Academic literature on the topic 'Gene transfer, viral genome'
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Journal articles on the topic "Gene transfer, viral genome"
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Hohn, Barbara, Zdena Koukolíková-Nicola, Guus Bakkeren, and Nigel Grimsley. "Agrobacterium-mediated gene transfer to monocots and dicots." Genome 31, no. 2 (January 15, 1989): 987–93. http://dx.doi.org/10.1139/g89-172.
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The interaction of the soil bacterium Agrobacterium tumefaciens with plants constitutes a unique kind of genetic flux: the bacterium transfers the T-DNA part of its Ti plasmid to plant cells, where it is integrated into the genome. Possible transfer intermediates, isolated from bacteria and from plants early after transfer, are described. Agroinfection, Agrobacterium-mediated delivery of plant viral genomes, is employed to monitor early events in T-DNA transfer in dicot plants. Graminaceous monocots, so far excluded from Agrobacterium's host range because of lack of tumor formation, have been shown to be agroinfectable. This newly discovered interaction between grasses and the pathogen is described in terms of the efficiency of gene transfer as compared with dicot hosts, the involvement of the bacterium's virulence genes, the susceptibility of various developmental stages of the host, the implications for biotechnology, and the evolutionary aspects of this host–parasite relationship.Key words: T-DNA, agroinfection, maize streak virus, plant transformation, Zea mays.
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Liu, Huiquan, Yanping Fu, Daohong Jiang, Guoqing Li, Jiatao Xie, Jiasen Cheng, Youliang Peng, Said A. Ghabrial, and Xianhong Yi. "Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes." Journal of Virology 84, no. 22 (September 1, 2010): 11876–87. http://dx.doi.org/10.1128/jvi.00955-10.
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ABSTRACT Horizontal gene transfer commonly occurs from cells to viruses but rarely occurs from viruses to their host cells, with the exception of retroviruses and some DNA viruses. However, extensive sequence similarity searches in public genome databases for various organisms showed that the capsid protein and RNA-dependent RNA polymerase genes from totiviruses and partitiviruses have widespread homologs in the nuclear genomes of eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification and sequencing as well as comparative evidence of junction coverage between virus and host sequences support the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis suggest that these genes were likely transferred horizontally from viruses to eukaryotic genomes. Furthermore, we present evidence showing that some of the transferred genes are conserved and expressed in eukaryotic organisms and suggesting that these viral genes are also functional in the recipient genomes. Our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.
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Bobay, Louis-Marie, and Howard Ochman. "Biological species in the viral world." Proceedings of the National Academy of Sciences 115, no. 23 (May 21, 2018): 6040–45. http://dx.doi.org/10.1073/pnas.1717593115.
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Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.
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Shayakhmetov, Dmitry M., Zong-Yi Li, Anuj Gaggar, Helen Gharwan, Vladimir Ternovoi, Volker Sandig, and André Lieber. "Genome Size and Structure Determine Efficiency of Postinternalization Steps and Gene Transfer of Capsid-Modified Adenovirus Vectors in a Cell-Type-Specific Manner." Journal of Virology 78, no. 18 (September 15, 2004): 10009–22. http://dx.doi.org/10.1128/jvi.78.18.10009-10022.2004.
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ABSTRACT Adenovirus serotype 5 (Ad5) vectors containing Ad B-group fibers have become increasingly popular as gene transfer vectors because they efficiently transduce human cell types that are relatively refractory to Ad5 infection. So far, most B-group fiber-containing vectors have been first-generation vectors, deleted of E1 and/or E3 genes. Transduction with these vectors, however, results in viral gene expression and is associated with cytotoxicity and immune responses against transduced cells. To circumvent these problems, we developed fiber-chimeric Ad vectors devoid of all viral genes that were produced either by the homologous recombination of first-generation vectors or by using the Cre/lox-based helper virus system. In this study we compared early steps of infection between first-generation (35-kb genome) and Ad vectors devoid of all viral genes with genome sizes of 28 kb and 12.6 kb. All vectors possessed an Ad35-derived fiber knob domain, which uses CD46 as a primary attachment receptor. Using immortalized human hematopoietic cell lines and primary human CD34-positive hematopoietic cells, we found that the Ad genome size did not affect the efficiency of virus attachment to and internalization into cells. Furthermore, independently of the genome length and structure, all vectors migrated to the nucleus through late endosomal and lysosomal cellular compartments. However, the vector containing the short 12.6-kb genome was unable to efficiently escape from endosomes and deliver its DNA into the nucleus. Moreover, compared to other vectors, these Ad particles were less stable and had an abnormal capsid protein composition, including a lack of capsid-stabilizing protein IX. Our data indicate that the size and structure of the packaged viral genomes can affect the integrity of Ad particles, which in turn results in lower infectivity of Ad vectors.
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Shettima, Abubakar, Muhammad M. Ibrahim, and Musa Ibn Abbas. "Features and properties of viral and non-viral gene delivery systems towards effective gene therapy." International Journal of Medicine 5, no. 1 (February 8, 2017): 45. http://dx.doi.org/10.14419/ijm.v5i1.7189.
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Gene therapy has revolutionized the treatment of hereditary and genetic link disorders by consciously swapping, fixing, adding or deleting the genetic sequences responsible for the condition. The culprit cells are altered by inserting purposeful genes and incorporated into their genome for proper expression. Germ line therapy ensures the genotypic changes to be transferred to the next generation (offspring) while the somatic type adequately rest on corrective pedestals and as such not advantageous to the offspring. The earlier was constrained by technical difficulties as well as ethical consideration. The accomplishment of the therapeutic benefits of gene therapy requires a special ferry system “vectors”. Vectors are designed to transfer the desired gene into its target cell without exposing it to some degrading enzymes, and must allow transcription to successfully take place. A model vector must not be immunogenic, it must not trigger high immune response detrimental to the patient and a specific tropism must be a pre-requisite. The choice of a vector should be based on safety, cost and availability as well as the accessibility of possible options. Mainly for viral carriers, host immune response trigger are the main concern. Viral vectors most frequently used in gene therapy include adenoviruses, retroviruses, poxviruses, adeno-associated viruses and herpes simplex viruses.
