Academic literature on the topic 'DNA Virus Genomes'
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Journal articles on the topic "DNA Virus Genomes"
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Weitzman, Matthew D., and Amélie Fradet-Turcotte. "Virus DNA Replication and the Host DNA Damage Response." Annual Review of Virology 5, no. 1 (September 29, 2018): 141–64. http://dx.doi.org/10.1146/annurev-virology-092917-043534.
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Viral DNA genomes have limited coding capacity and therefore harness cellular factors to facilitate replication of their genomes and generate progeny virions. Studies of viruses and how they interact with cellular processes have historically provided seminal insights into basic biology and disease mechanisms. The replicative life cycles of many DNA viruses have been shown to engage components of the host DNA damage and repair machinery. Viruses have evolved numerous strategies to navigate the cellular DNA damage response. By hijacking and manipulating cellular replication and repair processes, DNA viruses can selectively harness or abrogate distinct components of the cellular machinery to complete their life cycles. Here, we highlight consequences for viral replication and host genome integrity during the dynamic interactions between virus and host.
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Ma, Zhe, Guoxin Ni, and Blossom Damania. "Innate Sensing of DNA Virus Genomes." Annual Review of Virology 5, no. 1 (September 29, 2018): 341–62. http://dx.doi.org/10.1146/annurev-virology-092917-043244.
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DNA viruses are linked to many infectious diseases and contribute significantly to human morbidity and mortality worldwide. Moreover, DNA viral infections are usually lifelong and hard to eradicate. Under certain circumstances, these viruses can cause fatal disease, especially in children and immunocompromised patients. An efficient innate immune response against these viruses is critical, not only as the first line of host defense against viral infection but also for mounting more specific and robust adaptive immunity against the virus. Recognition of the viral DNA genome is the very first step of this whole process and is crucial for understanding viral pathogenesis as well as for preventing and treating DNA virus–associated diseases. This review focuses on the current state of our knowledge on how human DNA viruses are sensed by the host innate immune system and how viral proteins counteract this immune response.
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Lefeuvre, P., J. M. Lett, A. Varsani, and D. P. Martin. "Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses." Journal of Virology 83, no. 6 (December 30, 2008): 2697–707. http://dx.doi.org/10.1128/jvi.02152-08.
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ABSTRACT The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.
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Lynch, Kevin J., Sheryl Haggerty, and Richard J. Frisque. "DNA Replication of Chimeric JC Virus-Simian Virus 40 Genomes." Virology 204, no. 2 (November 1994): 819–22. http://dx.doi.org/10.1006/viro.1994.1600.
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Rosario, Karyna, Milen Marinov, Daisy Stainton, Simona Kraberger, Elizabeth J. Wiltshire, David A. Collings, Matthew Walters, Darren P. Martin, Mya Breitbart, and Arvind Varsani. "Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)." Journal of General Virology 92, no. 6 (June 1, 2011): 1302–8. http://dx.doi.org/10.1099/vir.0.030338-0.
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Dragonfly cyclovirus (DfCyV), a new species of ssDNA virus discovered using viral metagenomics in dragonflies (family Libellulidae) from the Kingdom of Tonga. Metagenomic sequences of DfCyV were similar to viruses of the recently proposed genus Cyclovirus within the family Circoviridae. Specific PCRs resulted in the recovery of 21 DfCyV genomes from three dragonfly species (Pantala flavescens, Tholymis tillarga and Diplacodes bipunctata). The 1741 nt DfCyV genomes share >95 % nucleotide identity and are classified into 11 subtypes representing a single strain. The DfCyV genomes share 48–63 % genome-wide nucleotide identity with cycloviruses identified in human faecal samples. Recombination analysis revealed three recombinant DfCyV genomes, suggesting that recombination plays an important role in cyclovirus evolution. To our knowledge, this is the first report of a circular ssDNA virus identified in insects, and the data may help elucidate evolutionary links among novel Circoviridae recently identified in animals and environmental samples.
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Coursey, Tami L., and Alison A. McBride. "Hitchhiking of Viral Genomes on Cellular Chromosomes." Annual Review of Virology 6, no. 1 (September 29, 2019): 275–96. http://dx.doi.org/10.1146/annurev-virology-092818-015716.
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Persistent viral infections require a host cell reservoir that maintains functional copies of the viral genome. To this end, several DNA viruses maintain their genomes as extrachromosomal DNA minichromosomes in actively dividing cells. These viruses typically encode a viral protein that binds specifically to viral DNA genomes and tethers them to host mitotic chromosomes, thus enabling the viral genomes to hitchhike or piggyback into daughter cells. Viruses that use this tethering mechanism include papillomaviruses and the gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. This review describes the advantages and consequences of persistent extrachromosomal viral genome replication.
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Xiao, Ke, Dan Xiong, Gong Chen, Jinsong Yu, Yue Li, Kening Chen, Lu Zhang, et al. "RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription." Science Advances 7, no. 26 (June 2021): eabf8962. http://dx.doi.org/10.1126/sciadv.abf8962.
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Like most DNA viruses, herpesviruses precisely deliver their genomes into the sophisticatedly organized nuclei of the infected host cells to initiate subsequent transcription and replication. However, it remains elusive how the viral genome specifically interacts with the host genome and hijacks host transcription machinery. Using pseudorabies virus (PRV) as model virus, we performed chromosome conformation capture assays to demonstrate a genome-wide specific trans-species chromatin interaction between the virus and host. Our data show that the PRV genome is delivered by the host DNA binding protein RUNX1 into the open chromatin and active transcription zone. This facilitates virus hijacking host RNAPII to efficiently transcribe viral genes, which is significantly inhibited by either a RUNX1 inhibitor or RNA interference. Together, these findings provide insights into the chromatin interaction between viral and host genomes and identify new areas of research to advance the understanding of herpesvirus genome transcription.
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Tillieux, Sueli L., Wendy S. Halsey, Elizabeth S. Thomas, John J. Voycik, Ganesh M. Sathe, and Ventzislav Vassilev. "Complete DNA Sequences of Two Oka Strain Varicella-Zoster Virus Genomes." Journal of Virology 82, no. 22 (September 10, 2008): 11023–44. http://dx.doi.org/10.1128/jvi.00777-08.
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ABSTRACT Varicella-zoster virus (VZV) is a herpesvirus and is the causative agent of chicken pox (varicella) and shingles (herpes zoster). Active immunization against varicella became possible with the development of live attenuated varicella vaccine. The Oka vaccine strain was isolated in Japan from a child who had typical varicella, and it was then attenuated by serial passages in cell culture. Several manufacturers have obtained this attenuated Oka strain and, following additional passages, have developed their own vaccine strains. Notably, the vaccines Varilrix and Varivax are produced by GlaxoSmithKline Biologicals and Merck & Co., Inc., respectively. Both vaccines have been well studied in terms of safety and immunogenicity. In this study, we report the complete nucleotide sequence of the Varilrix (Oka-VGSK) and Varivax (Oka-VMerck) vaccine strain genomes. Their genomes are composed of 124,821 and 124,815 bp, respectively. Full genome annotations covering the features of Oka-derived vaccine genomes have been established for the first time. Sequence analysis indicates 36 nucleotide differences between the two vaccine strains throughout the entire genome, among which only 14 are involved in unique amino acid substitutions. These results demonstrate that, although Oka-VGSK and Oka-VMerck vaccine strains are not identical, they are very similar, which supports the clinical data showing that both vaccines are well tolerated and elicit strong immune responses against varicella.
