to reveal the impact of TSV infection in relation to other populations and diseases...
- Yang T, Maluf N. Self-association of the adenoviral L4-22K protein. Biochemistry. 2010;49:9830-8 pubmed publisher..Assembly of virus particles requires condensation and encapsidation of the linear viral genome. This process requires sequence specific binding of two viral proteins, called IVa2 and L4-22K, to a conserved ..
- Manrubia S, Domingo E, Lázaro E. Pathways to extinction: beyond the error threshold. Philos Trans R Soc Lond B Biol Sci. 2010;365:1943-52 pubmed publisher..Altogether, it turns out that the pathways through which viral quasispecies go extinct are multiple and diverse. ..
- Cohen J. The varicella-zoster virus genome. Curr Top Microbiol Immunol. 2010;342:1-14 pubmed publisher..Further studies of the VZV genome, using recombinant viruses, may facilitate the development of safer and more effective VZV vaccines. Furthermore, VZV might be useful as a vaccine vector to immunize against both VZV and other viruses. ..
- Vu T, Holmes E, Duong V, Nguyen T, Tran T, Quail M, et al. Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia. PLoS Negl Trop Dis. 2010;4:e757 pubmed publisher..These results provide a mechanistic basis to a marked change in the genetic structure of DENV-2 and more broadly underscore that an understanding of DENV evolutionary dynamics can inform the development of vaccines and anti-viral drugs. ..
- Li J, Cheng W, Yao D, Lan B, Yu J, Liu Y, et al. [Sequence the complete sequence of bocavirus I with SISPA-PCR]. Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi. 2010;24:14-6 pubmed..The sequences were alighmented in nr with blastn and assembled with DNAstar. A 4834bp sequence of bocavirus I were assembled. SISPA-PCR is an economical and efficient technique for sequence a virus complete genome. ..
- Wang S, Zhou J, Hou X. [Application of a simple method for detection of rubella virus genome by loop-mediated isothermal amplification (LAMP)]. Zhongguo Yi Miao He Mian Yi. 2009;15:518-20 pubmed..The nucleic acid positive rates of all 11 strains of rubella virus were 100% by the two methods, the positive rate was 55%. RT-LAMP is more simple and convenient than RT-PCR. ..
- Okano Y, Maejima K, Shiraishi T, Hashimoto M, Senshu H, Ozeki J, et al. Genetic heterogeneity found in the replicase gene of poinsettia mosaic virus isolates. Arch Virol. 2010;155:1367-70 pubmed publisher..This suggests that PnMV might have evolved by creating variations in its genome by such translational frameshifts...
- Blacklaws B, Harkiss G. Small ruminant lentiviruses and human immunodeficiency virus: cousins that take a long view. Curr HIV Res. 2010;8:26-52 pubmed
- ..This suggests that mutation pressure is the main factor influencing codon usage bias in herpesviruses. ..
- Lucinda N, Inoue Nagata A, Kitajima E, Nagata T. Complete genome sequence of Brugmansia suaveolens mottle virus, a potyvirus from an ornamental shrub. Arch Virol. 2010;155:1729-32 pubmed publisher..These results and phylogenetic analyses based on the complete genome sequence of the most closely related potyviruses confirmed that BsMoV should be considered a member of a distinct species of the genus Potyvirus...
- Villordo S, Alvarez D, Gamarnik A. A balance between circular and linear forms of the dengue virus genome is crucial for viral replication. RNA. 2010;16:2325-35 pubmed publisher..virus as a model, we investigated the relevance of the interplay between two alternative conformations of the viral genome during replication...
- Shi C, Jia K, Yang B, Huang J. Complete genome sequence of a Megalocytivirus (family Iridoviridae) associated with turbot mortality in China. Virol J. 2010;7:159 pubmed publisher..We here sequenced and analyzed the complete genome of TRBIV, which was identified in Shandong province, China...
- Wang S, An X, Mi Z, Liu D, Zhang B, Lv J, et al. [Construction of HCV-producing cell model based on self-cleaving ribozyme]. Zhonghua Gan Zang Bing Za Zhi. 2010;18:437-9 pubmed publisher..IFN-treating experiment demonstrated that the HCV RNA level decreased with the increasing concentration of IFN alpha. We constructed a stable HCV-producing cell model which can be used for anti-HCV drug research. ..
- Li Y, Xue C, Wang L, Chen X, Chen F, Cao Y. Genomic analysis of two Chinese strains of porcine reproductive and respiratory syndrome viruses with different virulence. Virus Genes. 2010;40:374-81 pubmed publisher..The genomic variations of GDQJ strain provided the basis for further studies of virulence determinants for PRRSVs...
- Tao Z, Cui N, Xu A, Wang H, Song L, Li Y, et al. Genomic characterization of an enterovirus 97 strain isolated in Shandong, China. Virus Genes. 2010;41:158-64 pubmed publisher..Similarity plot analysis further provided the evidence of recombination with other strains of HEV-B in P2 and P3 coding region. This is the first finding of EV97 in China and the third genomic sequence of EV97 reported. ..
- Schlub T, Smyth R, Grimm A, Mak J, Davenport M. Accurately measuring recombination between closely related HIV-1 genomes. PLoS Comput Biol. 2010;6:e1000766 pubmed publisher..We demonstrate that this system is applicable to other studies to accurately measure the recombination rate and show that recombination does not occur randomly within the HIV genome. ..
- Kapoor A, Simmonds P, Lipkin W, Zaidi S, Delwart E. Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. J Virol. 2010;84:10322-8 pubmed publisher..As metagenomic analyses of different environments and organisms continue to yield highly divergent viral genomes NCA provides a rapid and robust method to identify their likely cellular hosts. ..
- Njouom R, Mba S, Nerrienet E, Foupouapouognigni Y, Rousset D. Detection and characterization of hepatitis B virus strains from wild-caught gorillas and chimpanzees in Cameroon, Central Africa. Infect Genet Evol. 2010;10:790-6 pubmed publisher..We demonstrated the existence of gorillas' specific HBV strains distinct but related to those found in chimpanzees living in the same habitat in Cameroon, providing substantial evidence of species association of HBV in NHPs. ..