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Yang, Grace S., Michael Schmidt, Ziying Yan, Jonathan D. Lindbloom, Thomas C. Harding, Brian A. Donahue, John F. Engelhardt, Robert Kotin, and Beverly L. Davidson. "Virus-Mediated Transduction of Murine Retina with Adeno-Associated Virus: Effects of Viral Capsid and Genome Size." Journal of Virology 76, no. 15 (August 1, 2002): 7651–60. http://dx.doi.org/10.1128/jvi.76.15.7651-7660.2002.
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ABSTRACT Gene therapy vectors based on adeno-associated viruses (AAVs) show promise for the treatment of retinal degenerative diseases. In prior work, subretinal injections of AAV2, AAV5, and AAV2 pseudotyped with AAV5 capsids (AAV2/5) showed variable retinal pigmented epithelium (RPE) and photoreceptor cell transduction, while AAV2/1 predominantly transduced the RPE. To more thoroughly compare the efficiencies of gene transfer of AAV2, AAV3, AAV5, and AAV6, we quantified, using stereological methods, the kinetics and efficiency of AAV transduction to mouse photoreceptor cells. We observed persistent photoreceptor and RPE transduction by AAV5 and AAV2 up to 31 weeks and found that AAV5 transduced a greater volume than AAV2. AAV5 containing full-length or half-length genomes and AAV2/5 transduced comparable numbers of photoreceptor cells with similar rates of onset of expression. Compared to AAV2, AAV5 transduced significantly greater numbers of photoreceptor cells at 5 and 15 weeks after surgery (greater than 1,000 times and up to 400 times more, respectively). Also, there were 30 times more genome copies in eyes injected with AAV2/5 than in eyes injected with AAV2. Comparing AAVs with half-length genomes, AAV5 transduced only four times more photoreceptor cells than AAV2 at 5 weeks and nearly equivalent numbers at 15 weeks. The enhancement of transduction was seen at the DNA level, with 50 times more viral genome copies in retinas injected with AAV having short genomes than in retinas injected with AAV containing full-length ones. Subretinal injection of AAV2/6 showed only RPE transduction at 5 and 15 weeks, while AAV2/3 did not transduce retinal cells. We conclude that varying genome length and AAV capsids may allow for improved expression and/or gene transfer to specific cell types in the retina.
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Monier, Adam, Aurélie Chambouvet, David S. Milner, Victoria Attah, Ramón Terrado, Connie Lovejoy, Hervé Moreau, Alyson E. Santoro, Évelyne Derelle, and Thomas A. Richards. "Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton." Proceedings of the National Academy of Sciences 114, no. 36 (August 21, 2017): E7489—E7498. http://dx.doi.org/10.1073/pnas.1708097114.
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Phytoplankton community structure is shaped by both bottom–up factors, such as nutrient availability, and top–down processes, such as predation. Here we show that marine viruses can blur these distinctions, being able to amend how host cells acquire nutrients from their environment while also predating and lysing their algal hosts. Viral genomes often encode genes derived from their host. These genes may allow the virus to manipulate host metabolism to improve viral fitness. We identify in the genome of a phytoplankton virus, which infects the small green alga Ostreococcus tauri, a host-derived ammonium transporter. This gene is transcribed during infection and when expressed in yeast mutants the viral protein is located to the plasma membrane and rescues growth when cultured with ammonium as the sole nitrogen source. We also show that viral infection alters the nature of nitrogen compound uptake of host cells, by both increasing substrate affinity and allowing the host to access diverse nitrogen sources. This is important because the availability of nitrogen often limits phytoplankton growth. Collectively, these data show that a virus can acquire genes encoding nutrient transporters from a host genome and that expression of the viral gene can alter the nutrient uptake behavior of host cells. These results have implications for understanding how viruses manipulate the physiology and ecology of phytoplankton, influence marine nutrient cycles, and act as vectors for horizontal gene transfer.
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Pchelin, Ivan M., Pavel V. Tkachev, Daniil V. Azarov, Andrey N. Gorshkov, Daria O. Drachko, Vasily V. Zlatogursky, Alexander V. Dmitriev, and Artemiy E. Goncharov. "A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences." Viruses 15, no. 1 (January 12, 2023): 216. http://dx.doi.org/10.3390/v15010216.
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In the human gut, temperate bacteriophages interact with bacteria through a predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in the phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of a viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus “Vespunovirus”, consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.
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Arhab, Yani, Alexander G. Bulakhov, Tatyana V. Pestova, and Christopher U. T. Hellen. "Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer." Viruses 12, no. 6 (June 4, 2020): 612. http://dx.doi.org/10.3390/v12060612.
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Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5′-untranslated region (5′UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5′-end-independent initiation of translation by a different mechanism. Picornavirus 5′UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.
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Bertani, Giuseppe. "Transduction-Like Gene Transfer in the MethanogenMethanococcus voltae." Journal of Bacteriology 181, no. 10 (May 15, 1999): 2992–3002. http://dx.doi.org/10.1128/jb.181.10.2992-3002.1999.
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ABSTRACT Strain PS of Methanococcus voltae (a methanogenic, anaerobic archaebacterium) was shown to generate spontaneously 4.4-kbp chromosomal DNA fragments that are fully protected from DNase and that, upon contact with a cell, transform it genetically. This activity, here called VTA (voltae transfer agent), affects all markers tested: three different auxotrophies (histidine, purine, and cobalamin) and resistance to BES (2-bromoethanesulfonate, an inhibitor of methanogenesis). VTA was most effectively prepared by culture filtration. This process disrupted a fraction of the M. voltae cells (which have only an S-layer covering their cytoplasmic membrane). VTA was rapidly inactivated upon storage. VTA particles were present in cultures at concentrations of approximately two per cell. Gene transfer activity varied from a minimum of 2 × 10−5 (BES resistance) to a maximum of 10−3 (histidine independence) per donor cell. Very little VTA was found free in culture supernatants. The phenomenon is functionally similar to generalized transduction, but there is no evidence, for the time being, of intrinsically viral (i.e., containing a complete viral genome) particles. Consideration of VTA DNA size makes the existence of such viral particles unlikely. If they exist, they must be relatively few in number;perhaps they differ from VTA particles in size and other properties and thus escaped detection. Digestion of VTA DNA with the AluI restriction enzyme suggests that it is a random sample of the bacterial DNA, except for a 0.9-kbp sequence which is amplified relative to the rest of the bacterial chromosome. A VTA-sized DNA fraction was demonstrated in a few other isolates of M. voltae.