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Blois, Sylvain, Benjamin M. Goetz, James J. Bull, and Christopher S. Sullivan. "Interpreting and de-noising genetically engineered barcodes in a DNA virus." PLOS Computational Biology 18, no. 11 (November 22, 2022): e1010131. http://dx.doi.org/10.1371/journal.pcbi.1010131.
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The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5000 barcodes–necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.
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Everett, Roger D., and Jill Murray. "ND10 Components Relocate to Sites Associated with Herpes Simplex Virus Type 1 Nucleoprotein Complexes during Virus Infection." Journal of Virology 79, no. 8 (April 15, 2005): 5078–89. http://dx.doi.org/10.1128/jvi.79.8.5078-5089.2005.
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ABSTRACT Infections with DNA viruses commonly result in the association of viral genomes and replication compartments with cellular nuclear substructures known as promyelocytic leukemia protein (PML) nuclear bodies or ND10. While there is evidence that viral genomes can associate with preexisting ND10, we demonstrate in this study by live-cell microscopy that structures resembling ND10 form de novo and in association with viral genome complexes during the initial stages of herpes simplex virus type 1 (HSV-1) infection. Consistent with previous studies, we found that the major ND10 proteins PML, Sp100, and hDaxx are exchanged very rapidly between ND10 foci and the surrounding nucleoplasm in live cells. The dynamic nature of the individual protein molecule components of ND10 provides a mechanism by which ND10 proteins can be recruited to novel sites during virus infection. These observations explain why the genomes and replication compartments of DNA viruses that replicate in the cell nucleus are so commonly found in association with ND10. These findings are discussed with reference to the nature, location, and potential number of HSV-1 prereplication compartments and to the dynamic aspects of HSV-1 genomes and viral products during the early stages of lytic infection.
Dissertations / Theses on the topic "DNA Virus Genomes"
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Upadhyay, Mohita. "Dinucleotide frequencies in DNA virus genomes: implications on virus evolution." Thesis, IIT Delhi, 2016. http://localhost:8080/xmlui/handle/12345678/6989.
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Altan, Eda, Valle Mendoza Juana Mercedes Del, Xutao Deng, Tung G. Phan, Mohammadreza Sadeghi, and Eric L. Delwart. "Small Circular Rep-Encoding Single-Stranded DNA Genomes in Peruvian Diarrhea Virome." American Society for Microbiology, 2017. http://hdl.handle.net/10757/622307.
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Metagenomic analysis of diarrhea samples revealed the presence of numerous human enteric viruses and small circular Rep-encoding single-stranded DNA (CRESS-DNA) genomes. One such genome was related to smacoviruses, while eight others were related to genomes reported in the feces of different mammals. The tropism of these CRESS-DNA viruses remains unknown.
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Karan, Mirko. "Sequence diversity of DNA components associated with banana bunchy top virus." Thesis, Queensland University of Technology, 1995.
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Jackson, Ronald James. "Analysis of hepatitis B virus DNA integrated into the genomes of rodent cells." Thesis, University of Edinburgh, 1987. http://hdl.handle.net/1842/15098.
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Tuthill, Tobias J. "Construction expression and preliminary biological analysis of HCV and HCV-dengue chimeric virus genomes." Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368893.
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Yoosuf, Niyaz. "Genomes of mimiviruses of amoeba." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5072/document.
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Les membres des familles Mimiviridae et Marseilleviridae, qui infectent et se répliquent dans Acanthamoeba spp. et d’autres protistes phagocytaires, ont été découverts au cours de la dernière décennie et rattachés à un groupe monophylétique de virus nommés les grands virus à ADN nucléocytoplasmiques (NCLDVs), qui infectent un large éventail d’eukaryotes y compris différents organismes unicellulaires. Récemment, il a été proposé de reclasser les NCLDVs dans un nouvel ordre viral nommé les Megavirales. Plusieurs dizaines de virus géants des amibes ont été isolés, mais le génome de peu d’entre eux a été étudié de façon approfondie. Nous avons étudié les génomes de ces virus géants d'amibe afin d’acquérir une meilleure compréhension de leur répertoire de gènes et leur importance évolutionnaire. L'analyse phylogénétique des virus géants d'amibe distingue clairement trois lignées, nommées A, B et C. Nous avons étudié en détail le génome de Acanthamoeba polyphaga moumouvirus, le membre fondateur de la lignée B et avons déchiffré son contenu en gènes et sa relation évolutive avec d'autres organismes. Nous avons également étudié les génomes de Terra1 virus et Terra2 virus, qui appartiennent respectivement aux lignées C et A, et ont été isolés à partir d'échantillons de sol alors que les mimivirus décrits aupravant ont été isolés à partir d'eau douce ou de mer. En outre, nous avons décrit le génome du virus Courdo11, qui appartient à la lignée C, et est étroitement lié au premier Mimivirus isolé d'un humain, qui présentait une pneumonie inexpliquéeThe members of families Mimiviridae and Marseilleviridae, which infect and replicate in Acanthamoeba spp. and other phagocytic protists, were discovered during the past decade and linked to a monophyletic group of viruses named the Nucleocytoplasmic Large DNA viruses (NCLDVs), which infect a broad variety of eukaryotes including diverse unicellular organisms. Recently, it has been proposed to reclassify the NCLDVs into a new viral order named the Megavirales. Several dozens of giant viruses of amoeba have been isolated but the genome of very few has been extensively studied. We studied the genomes of these giant viruses of amoeba to gain a better understanding of their gene repertoire and evolutionary importance. The phylogenetic analysis of giant viruses of amoeba clearly distinguished three lineages, named lineages A, B and C. We studied in detail the genome of Acanthamoeba polyphaga moumouvirus, the leader member of lineage B to decipher its gene content and its evolutionary relationship with other organisms. We further studied the genomes of Terra1 virus and Terra2 virus, which belong to lineages C and A, respectively, and were isolated from soil samples whereas previously described mimiviruses of amoeba were isolated from fresh or marine water. Furthermore, we described the genome of Courdo11 virus, which belongs to lineage C, and is closely related to the first mimivirus isolated from a human, who exhibited unexplained pneumonia
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Pereira, Bruna Tibirica. "Sequenciamento do baculovírus que infecta a broca-da-cana-de-açúcar Diatraea saccharalis." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-16052014-082057/.