Dissertations / Theses on the topic "Gene transfer, viral genome"
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Pelliccia, M. "STRATEGIES FOR ENHANCING VIRAL GENE TRANSFER AND THE THERMOSTABILITY OF VIRAL VECTORS IN VACCINE APPLICATIONS." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/265518.
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At the most basic level viruses are biological nano-containers constituted by genetic material enclosed in a protein shell, capsid. A peculiar feature of viruses, both bacterial and some eukaryotic viruses, lies in the high packaging density of the genome in order to fit itself in the small capsid and hence the high internal osmotic pressure. Virus is a relatively stable particle equipped with fascinating mechanical properties of the capsid that are crucial for the virus lifecycle. Viruses have only one purpose: infect a host cell for reproducing themselves in order to generate new viral progeny (Roos et al. 2007). Therefore, the first and foremost consideration arising from the concept of virus reflects its pathogenesis and virulence that can ultimately result in many important infectious diseases such as common cold, influenza, hepatitis, rabies, measles, cancer and AIDS. As a consequence, pathogenic viruses represent a heavy hurdle for the global health and there is a strong need for developing robust strategies such as vaccines or antiviral drugs against virus infections (Baram- Pinto et al. 2010). On the other hand, viruses in the course of evolution have become efficient specialized gene delivery agents. Therefore they represent powerful tools in biomedicine for gene therapy and vaccine purposes (Schaffer et al. 2008). For successful gene therapy and immunization programs, the efficiency and stability of viral vectors are fundamental aspects (Jorio et al. 2006).
To address this challenge, in the present research project we have investigated the interaction between viruses and nanomaterials. In the last years materials on the nanoscale for their unique properties have provided a broad range of potential biomedical uses (Verma et al. 2008) and for that reason we decided to explore their application with viruses. More specifically, we have examined three types of sulfonate- functionalized gold nanoparticles (AuNPs), namely, MUS:OT, MUS and MUS:brOT NPs, which are less than 5 nm in size, negatively charged and poorly cytotoxic (Verma et al. 2008). The NPs are coated with self-assembled monolayer (SAM) of thiolated organic molecules and one of the ligand is a sulfonated molecule, MUS (Verma et al. 2008). The MUS ligand itself was tested in our experiments as well. As virus models we focused on human recombinant adenovirus type 5 (Ad), one of the most promising viral vector as vaccine and gene therapy carrier and two picornaviruses of the genus enterovirus, namely, EV1 and CVB3, important human pathogens associated with several infectious diseases (e.g. myocarditis, aseptic meningitis, encephalitis, paralysis)(Kossila et al. 2002)(Marjomäki et al. 2014a). In spite of their medical impact, there are no therapeutic treatments available against picornavirus infections and the only vaccine products are against three types of poliovirus and hepatitis A virus (Merilahti et al. 2012).
Two sets of experiments were carried out: (1) Short-term incubation of Ad with nanomaterials for 1 h at 37°C prior
transducing HeLa cells or before in vivo administration in zebrafish and mice. The results demonstrated that Ad shortly pre-treated with nanomaterials showed a significant increase in the gene expression in vitro and in vivo The NPs’enhanced adenovirus transduction aims to reduce Ad vector doses in vivo thereby minimizing the adverse reactions of the immune response due to high vector dosage; (2) Long-term thermostabilization studies of Ad, EV1 and CVB3 in vitro in the presence and in the absence of our nanomaterials and other substances such as sugars (sucrose, glucose, glycerol) and Polyethylene glycol (PEG) molecules at 37°C or room temperature for extensive periods of time. Our results showed the capability of the nanomaterials and sucrose to increase substantially the heat stability of the viruses. In order to elucidate the thermal inactivation mechanism of viral particles and the stabilizing effect provided by some compounds on viruses we set out to formulate an analytical theory. This line of research fits in the context of developing more thermo-stable viral vector preparations for vaccine purposes that do not require the maintenance of the challenging cold chain system in order to preserve the effectiveness of viral vaccines during the storage, shipment and administration to the patients and hence to ensure the success of global immunization programs (Alcock et al. 2010).
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Monjezi, Razieh [Verfasser], and Michael [Gutachter] Hudecek. "Engineering of chimeric antigen receptor T cells with enhanced therapeutic index in cancer immunotherapy using non-viral gene transfer and genome editing / Razieh Monjezi ; Gutachter: Michael Hudecek." Würzburg : Universität Würzburg, 2018. http://d-nb.info/1162062231/34.
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Ibraheim, Raed R. "Genome Engineering Goes Viral: Repurposing of Adeno-associated Viral Vectors for CRISPR-mediated in Vivo Genome Engineering." eScholarship@UMMS, 2020. https://escholarship.umassmed.edu/gsbs_diss/1114.