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Baculovírus são vírus específicos de inseto que infectam principalmente membros da ordem Lepidoptera. Diatraea saccharalis granulovírus (DsGV) foi isolado de larvas de Diatraea saccharalis (Lepidoptera: Crambidae), a broca-da-cana-de-açúcar, um dos insetos-praga de maior importância na cultura de cana-de-açúcar no Brasil. O genoma completo de DsGV foi obtido através do sequenciamento 454 (Roche). O genoma de DsGV apresentou 98.463 pb e potencialmente codifica 116 genes. Foram identificados os 37 genes conservados em todos os baculovírus, 19 genes específicos de betabaculovírus e 17 genes únicos. DsGV é o primeiro betabaculovírus que possui o gene gp64, que codifica uma proteína de fusão, originalmente encontrado apenas em alfabaculovírus do grupo I. A análise filogenética utilizando a concatenação das sequências deduzidas de aminoácidos de 30 genes conservados em 61 baculovírus totalmente sequenciados sugere que DsGV está inserido no clado b do grupo dos betabaculovírus e parece estar mais estritamente relacionado a 5 GVs (ChocGV, PiraGV, ClanGV, CpGV e CrleGV).Baculoviruses are insect specific viruses that infect mainly members of the Order Lepidoptera. Diatraea saccharalis granulovirus (DsGV) was isolated from Diatraea saccharalis (Lepidoptera: Crambidae), one of the most important insect pest of the sugar cane culture in Brazil. The genome of DsGV was obtained by the 454 sequencing system (Roche). Our results showed that the nucleotide sequence of the DsGV genome is 98.463 bp in length and potentially encodes 116 putative genes. It contains the 37 baculovirus core genes, a set of 19 betabaculovirus-specific genes and 17 putative DsGV genes were not found in any genome of the baculoviruses sequenced up to the present. DsGV is the first betabaculovirus sequenced so far that has the gp64 envelope fusion protein gene, originally found only in alphabaculovirus group I. Phylogenetic analysis performed with concatamers of 30 conserved proteins from 61 fully sequenced baculovirus genomes suggests that DsGV is a member of clade b of the betabaculovirus and seems to be closer to 5 GVs (ChocGV, PiraGV, ClanGV, CpGV e CrleGV).
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Anderson, Marie June. "Complementary DNA cloning, sequencing, and analysis of the Pelargonium flower-break virus genome /." The Ohio State University, 1993. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487842372897839.
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Akahata, Wataru. "DNA vaccination of macaques by full genome plasmids which produce noninfectious virus particles." Kyoto University, 2002. http://hdl.handle.net/2433/149869.
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Kyoto University (京都大学)0048
新制・課程博士
博士(人間・環境学)
甲第9661号
人博第145号
13||130(吉田南総合図書館)
新制||人||35(附属図書館)
UT51-2002-G419
京都大学大学院人間・環境学研究科人間・環境学専攻
(主査)教授 速水 正憲, 教授 津田 謹輔, 教授 松村 道一, 助教授 三浦 智行
学位規則第4条第1項該当
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Fick, Wilhelmina Christina. "Characterisation of promoter sequences in a Capripoxvirus genome." Master's thesis, University of Cape Town, 1992. http://hdl.handle.net/11427/25623.
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Capripoxviruses are of particular interest as live recombinant vectors for use in the veterinary field, since their host-range is restricted to cattle, goats and sheep. The work presented in this thesis is a preliminary study undertaken on the South African Neethling vaccine strain of lumpy skin disease virus (LSDV). As a departure point towards the eventual identification of strong promoter areas in the 143 kb genome of LSDV, a portion of its genome was cloned. Three methods for purification of LSDV DNA were compared, to determine which yielded the best quality DNA for cloning. DNA extracted directly from infected cells was excessively contaminated with bovine host-DNA, complicating the cloning of LSDV DNA. The use of pulsed field gel electrophoresis solved the contamination problem, by separating viral DNA from bovine DNA. However, insufficient amounts of viral DNA for cloning purposes, could be recovered from the gel. Sufficient amounts of good quality LSDV DNA was obtained by extraction from purified virions. Purified LSDV DNA was digested with various restriction enzymes to identify those which yielded several 4-1 0 kb fragments, for cloning into the Bluescribe plasmid transcription vector. Enrichment for large fragments (8-1 0 kb) was achieved by sucrose density centrifugation. Cloned fragments were analysed by Southern blot hybridisation to verify their viral origin. Hybridisation studies indicated that several unique regions of the LSDV genome were cloned as Pst I and Bam HI fragments respectively, i.e. the cloned fragments contained no overlapping regions. In total, 71.25 kb of the DNA of the LSDV Neethling vaccine strain has been cloned, representing approximately 50% of the viral genome. The availability of these clones now paves the way for further molecular investigations of the LSDV Neethling genome, including identification of promoter regions. A trial gene, which will be cloned and expressed in LSDV, namely the cloned VPS-gene of bluetongue virus serotype 4, was prepared and its nucleotide sequence determined. Homopolymer sequences present at the terminal ends of the gene as a result of the original cloning strategy, are known to interfere with expression and were removed by means of the polymerase chain reaction (PCR). The nucleotide sequence of the resulting PCR-tailored BTV4 VPS-genewas determined and used to deduce the amino acid sequence of the protein. The gene is 1638 bp in length and encodes a protein of 526 aa. Conserved sequences, 6 bp in length and unique to the 5'- and 3'terminal ends of all BTV genes, were detected at the termini of the tailored gene, confirming that the original clone was a full-length copy of the gene. Amplification by PCR did not mutate the open reading frame (OAF) of the gene, since it was of similar length to that reported for 5 other BTV serotypes. With a view to future investigations, including the identification of promoter sequences in the LSDV genome, a preliminary investigation of LSDV protein synthesis was undertaken, to acquire some knowledge of the growth cycle of the virus. Eighteen putative virus-specific proteins were identified by radio-labelling infected cells with [³⁵S]-methionine. By pulse-labelling infected cells with [³⁵S]methionine at various times post infection (p.i.), viral proteins were first detected at 16 hr p.i. It is, however, unlikely that the early phase of viral replication commences as late as 16 hr p.i. and these results might be attributed to various problems, such as the low multiplicity of infection used and that host protein shut-down was inefficient, thus masking the presence viral proteins. In conclusion, this investigation resulted in the cloning of 71,25 kb of the LSDV genome, the tailoring and sequencing of the BTV4 VPS gene and the identification of 18 putative LSDV proteins. This now paves the way for further research to develop LSDV as a vaccine vector.
Books on the topic "DNA Virus Genomes"
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Enrique, Catalano Carlos, ed. Viral genome packaging machines: Genetics, structure, and mechanism. Georgetown, Tex: Landes Bioscience/Eurekah.com, 2005.
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Foreign DNA in mammalian systems. Weinheim: Wiley-VCH, 2000.
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Virus Replication and Genome Interaction. The Company of Biologists Limited, 1987.
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Becker, Yechiel. Replication of Viral and Cellular Genomes: Molecular Events at the Origins of Replication and Biosynthesis of Viral and Cellular Genomes. Springer, 2011.
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Vinod, Nikhra. COVID-19: Perspective, Patterns and Evolving strategies. Heighten Science Publications Inc., 2020. http://dx.doi.org/10.29328/ebook1003.