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One of the major challenges facing medicine and drug discovery is the large number of genetic diseases caused by inherited mutations leading to a toxic gain-of-function, or loss-of-function of the disease protein. Microbiology offered a new glimpse of hope to address those disorders with the adaptation of the bacterial CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) defense system as a genome editing tool. Cas9 is a unique CRISPR-associated endonuclease protein that can be easily programmed with an RNA [a single-guide RNA (sgRNA)] that is complementary to nearly any DNA locus. Cas9 creates a double-stranded break (DSB) that can be exploited to knock out toxic genes or replenish therapeutic expression levels of essential proteins. In addition to a matching sgRNA sequence, Cas9 requires the presence of a short signature sequence [a protospacer adjacent motif (PAM)] flanking the target locus. Over the past few years, several Cas9-based therapeutic platforms have emerged to correct DNA mutations in a wide range of mammalian cell lines, ex vivo, and in vivo by adapting recombinant adeno-associated virus (rAAV). However, most of the applications of Cas9 in the field have been limited to Streptococcus pyogenes (SpyCas9), which, in its wild-type form, suffers from inaccurate editing at off-target sites. It is also difficult to deliver via an all-in-one (sgRNA+Cas9) rAAV approach due to its large size. In this thesis, I describe other Cas9 nucleases and their development as new AAV-based genome editing platforms for therapeutic editing in vivo in mouse disease models. In the first part of this thesis, I develop the all-in-one AAV strategy to deliver a Neisseria meningitidis Cas9 ortholog (Nme1Cas9) in mice to reduce the level of circulating cholesterol in blood. I also help characterize an enhanced Cas9 from another meningococcus strain (Nme2Cas9) and show that it is effective in performing editing not only in mammalian cell culture, but also in vivo by all-in-one AAV delivery. Additionally, I describe two AAV platforms that enable advanced editing modalities in vivo: 1) segmental DNA deletion by delivering two sgRNAs (along with Nme2Cas9) in one AAV, and 2) precise HDR-based repair by fitting Nme2Cas9, sgRNA and donor DNA within a single AAV capsid. Using these tools, we successfully treat two genetic disorders in mice, underscoring the importance of this powerful duo of AAV and Cas9 in gene therapy to advance novel treatment. Finally, I present preliminary data on how to use these AAV.Nme2Cas9 vectors to treat Alexander Disease, a rare progressive neurological disorder. These findings provide a platform for future application of gene editing in therapeutics.
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Mills, Ryan Edward. "New AB initio methods of small genome sequence interpretation." Diss., Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-04062006-182528/.
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Thesis (Ph. D.)--Biomedical Engineering, Georgia Institute of Technology, 2006.Tannenbaum, Allen, Committee Member ; Choi, Jung, Committee Member ; Borodovsky, Mark, Committee Chair ; Voit, Eberhard, Committee Member ; Lee, Eva, Committee Member.
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Bremner, K. Helen. "Application of nuclear localization sequences to non-viral gene delivery systems." Thesis, University of Birmingham, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273725.
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Bowden, Jonathan Kirk. "Development of a viral and a non-viral based gene transfer systems using the yeast Saccharomyces cerevisiae." Thesis, Brunel University, 2016. http://bura.brunel.ac.uk/handle/2438/14538.
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VSV-G has been used for several years to pseudotype reteroviral and lentiviral vectors to increase the range of cell types that these vectors can be targeted to as well as increasing transfection efficiency and serum resistance. It has previously been shown that purified VSV-G protein can be added to several types of non-viral complexes to produce these same advantages. VSV-G therefore holds great potential in gene therapy for both viral and non-viral vectors. Due to the cellular toxicity of VSV-G in mammalian cells VSV-G pseudotyped viral vectors are generally produced from transiently transfected cells which greatly limit the scale of viral production. VSV-G for non-viral vectors is also limited in the same manner but also suffer from expensive and time consuming methods to purify the VSV-G from the expression media. To address these problems with production we attempted to generate strains of the yeast Saccharomyces cerevisiae that can produce VSV-G pseudotyped lentivirus and VSV-G protein from inducible integrated vectors. We theorised that the cell wall of Saccharomyces cerevisiae would prevent syncytia and cellular toxicity of VSV-G during production, allowing the continuous production of virus or protein. In this report we show that this new production method allows us to produce and purify VSV-G from yeast using simple and scalable methods and that this produces a greater enhancement of transfection efficiency than mammalian derived VSV-G. However we were not able to demonstrate the production of VSV-G pseudotyped virus, seemingly due to the genotoxic effects of viral integrase.
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Xenariou, Stefania. "Magnetofection and sonoporation to enhance non-viral gene transfer to airway epithelium." Thesis, Imperial College London, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.433595.
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Collins, Louise. "A non-viral vector system for efficient gene transfer via membrane integrins." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321961.
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Odom, Mary Rebecca. "Poxvirus evolution the role of horizontal gene transfer /." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2010. https://www.mhsl.uab.edu/dt/2010p/odom.pdf.
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Zhou, Chen, and 周辰. "Genome-informed studies on Penicillium marneffei: horizontal gene transfer survey and differentialsecretomics." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B41633672.
Full textBooks on the topic "Gene transfer, viral genome"
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Leaf, Huang, Hung Mien-chie, and Wagner Ernst 1960-, eds. Non-viral vectors for gene therapy. 2nd ed. Amsterdam: Elsevier Academic Press, 2005.
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Viral vectors for gene therapy: Methods and protocols. New York: Humana Press, 2011.
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1963-, March Keith Leonard, ed. Gene transfer in the cardiovascular system: Experimental approaches and therapeutic implications. Boston: Kluwer Academic Publishers, 1997.
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A, Machida Curtis, ed. Viral vectors for gene therapy: Methods and protocols. Totowa, N.J: Humana Press, 2003.
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A, Machida Curtis, ed. Viral vectors for gene therapy: Methods and protocols. Totowa, N.J: Humana Press, 2003.
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A, Machida Curtis, ed. Viral vectors for gene therapy: Methods and protocols. Totowa, New Jersey: Humana Press, 2003.
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G, Kaplitt Michael, and During Matthew J, eds. Gene therapy of the central nervous system: From bench to bedside. Amsterdam: Academic Press, 2006.
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Brambilla, Riccardo. Viral vector approaches in neurobiology and brain diseases. New York: Humana Press, 2013.
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Joset, Françoise. Prokaryotic genetics: Genome organization, transfer, and plasticity. Oxford: Blackwell Scientific Publications, 1993.