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The Global Virome: The viruses have a global distribution, phylogenetic diversity, and host specificity. They are obligate intracellular parasites with single- or double-stranded DNA or RNA genomes, and afflict bacteria, plants, animals, and human population. The infecting virus binds to receptor proteins on the host cell surface, followed by internalisation, replication, and cell lysis. Further, trans-species interactions of viruses with bacteria, small eukaryotes and host are linked with various zoonotic viral diseases and disease progression.
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Leisy, Douglas J. Gene expression, genome organization, and evolution of the Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus. 1986.
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Livingston, Schuyler, Benjamin Young, Martin Markowitz, Poonam Mathur, and Bruce L. Gilliam. HIV Virology. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190493097.003.0017.
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HIV is a member of the lentivirus subfamily of retroviruses. Two distinct groups of viruses are pathogenic in humans: HIV-1 and HIV-2. Both are transmitted sexually and known to cause immunodeficiency disease. HIV enters the cell through use of the CD4 receptor and chemokine co-receptors, primarily CCR5 and CXCR4. The viral genome is transcribed from RNA to DNA by reverse transcriptase and integrated into the host genome by integrase. The HIV genome encodes 15 proteins, comprising three categories: structural, regulatory, and accessory. After budding from the host cell, the virus matures into its infectious form through cleavage of viral precursor proteins by protease.
Book chapters on the topic "DNA Virus Genomes"
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Hirth, Léon. "Cloning of Plant-Virus Genomes Other than that of Cauliflower Mosaic Virus." In Recombinant DNA Research and Viruses, 277–92. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4613-2565-9_14.
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Lecomte, Emilie, Adrien Leger, Magalie Penaud-Budloo, and Eduard Ayuso. "Single-Stranded DNA Virus Sequencing (SSV-Seq) for Characterization of Residual DNA and AAV Vector Genomes." In Methods in Molecular Biology, 85–106. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9139-6_5.
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Sample, Jeffery T., Elessa M. Marendy, David J. Hughes, and Clare E. Sample. "The Epstein–Barr Virus Genome." In DNA Tumor Viruses, 241–58. New York, NY: Springer US, 2008. http://dx.doi.org/10.1007/978-0-387-68945-6_11.
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Weller, Sandra K. "Herpes Simplex Virus DNA Replication and Genome Maturation." In The DNA Provirus, 189–213. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818302.ch14.
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Hofschneider, P. H., M. Wollersheim, and P. Zahm. "Transactivation by Hepatitis B Virus DNA." In Organization and Function of the Eucaryotic Genome, 19–20. Berlin, Heidelberg: Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-46611-3_23.
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Digard, Paul, William Bebrin, Connie Chow, and Donald M. Coen. "Functional Analysis of the Herpes Simplex Virus DNA Polymerase." In Viral Genome Methods, 241–51. Boca Raton: CRC Press, 2023. http://dx.doi.org/10.1201/9781003420163-14.
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Liu, Shenping, and Fred L. Homa. "Atomic Structure of the Herpes Simplex Virus 1 DNA Polymerase." In Viral Genome Replication, 365–81. Boston, MA: Springer US, 2009. http://dx.doi.org/10.1007/b135974_17.
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Godfrey, Anja, Sharada Ramasubramanyan, and Alison J. Sinclair. "The Use of Chromatin Precipitation Coupled to DNA Sequencing (ChIP-Seq) for the Analysis of Zta Binding to the Human and EBV Genome." In Epstein Barr Virus, 191–206. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6655-4_14.
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Johannsen, Eric, Michael Calderwood, Myung-Soo Kang, Bo Zhao, Daniel Portal, and Elliott Kieff. "Epstein–Barr Virus Latent Infection Nuclear Proteins: Genome Maintenance and Regulation of Lymphocyte Cell Growth and Survival." In DNA Tumor Viruses, 317–53. New York, NY: Springer US, 2008. http://dx.doi.org/10.1007/978-0-387-68945-6_14.
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Fleming, Jo-Ann G. W., and Max D. Summers. "The Integration of the Genome of a Segmented DNA Virus in the Host Insect’s Genome." In Molecular Insect Science, 99–105. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4899-3668-4_12.
Full textConference papers on the topic "DNA Virus Genomes"
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Chen, Chun-Cheng, and Gou-Jen Wang. "PCR Free Detection of Hepatitis B Virus DNA Using a Nanostructured Impedance Biosensor." In ASME 2014 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/detc2014-34866.
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In this study, a PCR free technique for effective detection of hepatitis B virus (HBV) DNA obtained directly from clinical samples was presented. The honeycomb-like barrier layer of an anodic aluminum oxide (AAO) film having a uniform nanohemisphere array was used as the substrate of the sensing electrode. A gold thin film about 30 nm thick was radio-frequency (RF) magnetron sputtered onto the AAO barrier-layer surface as the electrode for the successive deposition of gold nanoparticles (GNPs) on the hemisphere surface. A specially designed single-strand 96-mer gene fragment of the target genomic DNA of HBV based on the genome sequences of HBV from the National Center for Biotechnology Information (NCBI) was immobilized on the nanostructured electrode as the capture probe. Complementary target HBV DNA (3020–3320 mer) obtained from clinical samples were further hybridized to the sensing probes. Detection results through electrochemical impedance spectroscopy (EIS) illustrate that two dynamic linear ranges, 0–103 and 103–105 copies/mL, having R2 values of 0.973 and 0.998, respectively, could be obtained. A detection limit of 186 copies/mL could be achieved. The proposed simple and high performance HBV DNA detection technique in this study is highly feasible for future clinical applications.
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Tyumentseva, M. A., A. I. Tyumentsev, and V. G. Akimkin. "DEVELOPMENT OF APPROACHES FOR DETECTION OF GENOME-INTEGRATED PROVIRAL DNA OF THE HUMAN IMMUNODEFICIENCY VIRUS (HIV-1) IN ULTRA LOW CONCENTRATIONS USING THE CRISPR/CAS SYSTEM." In Molecular Diagnostics and Biosafety. Federal Budget Institute of Science 'Central Research Institute for Epidemiology', 2020. http://dx.doi.org/10.36233/978-5-9900432-9-9-118.
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For the effective functioning of supervisory and health monitoring services, it is necessary to introduce modern molecular technologies into their practice. Therefore, the task of developing new effective methods for detecting pathogen, for example HIV, based on CRISPR/CAS genome editing systems, remains urgent. In the present work, guide RNAs and specific oligonucleotides were developed for preliminary amplification of highly conserved regions of the HIV-1 genome. The developed guide RNAs make it possible to detect single copies of HIV-1 proviral DNA in vitro as part of CRISPR/CAS ribonucleoprotein complexes in biological samples after preliminary amplification.
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Arai, Eri, Ying Tian, Masahiro Gotoh, Yoriko Takahashi, Hidenori Ojima, Tomoo Kosuge, and Yae Kanai. "Abstract 1055: Genome-wide DNA methylation analysis in precancerous conditions associated with hepatitis B virus and hepatitis C virus infection." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-1055.
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Kuramoto, Junko, Eri Arai, Ying Tian, Nobuaki Funahashi, Masaki Hiramoto, Takao Nammo, Yuichi Nozaki, et al. "Abstract 5320: Genome-wide DNA methylation analysis during nonalcoholic steatohepatitis-related multistage hepatocarcinogenesis: Comparison with hepatitis virus-related carcinogenesis." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-5320.
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Nogueira, Raniery Augusto dos Santos Beserra, Ana Beatriz Silva Barbosa, Francisco Das Chagas Diassis Jácome Valentim, Sâmya Pires Batista De Azevêdo, and Jamile Rodrigues Cosme De Holanda. "MECANISMOS DE MANUTENÇÃO DA LATÊNCIA DO VÍRUS VARICELA ZÓSTER: UMA ADAPTAÇÃO NECESSÁRIA." In I Congresso Nacional de Microbiologia Clínica On-Line. Revista Multidisciplinar em Saúde, 2021. http://dx.doi.org/10.51161/rems/1182.
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Introdução: O Vírus Varicela Zóster pertence à subfamília α-herpesviridae e é um DNA-vírus de fita dupla, possuindo 68 Fases de Leitura Aberta (ORF) únicas. Sendo responsável por varicela, em um primeiro contato, o vírus mantém-se latente por um longo período em gânglios das raízes dorsais e de nervos cranianos, disseminando-se por essas estruturas após décadas, quando reativado, configurando Herpes Zóster, cujas complicações prejudicam a qualidade de vida dos pacientes. Posteriormente à infecção primária, o vírus classifica-se como neurotrópico e seus meios de sobrevida em neurônios, ainda não são claros. Objetivo: Este estudo busca elucidar os mecanismos de latência desse patógeno, visando ao desenvolvimento do conhecimento científico no assunto. Material e Métodos: Utilizando-se da plataforma online PubMed, foram pesquisados os descritores “varicella zoster virus”, em adição a “apoptosis”, e “herpes zoster infection”, com o operador booleano “AND” tendo como filtro a delimitação temporal entre 01/01/2018 e 01/05/2021. Resultados: Ao longo do período de latência, o DNA viral é encontrado em células neuronais, estando em forma não-integrada (cita-se epissoma infinito ou comprimento concateméro) e sua transcrição é fortemente restrita. Em meio ao genoma viral, o ORF63 mostrou-se de grande relevância na proteção de neuronal em humanos. Durante monitorização, foi-se percebido a migração da proteína OFR63 quando se induz apoptose na célula, tornando-se mais citoplasmática. A partir disso, percebeu-se interação inibitória entre a proteína ORF63 e a estaurosporina, molécula indutora da apoptose. O que até então se mostrava como hipótese, foi melhor embasado pela redução dos níveis de caspase-3, marcador apoptótico celular, em neurônios infectados pelo VVZ quando comparados a outras células (infectadas ou não). Conclusão: Diante de todas as questões, ainda cientificamente obscuras, acerca da capacidade desse vírus de sobreviver durante décadas nos gânglios nervosos, ressalta-se a necessidade de mais pesquisas na área, para que se tenha melhor manejo de pacientes infectados com o Vírus Varicela Zóster. Ademais, não se pode negar que a inibição da apoptose é uma evolução adaptativa muito favorável ao microrganismo, já que as células neuronais são hospedeiras senescentes e seu aumento de vida significa aumento de vida do patógeno.
Reports on the topic "DNA Virus Genomes"
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Mawassi, Munir, and Valerian V. Dolja. Role of the viral AlkB homologs in RNA repair. United States Department of Agriculture, June 2014. http://dx.doi.org/10.32747/2014.7594396.bard.
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AlkB proteins that repair DNA via reversing methylation damage are conserved in a broad range of prokaryotes and eukaryotes including plants. Surprisingly, AlkB-domains were discovered in the genomes of numerous plant positive-strand RNA viruses, majority of which belong to the family Flexiviridae. The major goal of this research was to reveal the AlkB functions in the viral infection cycle using a range of complementary genetic and biochemical approaches. Our hypotheses was that AlkB is required for efficient replication and genetic stability of viral RNA genomes The major objectives of the research were to identify the functions of GVA AlkB domain throughout the virus infection cycle in N. benthamiana and grapevine, to investigate possible RNA silencing suppression activity of the viral AlkBs, and to characterize the RNA demethylation activity of the mutated GVA AlkBs in vitro and in vivo to determine methylation status of the viral RNA. Over the duration of project, we have made a very substantial progress with the first two objectives. Because of the extreme low titer of the virus particles in plants infected with the AlkB mutant viruses, we were unable to analyze RNA demethylation activity and therefore had to abandon third objective. The major achievements with our objectives were demonstration of the AlkB function in virus spread and accumulation in both experimental and natural hosts of GVA, discovery of the functional cooperation and physical interaction between AlkB and p10 AlkB in suppression of plant RNA silencing response, developing a powerful virus vector technology for grapevine using GLRaV-2-derived vectors for functional genomics and pathogen control in grapevine, and in addition we used massive parallel sequencing of siRNAs to conduct comparative analysis of the siRNA populations in grape plants infected with AlkB-containing GLRaV-3 versus GLRaV-2 that does not encode AlkB. This analysis revealed dramatically reduced levels of virus-specific siRNAs in plants infected with GLRaV-3 compared to that in GLRaV-2 infection implicating AlkB in suppression of siRNA formation. We are pleased to report that BARD funding resulted in 5 publications directly supported by BARD, one US patent, and 9 more publications also relevant to project. Moreover, two joint manuscripts that summarize work on GVA AlkB (led by Israeli PI) and on viral siRNAs in grapevine (led by US PI in collaboration with University of Basel) are in preparation.
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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, February 2022. http://dx.doi.org/10.18235/0003982.
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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.
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Bercovier, Herve, and Ronald P. Hedrick. Diagnostic, eco-epidemiology and control of KHV, a new viral pathogen of koi and common carp. United States Department of Agriculture, December 2007. http://dx.doi.org/10.32747/2007.7695593.bard.