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Principles of molecular virology. London: Academic Press, 1993.
Find full textBook chapters on the topic "Gene transfer, viral genome"
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Jacobsen, Linda B. "Plasmid and Other Non-Viral Vectors." In Gene Transfer in the Cardiovascular System, 85–110. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-6277-1_4.
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Nabel, Elizabeth G. "Viral Vector-Based Vascular Gene Delivery: Basic Studies and Therapeutic Applications." In Gene Transfer in the Cardiovascular System, 239–53. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-6277-1_10.
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Trapnell, Bruce C., and Michael N. Pensiero. "Development of Viral Vectors for Human Gene Therapy: Retrovirus and Adenovirus (Part I)." In Gene Transfer in the Cardiovascular System, 3–24. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-6277-1_1.
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Luebke, Anne E., Cherokee Rova, Peter G. Von Doersten, and David J. Poulsen. "Adenoviral and AAV-Mediated Gene Transfer to the Inner Ear: Role of Serotype, Promoter, and Viral Load on In Vivo and In Vitro Infection Efficiencies." In Gene Therapy of Cochlear Deafness, 87–98. Basel: KARGER, 2009. http://dx.doi.org/10.1159/000218209.
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Fernández-de-Bobadilla, Miguel D., Teresa M. Coque, and Val F. Lanza. "Statistical Analysis of Accessory Genome." In Horizontal Gene Transfer, 341–53. New York, NY: Springer US, 2019. http://dx.doi.org/10.1007/978-1-4939-9877-7_24.
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Güell, Marc. "Conjugative Assembly Genome Engineering (CAGE)." In Horizontal Gene Transfer, 399–409. New York, NY: Springer US, 2019. http://dx.doi.org/10.1007/978-1-4939-9877-7_28.
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Brimijoin, W. Stephen. "Viral Gene Transfer of Enzymes." In Biologics to Treat Substance Use Disorders, 167–85. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-23150-1_11.
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Lu, Yuanan, and Lynn F. Gottfried. "Viral Vector-Mediated Gene Transfer." In Encyclopedia of Cancer, 1–4. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-642-27841-9_6193-2.
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Lu, Yuanan, and Lynn F. Gottfried. "Viral Vector-Mediated Gene Transfer." In Encyclopedia of Cancer, 4812–15. Berlin, Heidelberg: Springer Berlin Heidelberg, 2017. http://dx.doi.org/10.1007/978-3-662-46875-3_6193.
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Lu, Yuanan, and Lynn Sniderhan. "Viral Vector-mediated Gene Transfer." In Encyclopedia of Cancer, 3912–14. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-16483-5_6193.
Full textConference papers on the topic "Gene transfer, viral genome"
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Howard, Candace M., Flemming Forsberg, Ji-Bin Liu, Daniel A. Merton, Corrado Minimo, and Pier P. Claudio. "Using a Commercial Ultrasound Contrast Agent for Viral-Mediated Gene Transfer In Vitro and In Vivo." In 6TH INTERNATIONAL SYMPOSIUM ON THERAPEUTIC ULTRASOUND. AIP, 2007. http://dx.doi.org/10.1063/1.2744325.
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"Reconstruction and analysis of the gene network of the external pathway of apoptosis in viral hepatitis C." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-103.
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"Bacteriophages as vectors of gene transfer from prokaryotes to eukaryotes." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-074.
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Khalid, Muhammad, Chenn Zhou, Ashish Bassi, San Ming Wang, Howard Gerber, and Charles Tseng. "Heat Transfer Analysis of Human Cell Culture Under RF Exposure." In ASME 2005 Summer Heat Transfer Conference collocated with the ASME 2005 Pacific Rim Technical Conference and Exhibition on Integration and Packaging of MEMS, NEMS, and Electronic Systems. ASMEDC, 2005. http://dx.doi.org/10.1115/ht2005-72655.
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A 2.45 GHz radio frequency (RF) exposure system was designed and used to study the RF effects on the genome-wide gene expression in cultured human cells. In this system, a T-25 culture flask, which contains 10 × 106 cells in a 10ml medium, is placed in a WR 340 waveguide. The waveguide serves as an environmental chamber. The source is a pulsed magnetron for obtaining a high electric field with the specific absorption rate (SAR) at approximately 10 W/kg. In order to ensure the non-thermal effect, the system was designed to maintain a temperature of 37°C. In this research, the heat transfer analysis of the system was conducted using the computational fluid dynamic (CFD) software FLUENT® coupled with the finite element software, High Frequency Structural Simulation (HFSS) by Ansoft. The electric field was first analyzed by using HFSS to calculate the SAR distribution as a heat source input for CFD calculations. The fluid flow and temperature distributions within the flask were then analyzed using FLUENT®. The results were validated experimentally by measuring the temperatures with fluoroptic thermometer probes as well as by examining the level of heat shock gene expression. These results provide useful information for a better understanding and controlling of the operating conditions of the system.
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Wijeratne, Shalini. "A Comparative Analysis of Nanoluc Luciferase and Alkaline Phosphatase as Reporter Proteins for Phage-based Pathogen Detection." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/iibu6123.
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Rapid and specific detection of pathogenic bacteria in food and water sources can be crucial to disease diagnosis and prevention. Genetically modified bacteriophage-based assays are a promising alternative over standard overnight culture-based assays as they can provide comparatively rapid detection. Bacteriophage (phage) viruses specifically infect live bacterial cells for the rapid replication of their viral genome. Scientists exploit this in-built molecular amplification system by genetically modifying phage genes to express certain reporter proteins during an infection. The expression of reporter proteins is confirmed through enzymatic and/or sensory assays, indicating the presence of the pathogenic bacteria. The sensitivity of the reporter phage assays depend on the ability of the genetically engineered phage to successfully express its reporter protein with conserved activity. In this study, we compared two enzymes, alkaline phosphatase (ALP) and nanoluc luciferase (NLuc) as reporter proteins in the context of the above criteria. We genetically modified T7 phage genome to overexpress these enzymes upon infecting BL21 E. coli cells. The reporter proteins were quantified and detected by measuring its luminescence activities. NLuc phage was significantly better at its gene expression in comparison to ALP phage, averaging at 9.8 × 105 molecules of protein/CFU of E. coli and providing a limit of detection at 107 CFU of E. coli/mL. On the other hand, ALP phage was only able to produce 8.6 × 104 molecules of protein/CFU of E. coli and provide a limit of detection at 109 CFU of E. coli/mL. These findings will allow researchers to select their choice of reporter proteins to improve phage-based assays and continue their progress in the field of pathogen detection.