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Original objectives and revisions-The proposed research included these original objectives: field validation of diagnostic tests (PCR), the development and evaluation of new sensitive tools (LC-PCR/TaqManPCR, antibody detection by ELISA) including their use to study the ecology and the epidemiology of KHV (virus distribution in the environment and native cyprinids) and the carrier status of fish exposed experimentally or naturally to KHV (sites of virus replication and potential persistence or latency). In the course of the study we completed the genome sequence of KHV and developed a DNA array to study the expression of KHV genes in different conditions. Background to the topics-Mass mortality of koi or common carp has been observed in Israel, USA, Europe and Asia. These outbreaks have reduced exports of koi from Israel and have created fear about production, import, and movements of koi and have raised concerns about potential impacts on native cyprinid populations in the U.S.A. Major conclusions-A suite of new diagnostic tools was developed that included 3 PCR assays for detection of KHV DNA in cell culture and fish tissues and an ELISA assay capable of detecting anti-KHV antibodies in the serum of koi and common carp. The TKPCR assay developed during the grant has become an internationally accepted gold standard for detection of viral DNA. Additionally, the ELISA developed for detecting serum anti-KHV antibodies is now in wide use as a major nonlethal screening tool for evaluating virus status of koi and common carp populations. Real time PCR assays have been able to detect viral DNA in the internal organs of survivors of natural and wild type vaccine exposures at 1 and 10³ genome equivalents at 7 months after exposure. In addition, vaccinated fish were able to transmit the virus to naive fish. Potential control utilizing hybrids of goldfish and common carp for production demonstrated they were considerably more resistant than pure common carp or koi to both KHV (CyHV-3). There was no evidence that goldfish or other tested endemic cyprinids species were susceptible to KHV. The complete genomic sequencing of 3 strains from Japan, the USA, and Israel revealed a 295 kbp genome containing a 22 kbp terminal direct repeat encoding clear gene homologs to other fish herpesviruses in the family Herpesviridae. The genome encodes156 unique protein-coding genes, eight of which are duplicated in the terminal repeat. Four to seven genes are fragmented and the loss of these genes may be associated with the high virulence of the virus. Viral gene expression was studies by a newly developed chip which has allowed verification of transcription of most all hypothetical genes (ORFs) as well as their kinetics. Implications, both scientific and agricultural- The results from this study have immediate application for the control and management of KHV. The proposal provides elements key to disease management with improved diagnostic tools. Studies on the ecology of the virus also provide insights into management of the virus at the farms that farmers will be able to apply immediately to reduce risks of infections. Lastly, critical issues that surround present procedures used to create “resistant fish” must be be resolved (e.g. carriers, risks, etc.). Currently stamping out may be effective in eradicating the disease. The emerging disease caused by KHV continues to spread. With the economic importance of koi and carp and the vast international movements of koi for the hobby, this disease has the potential for even further spread. The results from our studies form a critical component of a comprehensive program to curtail this emerging pathogen at the local, regional and international levels.
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Hedrick, Ronald, and Herve Bercovier. Characterization and Control of KHV, A New Herpes Viral Pathogen of Koi and Common Carp. United States Department of Agriculture, January 2004. http://dx.doi.org/10.32747/2004.7695871.bard.
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In this project we proposed to characterize the virus genome and the structural virion polypeptides to allow development of improved diagnostic approaches and potential vaccination strategies. These goals have been mostly achieved and the corresponding data were published in three papers (see below) and three more manuscripts are in preparation. The virion polypeptides of KHV strains isolated from USA (KHV-U) and Israel (KHV-I) were found to be identical. Purified viral DNA analyzed with a total of 5 restriction enzymes demonstrated no fragment length polymorphism between KHV-I and KHV-U but both KHV isolates differed significantly from the cyprinid herpesvirus (CHV) and the ictalurid herpesvirus (channel catfish virus or CCV). Using newly obtained viral DNA sequences two different PCR assays were developed that need to be now further tested in the field. We determined by pulse field analysis that the size of KHV genome is around 280 kbp (1-1. Bercovier, unpublished results). Sequencing of the viral genome of KHV has reached the stage where 180 kbp are sequenced (twice and both strands). Four hypothetical genes were detected when DNA sequences were translated into amino acid sequences. The finding of a gene of real importance, the thymidine kinase (TK) led us to extend the study of this specific gene. Four other genes related to DNA synthesis were found. PCR assays based on defined sequences were developed. The PCR assay based on TK gene sequence has shown improved sensitivity in the detection of KHV DNA compared to regular PCR assays. </P> <P><SPAN>With the ability to induce experimental infections in koi with KHV under controlled laboratory conditions we have studied the progress and distribution of virus in host tissues, the development of immunity and the establishment of latent infections. Also, we have investigated the important role of water temperature on severity of infections and mortality of koi following infections with KHV. These initial studies need to be followed by an increased focus on long-term fate of the virus in survivors. This is essential in light of the current "controlled exposure program" used by farmers to produce KHV "naturally resistant fish" that may result in virus or DNA carriers. </SPAN></P> <P><SPAN>The information gained from the research of this project was designed to allow implementation of control measures to prevent the spread of the virus both by improved diagnostic approaches and preventive measures. We have accomplished most of these goals but further studies are needed to establish even more reliable methods of prevention with increased emphases on improved diagnosis and a better understanding of the ecology of KHV. </SPAN>
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Bar-Joseph, Moshe, William O. Dawson, and Munir Mawassi. Role of Defective RNAs in Citrus Tristeza Virus Diseases. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575279.bard.
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This program focused on citrus tristeza virus (CTV), the largest and one of the most complex RNA-plant-viruses. The economic importance of this virus to the US and Israeli citrus industries, its uniqueness among RNA viruses and the possibility to tame the virus and eventually turn it into a useful tool for the protection and genetic improvement of citrus trees justify these continued efforts. Although the overall goal of this project was to study the role(s) of CTV associated defective (d)-RNAs in CTV-induced diseases, considerable research efforts had to be devoted to the engineering of the helper virus which provides the machinery to allow dRNA replication. Considerable progress was made through three main lines of complementary studies. For the first time, the generation of an engineered CTV genetic system that is capable of infecting citrus plants with in vitro modified virus was achieved. Considering that this RNA virus consists of a 20 kb genome, much larger than any other previously developed similar genetic system, completing this goal was an extremely difficult task that was accomplished by the effective collaboration and complementarity of both partners. Other full-length genomic CTV isolates were sequenced and populations examined, resulting in a new level of understanding of population complexities and dynamics in the US and Israel. In addition, this project has now considerably advanced our understanding and ability to manipulate dRNAs, a new class of genetic elements of closteroviruses, which were first found in the Israeli VT isolate and later shown to be omnipresent in CTV populations. We have characterized additional natural dRNAs and have shown that production of subgenomic mRNAs can be involved in the generation of dRNAs. We have molecularly cloned natural dRNAs and directly inoculated citrus plants with 35S-cDNA constructs and have shown that specific dRNAs are correlated with specific disease symptoms. Systems to examine dRNA replication in protoplasts were developed and the requirements for dRNA replication were defined. Several artificial dRNAs that replicate efficiently with a helper virus were created from infectious full-genomic cDNAs. Elements that allow the specific replication of dRNAs by heterologous helper viruses also were defined. The T36-derived dRNAs were replicated efficiently by a range of different wild CTV isolates and hybrid dRNAs with heterologous termini are efficiently replicated with T36 as helper. In addition we found: 1) All CTV genes except of the p6 gene product from the conserved signature block of the Closteroviridae are obligate for assembly, infectivity, and serial protoplast passage; 2) The p20 protein is a major component of the amorphous inclusion bodies of infected cells; and 3) Novel 5'-Co-terminal RNAs in CTV infected cells were characterized. These results have considerably advanced our basic understanding of the molecular biology of CTV and CTV-dRNAs and form the platform for the future manipulation of this complicated virus. As a result of these developments, the way is now open to turn constructs of this viral plant pathogen into new tools for protecting citrus against severe CTV terms and development of virus-based expression vectors for other citrus improvement needs. In conclusion, this research program has accomplished two main interconnected missions, the collection of basic information on the molecular and biological characteristics of the virus and its associated dRNAs toward development of management strategies against severe diseases caused by the virus and building of novel research tools to improve citrus varieties. Reaching these goals will allow us to advance this project to a new phase of turning the virus from a pathogen to an ally.
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Jordan, Ramon L., Abed Gera, Hei-Ti Hsu, Andre Franck, and Gad Loebenstein. Detection and Diagnosis of Virus Diseases of Pelargonium. United States Department of Agriculture, July 1994. http://dx.doi.org/10.32747/1994.7568793.bard.
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Pelargonium (Geranium) is the number one pot plant in many areas of the United States and Europe. Israel and the U.S. send to Europe rooted cuttings, foundation stocks and finished plants to supply a certain share of the market. Geraniums are propagated mainly vegetatively from cuttings. Consequently, viral diseases have been and remain a major threat to the production and quality of the crop. Among the viruses isolated from naturally infected geraniums, 11 are not specific to Pelargonium and occur in other crops while 6 other viruses seem to be limited to geranium. However, several of these viruses are not sufficiently characterized to conclude that they are distinct agents and their nomenclature and taxonomy are confusing. The ability to separate, distinguish and detect the different viruses in geranium will overcome obstacles te developing effective detection and certification schemes. Our focus was to further characterize some of these viruses and develop better methods for their detection and control. These viruses include: isolates of pelargonium line pattern virus (PLPV), pelargonium ringspot virus (PelRSV), pelargonium flower break virus (PFBV), pelargonium leaf curl (PLCV), and tomato ringspot virus (TomRSV). Twelve hybridoma cell lines secreting monoclonal antibodies specific to a geranium isolate of TomRSV were produced. These antibodies are currently being characterized and will be tested for the ability to detect TomRSV in infected geraniums. The biological, biochemical and serological properties of four isometric viruses - PLPV, PelRSV, and PFBV (and a PelRSV-like isolate from Italy called GR57) isolated from geraniums exhibiting line and ring pattern or flower break symptoms - and an isolate ol elderbeny latent virus (ELV; which the literature indicates is the same as PelRSV) have been determined Cloned cDNA copies of the genomic RNAs of these viruses were sequenced and the sizes and locations of predicted viral proteins deduced. A portion of the putative replicase genes was also sequenced from cloned RT-PCR fragments. We have shown that, when compared to the published biochemical and serological properties, and sequences and genome organizations of other small isometric plant viruses, all of these viruses should each be considered new, distinct members of the Carmovirus group of the family Tombusviridae. Hybridization assays using recombinant DNA probes also demonstrated that PLPV, PelRSV, and ELV produce only one subgenomic RNA in infected plants. This unusual property of the gene expression of these three viruses suggests that they are unique among the Carmoviruses. The development of new technologies for the detection of these viruses in geranium was also demonstrated. Hybridization probes developed to PFBV (radioactively-labeled cRNA riboprobes) and to PLPV (non-radioactive digoxigenin-labeled cDNAs) were generally shown to be no more sensitive for the detection of virus in infected plants than the standard ELISA serology-based assays. However, a reverse transcriptase-polymerase chain reaction assay was shown to be over 1000 times more sensitive in detecting PFBV in leaf extracts of infected geranium than was ELISA. This research has lead to a better understanding of the identity of the viruses infecting pelargonium and to the development of new tools that can be used in an improved scheme of providing virus-indexed pelargonium plants. The sequence information, and the serological and cloned DNA probes generated from this work, will allow the application of these new tools for virus detection, which will be useful in domestic and international indexing programs which are essential for the production of virus-free germplasm both for domestic markets and the international exchange of plant material.
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Citovsky, Vitaly, and Yedidya Gafni. Nuclear Import of the Tomato Yellow Curl Leaf Virus in Tomato Plants. United States Department of Agriculture, September 1994. http://dx.doi.org/10.32747/1994.7568765.bard.
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Tomato yellow leaf curl geminivirus (TYLCV) is a major pathogen of cultivated tomato, causing up to 100% crop loss in many parts of the world. In Israel the disease is well known and has an economic significance. In recent years viral symptoms were found in countries of the "New World" and since 1997, in Florida. Surprisingly, little is known about the molecular mechanisms of TYLCV interaction with the host plant cells. This proposal was aimed at expanding our understanding of the molecular mechanisms by which TYLCV enters the host cell nucleus. The main objective was to elucidate the TYLCV protein(s) involved in transport of the viral genomic DNA into the host cell nucleus. This goal was best served by collaboration between our laboratories one of which (V.C.) was already investigating the nuclear import of the T-DNA ofAgrobacterium tumefaciens, and the other (Y.G.) was studying the effect of TYLCV capsid protein (CP) in transgenic plants, hypothesizing its involvement in the viral nuclear entry. Three years of our collaborative work have provided signifcant data that strongly support our original hypothesis of the involvement of TYLCtr CP in viral nuclear import. Furthermore, our results have laid a foundation to study fundamental, but as yet practically unresolved, questions about the role ofthe host cell factors in the nuclear import of geminiviruses within their host plant. As a result, this research may lead to development of new approaches for plant protection based on control of TYLCV import to the host plant cell nucleus.
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Mawassi, Munir, and Valerian Dolja. Role of RNA Silencing Suppression in the Pathogenicity and Host Specificity of the Grapevine Virus A. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592114.bard.
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RNA silencing is a defense mechanism that functions against virus infection and involves sequence-specific degradation of viral RNA. Diverse RNA and DNA viruses of plants encode RNA silencing suppressors (RSSs), which, in addition to their role in viral counterdefense, were implicated in the efficient accumulation of viral RNAs, virus transport, pathogenesis, and determination of the virus host range. Despite rapidly growing understanding of the mechanisms of RNA silencing suppression, systematic analysis of the roles played by diverse RSSs in virus biology and pathology is yet to be completed. Our research was aimed at conducting such analysis for two grapevine viruses, Grapevine virus A (GVA) and Grapevine leafroll-associated virus-2 (GLRaV- 2). Our major achievements on the previous cycle of BARD funding are as follows. 1. GVA and GLRaV-2 were engineered into efficient gene expression and silencing vectors for grapevine. The efficient techniques for grapevine infection resulting in systemic expression or silencing of the recombinant genes were developed. Therefore, GVA and GLRaV-2 were rendered into powerful tools of grapevine virology and functional genomics. 2. The GVA and GLRaV-2 RSSs, p10 and p24, respectively, were identified, and their roles in viral pathogenesis were determined. In particular, we found that p10 functions in suppression and pathogenesis are genetically separable. 3. We revealed that p10 is a self-interactive protein that is targeted to the nucleus. In contrast, p24 mechanism involves binding small interfering RNAs in the cytoplasm. We have also demonstrated that p10 is relatively weak, whereas p24 is extremely strong enhancer of the viral agroinfection. 4. We found that, in addition to the dedicated RSSs, GVA and GLRaV-2 counterdefenses involve ORF1 product and leader proteases, respectively. 5. We have teamed up with Dr. Koonin and Dr. Falnes groups to study the evolution and function of the AlkB domain presents in GVA and many other plant viruses. It was demonstrated that viral AlkBs are RNA-specific demethylases thus providing critical support for the biological relevance of the novel process of AlkB-mediated RNA repair.