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Saksaganskaia, Alla S., Victoria S. Muntyan, Alexey N. Muntyan, Boris V. Simarov, and Marina L. Roumiantseva. "ABUNDANCE OF PHAGE-RELATED SEQUENCES ON NON-SYMBIOTIC PLASMIDS OF SINORHIZOBIUM MELILOTI FROM CENTERS OF LEGUME PLANTS DIVERSITY." In 22nd SGEM International Multidisciplinary Scientific GeoConference 2022. STEF92 Technology, 2022. http://dx.doi.org/10.5593/sgem2022/6.1/s25.06.
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Genomes of alfalfa root nodule bacteria, Sinorhizobium meliloti, symbionts of alfalfa are enriched in non-symbiotic (cryptic) plasmids, which gene pool is remained weakly studied. S. meliloti strains are significantly varied in number and size of these plasmids. The goal of the study was to assess the occurrence of phage-related sequences (PRS) on cryptic plasmids. Whole genome sequences of 12 S. meliloti strains native to Caucasian and Kazakhstan centers of alfalfa diversity (NCG and PAG, correspondingly) were studied and 20 cryptic plasmids, which sizes varied from 17.2 to 453.8 kb, were assembled. In total 55 PRS were identified on cryptic plasmids, and these sequences were represented by intact, questionable and incomplete sequences according to PHASTER. Significant differences in the occurrence of above-mentioned types of PRS on cryptic plasmids was detected between strains native to NCG and PAG (X2 = 6.73, p = 0.03). The sizes of the desired PRS varied from 5.1 to 33 kb, and their number was from 1 to 11 per replicon in tested strains. It was revealed that PRS on plasmids of strains from NCG were predominantly related to Siphoviridae family (p smaller than 0.05), while PRS homologous to phages of Siphoviridae and Podoviridae families prevailed with equal frequencies on plasmids of strains from PAG. For 40% of tested PRS the attL/attR sequences were detected and that is proving their site-specific integration type. ORFs of PRS as it was revealed are encoded integrases, fiber protein and tail shaft, and nearly all PRS are contained ORFs encoded transposases. Summarizing, S. meliloti strains native to origins of alfalfa diversity are enriched in cryptic plasmids, and the latest are attractive for soil bacteriophages, that is strongly evident the participation of small size plasmids in horizontal gene transfer process.
Reports on the topic "Gene transfer, viral genome"
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.
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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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Petitte, James, Hefzibah Eyal-Giladi, and Malka Ginsburg. The Study of Primordial Germ Cell Development as a Tool for Gene Transfer in Chickens. United States Department of Agriculture, October 1991. http://dx.doi.org/10.32747/1991.7561071.bard.
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The ability to introduce novel genetic material into the genome of commercial poultry has been impeded by a lack of kowledge regarding the origin in the early embryo of the target cell of interest, namely, the germ cell. Hence, this project investigated the emergence of primordial germ cells (PGCs) during the early development of the avian embryo to aid in efforts to produce transgenic poultry on a routine basis. The strategy was to introduce foreign DNA into the area of the unincubated embryo that is destined to give rise to the germ line. The objectives of this project were: 1) to identify and localize a subpopulation of cells in the early embryo which will give rise to PGCs, 2) to determine the best location and stage of development to transfer donor cells for efficient germline chimerism, and 3) to transfect donor cells to produce transgenic/germline chimeric embryos. We show that by using the monoclonal antibody SSEA-1 and by various cell culture techniques that germ cells appear to segregate from the somatic lineages at St. X., a process that is gradual and continues through St. XIV. Using microsurgical transplantation between quail and chick embryos, we demonstrated that the inner 1/3 of the area pellucida between states X-XII gives rise to about 2/3 of the germ cell population at the time of their residence in the germinal crescent. Because of the non-localized emergence of PGCs, attempts to introduce foreign DNA into clonal precursors of germ cells through liposome-mediated transfection yielded unacceptable levels of efficiency. However, through our investigation of germ cell origins, an in vitro model of germ cell differentiation was developed that could offer a means of determining the factors required for the long term culture of avian PGCs thereby providing a convenient means of manipulating the avian genome.
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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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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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Mawassi, Munir, Adib Rowhani, Deborah A. Golino, Avichai Perl, and Edna Tanne. Rugose Wood Disease of Grapevine, Etiology and Virus Resistance in Transgenic Vines. United States Department of Agriculture, November 2003. http://dx.doi.org/10.32747/2003.7586477.bard.
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Rugose wood is a complex disease of grapevines, which occurs in all growing areas. The disease is spread in the field by vector transmission (mealybugs). At least five elongated-phloem- limited viruses are implicated in the various rugose wood disorders. The most fully characterized of these are Grapevine virus A (GV A) and GVB, members of a newly established genus, the vitivirus. GVC, a putative vitivirus, is much less well characterized than GV A or GVB. The information regarding the role of GVC in the etiology and epidemiology of rugose wood is fragmentary and no sequence data for GVC are available. The proposed research is aimed to study the etiology and epidemiology of rugose wood disease, and to construct genetically engineered virus-resistant grapevines. The objectives of our proposed research were to construct transgenic plants with coat protein gene sequences designed to induce post-transcriptional gene silencing (pTGS); to study the epidemiology and etiology of rugose wood disease by cloning and sequencing of GVC; and surveying of rugose wood- associated viruses in Californian and Israeli vineyards. In an attempt to experimentally define the role of the various genes of GV A, we utilized the infectious clone, inserted mutations in every ORF, and studied the effect on viral replication, gene expression, symptoms and viral movement. We explored the production of viral RNAs in a GV A-infected Nicotiana benthamiana herbaceous host, and characterized one nested set of three 5'-terminal sgRNAs of 5.1, 5.5 and 6.0 kb, and another, of three 3'-terminal sgRNAs of 2.2, 1.8 and 1.0 kb that could serve for expression of ORFs 2-3, respectively. Several GV A constructs have been assembled into pCAMBIA 230 I, a binary vector which is used for Angrobacterium mediated transformation: GV A CP gene; two copies of the GV A CP gene arranged in the same antisense orientation; two copies of the GV A CP gene in which the downstream copy is in an antigens orientation; GV A replicase gene; GV A replicase gene plus the 3' UTR sequence; and the full genome of GV A. Experiments for transformation of N. benthamiana and grapevine cell suspension with these constructs have been initiated. Transgenic N. benthamiana plants that contained the CP gene, the replicase gene and the entire genome of GV A were obtained. For grapevine transformation, we have developed efficient protocols for transformation and successfully grapevine plantlets that contained the CP gene and the replicase genes of GV A were obtained. These plants are still under examination for expression of the trans genes. The construction of transgenic plants with GV A sequences will provide, in the long run, a means to control one of the most prevalent viruses associated with grapevines. Our many attempts to produce a cDNA library from the genome of GVC failed. For surveying of rugose wood associated viruses in California vineyards, samples were collected from different grape growing areas and tested by RT-PCR for GV A, GVB and GVD. The results indicated that some of the samples were infected with multiple viruses, but overall, we found higher incidence of GVB and GV A infection in California vineyards and new introduction varieties, respectively. In this research we also conducted studies to increase our understanding of virus - induced rootstock decline and its importance in vineyard productivity. Our results provided supporting evidence that the rootstock response to virus infection depends on the rootstock genotype and the virus type. In general, rootstocks are differ widely in virus susceptibility. Our data indicated that a virus type or its combination with other viruses was responsible in virus-induced rootstock decline. As the results showed, the growth of the rootstocks were severely affected when the combination of more than one virus was present.
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Mawassi, Munir, Baozhong Meng, and Lorne Stobbs. Development of Virus Induced Gene Silencing Tools for Functional Genomics in Grapevine. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7613887.bard.
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Grapevine is perhaps the most widely grown fruit crop. To understand the genetic make-up so as to improve the yield and quality of grapes and grape products, researchers in Europe have recently sequenced the genomes of Pinot noir and its inbred. As expected, function of many grape genes is unknown. Functional genomics studies have become the major focus of grape researchers and breeders. Current genetic approaches for gene function studies include mutagenesis, crossing and genetic transformation. However, these approaches are difficult to apply to grapes and takes long periods of time to accomplish. It is thus imperative to seek new ways for grape functional genomics studies. Virus-induced gene silencing (VIGS) offers an attractive alternative for this purpose and has proven highly effective in several herbaceous plant species including tomato, tobacco and barley. VIGS offers several advantages over existing functional genomics approaches. First, it does not require transformation to silence a plant gene target. Instead, it induces silencing of a plant gene through infection with a virus that contains the target gene sequence, which can be accomplished within a few weeks. Second, different plant genes can be readily inserted into the viral genome via molecular cloning and functions of a large number of genes can be identified within a short period of time. Our long-term goal of this research is to develop VIGS-based tools for grapevine functional genomics, made of the genomes of Grapevine virus A (GVA) from Israel and Grapevine rupestris stem pitting-associated virus (GRSPaV) from Canada. GVA and GRSPaV are members of the Flexiviridae. Both viruses have single-stranded, positive sense RNA genomes, which makes them easy to manipulate genetically and excellent candidates as VIGS vectors. In our three years research, several major breakthroughs have been made by the research groups involved in this project. We have engineered a cDNA clone of GVA into a binary vector that is infectious upon delivery into plantlets of micropropagated Vitis viniferacv. Prime. We further developed the GVA into an expression vector that successfully capable to silence endogenous genes. We also were able to assemble an infectious full-length cDNA clones of GRSPaV. In the following sections Achievements and Detailed description of the research activities, we are presenting the outcome and results of this research in details.
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Lapidot, Moshe, and Vitaly Citovsky. molecular mechanism for the Tomato yellow leaf curl virus resistance at the ty-5 locus. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604274.bard.
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Tomato yellow leaf curl virus (TYLCV) is a major pathogen of tomato that causes extensive crop loss worldwide, including the US and Israel. Genetic resistance in the host plant is considered highly effective in the defense against viral infection in the field. Thus, the best way to reduce yield losses due to TYLCV is by breeding tomatoes resistant or tolerant to the virus. To date, only six major TYLCV-resistance loci, termed Ty-1 to Ty-6, have been characterized and mapped to the tomato genome. Among tomato TYLCV-resistant lines containing these loci, we have identified a major recessive quantitative trait locus (QTL) that was mapped to chromosome 4 and designated ty-5. Recently, we identified the gene responsible for the TYLCV resistance at the ty-5 locus as the tomato homolog of the gene encoding messenger RNA surveillance factor Pelota (Pelo). A single amino acid change in the protein is responsible for the resistant phenotype. Pelo is known to participate in the ribosome-recycling phase of protein biosynthesis. Our hypothesis was that the resistant allele of Pelo is a “loss-of-function” mutant, and inhibits or slows-down ribosome recycling. This will negatively affect viral (as well as host-plant) protein synthesis, which may result in slower infection progression. Hence we have proposed the following research objectives: Aim 1: The effect of Pelota on translation of TYLCV proteins: The goal of this objective is to test the effect Pelota may or may not have upon translation of TYLCV proteins following infection of a resistant host. Aim 2: Identify and characterize Pelota cellular localization and interaction with TYLCV proteins: The goal of this objective is to characterize the cellular localization of both Pelota alleles, the TYLCV-resistant and the susceptible allele, to see whether this localization changes following TYLCV infection, and to find out which TYLCV protein interacts with Pelota. Our results demonstrate that upon TYLCV-infection the resistant allele of pelota has a negative effect on viral replication and RNA transcription. It is also shown that pelota interacts with the viral C1 protein, which is the only viral protein essential for TYLCV replication. Following subcellular localization of C1 and Pelota it was found that both protein localize to the same subcellular compartments. This research is innovative and potentially transformative because the role of Peloin plant virus resistance is novel, and understanding its mechanism will lay the foundation for designing new antiviral protection strategies that target translation of viral proteins. BARD Report - Project 4953 Page 2
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Vakharia, Vikram, Shoshana Arad, Yonathan Zohar, Yacob Weinstein, Shamila Yusuff, and Arun Ammayappan. Development of Fish Edible Vaccines on the Yeast and Redmicroalgae Platforms. United States Department of Agriculture, February 2013. http://dx.doi.org/10.32747/2013.7699839.bard.