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Levin, Ilan, John Thomas, Moshe Lapidot, Desmond McGrath, and Denis Persley. Resistance to Tomato yellow leaf curl virus (TYLCV) in tomato: molecular mapping and introgression of resistance to Australian genotypes. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7613888.bard.
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Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomatoes. Although first identified in the Mediterranean region, it is now distributed world-wide. Sequence analysis of the virus by the Australian group has shown that the virus is now present in Australia. Despite the importance of the disease and extensive research on the virus, very little is known about the resistance genes (loci) that determine host resistance and susceptibility to the virus. A symptom-less resistant line, TY-172, was developed at the Volcani Center which has shown the highest resistance level among all tested varieties. Preliminary results show that TY-172 is a good candidate to confer resistance to both TYLCV and to Tomato leaf curl virus (ToLCV) in Queensland conditions. Furthermore, Segregation analysis has previously indicated that the resistance is determined by 2-3 genes. In this proposal we aimed to substantiate that TY-172 can contribute to resistance breeding against TYLCV in Queensland, to develop DNA markers to advance such resistance breeding in both Israel and Queensland, and to exploit these markers for resistant breeding in Australian and Israeli lines. To map quantitative trait loci (QTLs) controlling TYLCVresistance in TY172, appropriate segregating populations were analyzed using 69 polymorphic DNA markers spanning the entire tomato genome. Results show that TYLCV resistance in TY172 is controlled by a previously unknown major QTL, originating from the resistant line, and four additional minor QTLs. The major QTL, termed Ty-5, maps to chromosome 4 and accounts for 39.7-to-46.6% of the variation in symptom severity among segregating plants (LOD score: 33-to-35). The minor QTLs, originated either from the resistant or susceptible parents, were mapped to chromosomes 1, 7, 9 and 11, and contributed 12% to the variation in symptom severity in addition to Ty-5. Further analysis of parental lines as well as large F₁, BC₁F₁, F₂ and BC₁F₂ populations originating from crosses carried out, in reciprocal manner, between TY172 and the susceptible processing line M-82 (LA3475) during spring-summer 2010, indicated that: (1) the minor QTLs we have previously identified are in effect not reproducible, (2)Ty-5 alone can yield highly resistant plants with practically no extra-chromosomal effects, and (3) the narrow-sense heritability estimate of resistance levels, attributed to additive factors responsive to selection, does not significantly deviate from 1. All of these results point to Ty-5 as the sole resistance locus in TY172 thus significantly increasing the likelihood of its successful molecular dissection. The DNA markers developed during the course of this study were transferred together with the TY172 genotype to Queensland. TY172 was crossed to a panel of Australian genotypes and the resulting populations were subjected to segregation analysis. Results showed that resistant locus, Ty-5, is highly reproducible in the Australian conditions as well. The Australian group was also able to make improvements to the marker assays by re-designing primer pairs to provide more robust PCR fragments. The Ty-5 locus has now been introgressed into elite Australian germplasm and selection for TYLCV resistance has begun. Cumulatively, our results show that Ty-5 can be effectively used, together with the TY172 genotype to expedite TYLCV resistance breeding and improve our understanding of the genetics that underline the response of tomato to TYLCV. Contributions to agriculture include: (1) the development of tools for more efficient resistance breeding, allowing the incorporation of resistance to local tomato varieties in Australia, Israel and elsewhere; and (2) establish a solid framework for a future attempt to clone the genes that encode such resistance. The latter will enable to decipher the resistance mechanisms that could be applied to other geminiviruses in tomato and possibly in other plant species.
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Levin, Ilan, John W. Scott, Moshe Lapidot, and Moshe Reuveni. Fine mapping, functional analysis and pyramiding of genes controlling begomovirus resistance in tomato. United States Department of Agriculture, November 2014. http://dx.doi.org/10.32747/2014.7594406.bard.
Full textAbstract:
Abstract. Tomato yellow leaf curl virus (TYLCV), a monopartitebegomovirus, is one of the most devastating viruses of cultivated tomatoes and poses increasing threat to tomato production worldwide. Because all accessions of the cultivated tomato are susceptible to these viruses, wild tomato species have become a valuable resource of resistance genes. QTL controlling resistance to TYLCV and other begomoviruses (Ty loci) were introgressed from several wild tomato species and mapped to the tomato genome. Additionally, a non-isogenic F₁diallel study demonstrated that several of these resistance sources may interact with each other, and in some cases generate hybrid plants displaying lower symptoms and higher fruit yield compared to their parental lines, while their respective resistance genes are not necessarily allelic. This suggests that pyramiding genes originating from different resistance sources can be effective in obtaining lines and cultivars which are highly resistant to begomoviruses. Molecular tools needed to test this hypothesis have been developed by our labs and can thus significantly improve our understanding of the mechanisms of begomovirus resistance and how to efficiently exploit them to develop wider and more durable resistance. Five non-allelic Ty loci with relatively major effects have been mapped to the tomato genome using molecular DNA markers, thereby establishing tools for efficient marker assisted selection, pyramiding of multiple genes, and map based gene cloning: Ty-1, Ty-2, Ty-3, Ty-4, and ty-5. This research focused on Ty-3 and Ty-4 due to their broad range of resistance to different begomoviruses, including ToMoV, and on ty-5 due to its exceptionally high level of resistance to TYLCV and other begomoviruses. Our aims were: (1) clone Ty-3, and fine map Ty-4 and Ty-5 genes, (2)introgress each gene into two backgroundsand develop semi isogenic lines harboring all possible combinations of the three genes while minimizing linkage-drag, (3) test the resulting lines, and F₁ hybrids made with them, for symptom severity and yield components, and (4) identify and functionally characterize candidate genes that map to chromosomal segments which harbor the resistance loci. During the course of this research we have: (1) found that the allelic Ty-1 and Ty-3 represent two alternative alleles of the gene coding DFDGD-RDRP; (2) found that ty-5is highly likely encoded by the messenger RNA surveillance factor PELOTA (validation is at progress with positive results); (3) continued the map-based cloning of Ty-4; (4) generated all possible gene combinations among Ty-1, Ty-3 and ty-5, including their F₁ counterparts, and tested them for TYLCV and ToMoV resistance; (5) found that the symptomless line TY172, carrying ty-5, also carries a novel allele of Ty-1 (termed Ty-1ⱽ). The main scientific and agricultural implications of this research are as follows: (1) We have developed recombination free DNA markers that will substantially facilitate the introgression of Ty-1, Ty-3 and ty-5 as well as their combinations; (2) We have identified the genes controlling TYLCV resistance at the Ty-1/Ty-3 and ty-5 loci, thus enabling an in-depth analyses of the mechanisms that facilitate begomovirus resistance; (3) Pyramiding of Ty resistance loci is highly effective in providing significantly higher TYLCV resistance.