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Betanodaviruses are causative agents of viral nervous necrosis (VNN), a devastating disease of cultured marine fish worldwide. Betanodavirus (BTN) genome is composed of two single-stranded, positive-sense RNA molecules. The larger genomic segment, RNA1 (3.1 kb), encodes the RNA-dependent RNA polymerase, while the smaller genomic segment, RNA 2 (1.4kb), encodes the coat protein. This structural protein is the host-protective antigen of VNN which assembles to form virus-like particles (VLPs). BTNs are classified into four genotypes, designated red-spotted grouper nervous necrosis virus (RGNNV), barfin flounder nervous necrosis virus (BFNNV), tiger puffer nervous necrosis virus (TPNNV), and striped jack nervous necrosis virus (SJNNV), based on phylogenetic analysis of the coat protein sequences. RGNNV type is quite important as it has a broad host-range, infecting warm-water fish species. At present, there is no commercial vaccine available to prevent VNN in fish. The general goal of this research was to develop oral fish vaccines in yeast and red microalgae (Porphyridium sp.) against the RGNNV genotype. To achieve this, we planned to clone and sequence the coat protein gene of RGNNV, express the coat protein gene of RGNNV in yeast and red microalgae and evaluate the immune response in fish fed with recombinantVLPs antigens produced in yeast and algae. The collaboration between the Israeli group and the US group, having wide experience in red microalgae biochemistry, molecular genetics and large-scale cultivation, and the development of viral vaccines and eukaryotic protein expression systems, respectively, was synergistic to produce a vaccine for fish that would be cost-effective and efficacious against the betanodavirus infection.
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Whitham, Steven A., Amit Gal-On, and Tzahi Arazi. Functional analysis of virus and host components that mediate potyvirus-induced diseases. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7591732.bard.
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The mechanisms underlying the development of symptoms in response to virus infection remain to be discovered in plants. Insight into symptoms induced by potyviruses comes from evidence implicating the potyviral HC-Pro protein in symptom development. In particular, recent studies link the development of symptoms in infected plants to HC-Pro's ability to interfere with small RNA metabolism and function in plant hosts. Moreover, mutation of the highly conserved FRNK amino acid motif to FINK in the HC-Pro of Zucchini yellow mosaic virus (ZYMV) converts a severe strain into an asymptomatic strain, but does not affect virus accumulation in cucurbit hosts. The ability of this FINK mutation to uncouple symptoms from virus accumulation creates a unique opportunity to study symptom etiology, which is usually confounded by simultaneous attenuation of both symptoms and virus accumulation. Our goal was to determine how mutations in the conserved FRNK motif affect host responses to potyvirus infection in cucurbits and Arabidopsis thaliana. Our first objective was to define those amino acids in the FRNK motif that are required for symptoms by mutating the FRNK motif in ZYMV and Turnip mosaic virus (TuMV). Symptom expression and accumulation of resulting mutant viruses in cucurbits and Arabidopsis was determined. Our second objective was to identify plant genes associated with virus disease symptoms by profiling gene expression in cucurbits and Arabidopsis in response to mutant and wild type ZYMV and TuMV, respectively. Genes from the two host species that are differentially expressed led us to focus on a subset of genes that are expected to be involved in symptom expression. Our third objective was to determine the functions of small RNA species in response to mutant and wild type HC-Pro protein expression by monitoring the accumulation of small RNAs and their targets in Arabidopsis and cucurbit plants infected with wild type and mutant TuMV and ZYMV, respectively. We have found that the maintenance of the charge of the amino acids in the FRNK motif of HC-Pro is required for symptom expression. Reduced charge (FRNA, FRNL) lessen virus symptoms, and maintain the suppression of RNA silencing. The FRNK motif is involved in binding of small RNA species including microRNAs (miRNA) and short interfering RNAs (siRNA). This binding activity mediated by the FRNK motif has a role in protecting the viral genome from degradation by the host RNA silencing system. However, it also provides a mechanism by which the FRNK motif participates in inducing the symptoms of viral infection. Small RNA species, such as miRNA and siRNA, can regulate the functions of plant genes that affect plant growth and development. Thus, this binding activity suggests a mechanism by which ZYMVHC-Pro can interfere with plant development resulting in disease symptoms. Because the host genes regulated by small RNAs are known, we have identified candidate host genes that are expected to play a role in symptoms when their regulation is disrupted during viral infections. As a result of this work, we have a better understanding of the FRNK amino acid motif of HC-Pro and its contribution to the functions of HC-Pro, and we have identified plant genes that potentially contribute to symptoms of virus infected plants when their expression becomes misregulated during potyviral infections. The results set the stage to establish the roles of specific host genes in viral pathogenicity. The potential benefits include the development of novel strategies for controlling diseases caused by viruses, methods to ensure stable expression of transgenes in genetically improved crops, and improved potyvirus vectors for expression of proteins or peptides in plants.
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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.
Full textAbstract:
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.