Relevant bibliographies by topics / DNA sequences

Academic literature on the topic 'DNA sequences'

Author: Grafiati
Published: 4 June 2021
Last updated: 31 January 2023

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Journal articles on the topic "DNA sequences"

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He, Ping-an, and Jun Wang. "Characteristic Sequences for DNA Primary Sequence." Journal of Chemical Information and Computer Sciences 42, no. 5 (September 2002): 1080–85. http://dx.doi.org/10.1021/ci010131z.

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AUFFRAY, CHARLES. "DNA sequences." Nature 355, no. 6358 (January 1992): 292. http://dx.doi.org/10.1038/355292b0.

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Yablonsky, Michael D., and William J. Hone. "Patenting DNA Sequences." Nature Biotechnology 13, no. 7 (July 1995): 656–57. http://dx.doi.org/10.1038/nbt0795-656.

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King, D. G., and Y. Kashi. "Heretical DNA Sequences?" Science 326, no. 5950 (October 8, 2009): 229–30. http://dx.doi.org/10.1126/science.326_229.

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Hoss, Matthias, Svante Paabo, and N. K. Vereshchagin. "Mammoth DNA sequences." Nature 370, no. 6488 (August 1994): 333. http://dx.doi.org/10.1038/370333a0.

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Agris, Cheryl H. "Patenting DNA sequences." Nature Biotechnology 16, no. 9 (September 1998): 877. http://dx.doi.org/10.1038/nbt0998-877.

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Chen, William Y. C., and James D. Louck. "Necklaces, MSS Sequences, and DNA Sequences." Advances in Applied Mathematics 18, no. 1 (January 1997): 18–32. http://dx.doi.org/10.1006/aama.1996.0494.

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Churchill, Gary A., and Michael S. Waterman. "The accuracy of DNA sequences: Estimating sequence quality." Genomics 14, no. 1 (September 1992): 89–98. http://dx.doi.org/10.1016/s0888-7543(05)80288-5.

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He, Ping-an, and Jun Wang. "ChemInform Abstract: Characteristic Sequences for DNA Primary Sequence." ChemInform 33, no. 47 (May 19, 2010): no. http://dx.doi.org/10.1002/chin.200247209.

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Onozawa, Masahiro, Tamas Varga, Yoo Jung Kim, Zhenhua Zhang, and Peter Aplan. "Repair of DNA Double Strand Breaks by RNA/DNA Patches in U937 Cells." Blood 120, no. 21 (November 16, 2012): 2375. http://dx.doi.org/10.1182/blood.v120.21.2375.2375.

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Abstract Abstract 2375 It has been suggested that errors in the repair of DNA double strand breaks (DSB) can result in gross chromosomal rearrangements (GCR), including chromosomal amplifications, deletions, inversions, and translocations. To study repair of DNA DSB in vivo, we generated a vector containing the EF1a promoter driving expression of the herpes simplex thymidine kinase (HsTK); interspersed between the EF1a promoter and Hstk cDNA was the recognition site for the rare-cutting meganuclease I-SceI. This vector was electroporated into U937 cells, and a clone containing a single copy, of the EF1aTK vector, designated F5, was isolated. Transfection of the F5 cells with an I-SceI expression vector, followed by ganciclovir selection, identified clones that had lost expression of HsTK. We recovered no GCR with this approach; most of the GCV-resistant clones had partial or complete deletions of the EF1a promoter, the HsTK cDNA, or both. However we noted that ∼5–10% of repair elements involved insertions of DNA sequences derived from distant regions of the genome; the length of the inserted fragment varied from 47 to 756 bp. Surprisingly, all of the inserted fragments were derived from gene and/or retrotransposon repeat elements such as LINE (Long Interspersed Nuclear Element) or SINE (Short Interspersed Nuclear Element) sequences. Therefore, we hypothesized that the inserted sequences used to “patch” the DNA DSB could be based on reverse transcription of an RNA template. Since sequences derived from human RNA and human genomic DNA are identical (with the exception of RNA splice events, poly-A tails, and RNA-edited nucleotides), we co-transfected the F5 cells with murine RNA and an I-SceI expression vector to test the hypothesis that the patches at the DNA DSB sites could be derived from RNA. After hygromycin selection for successfully transfected cells, genomic DNA was isolated, and amplified with primers that flanked the I-SceI cleavage site. DNA fragments of 500–1000bp (larger than the size of the uncleaved EF!aTK PCR product, which was 400 bp) containing insertions at the I-SceI site were isolated, subcloned, and sequenced. We identified 51 independent sequences which had insertions of 23–266 bp at I-SceI cleavage site. Of these 51 insertions, 4 were vector capture events (derived form the expression vector), and 4 were too short to identify unambiguously. Of the remaining 43 insertions, 39 were derived from a single genomic loci, and 4 samples contained identifiable sequences from 2 distinct genomic regions. The sequences were derived from 16 of the 24 human chromosomes, with no clear preference for any specific chromosome. 62% of the sequences were found to contain sequences from a transcribed gene region, and 64% contained repeat sequences such as LINE, SINE, or LTR. The involvement of retrotransposon sequences, which are known to be reverse transcribed and integrated into the genome, supports the hypothesis that at least some of the insertions may be templated from RNA. Furthermore, 45 of the 47 inserted sequences were derived from endogenous human sequences; however 2 insertions matched to mouse sequences, and were derived from the co-transfected mouse RNA. One sample matched an intronic region of murine Vwa3b, which we confirmed was highly expressed in the mouse cells used to harvest the RNA used for the co-transfection. A second sample was not a gene sequence but contained a LINE element. Taken together, these findings demonstrate that I-SceI-induced DNA DSB can be repaired by “patches” derived from distant regions of the genome. This is the first systematic study focused on captured sequences at DNA DSB sites in the mammalian genome, and suggests that transcribed mRNA and retrotransposons can play an important role in the repair of DNA DSB and preservation of genomic integrity. Finally, the observation that I-SceI-induced DNA DSBs are often repaired by insertions suggests that these insertions could be mistaken for chromosome translocations, if only one “side” of the DNA DSB is sequenced. Disclosures: No relevant conflicts of interest to declare.
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Dissertations / Theses on the topic "DNA sequences"

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Cai, Zheng. "Repetitive sequence analysis for soybean genome sequences." Diss., Columbia, Mo. : University of Missouri-Columbia, 2005. http://hdl.handle.net/10355/4249.

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Thesis (M.S.)--University of Missouri-Columbia, 2005.
"May 2005" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Includes bibliographical references.
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Parsons, Jeremy David. "Computer analysis of molecular sequences." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282922.

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Leung, Chi-ming. "Motif discovery for DNA sequences." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3859755X.

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Leung, Chi-ming, and 梁志銘. "Motif discovery for DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B3859755X.

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Zainuddin, Zainul Fadziruddin. "Mycobacterial plasmids and related DNA sequences." Thesis, University of Surrey, 1988. http://epubs.surrey.ac.uk/843201/.

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An investigation into the presence of plasmids in Mycobacterium tuberculosis was conducted. No extrachromosomal DNA was found although some evidence for their presence were detected. Plasmid-related sequences were however found in the genomic DNA of M, tuberculosis. Isolation of plasmid-related sequences from a strain of M, tuberculosis resulted in two different DNA probes which showed high specificity for M, tuberculosis and related species. One of these probes gave banding patterns which suggest the presence of restriction fragment polymorphism in M, tuberculosis. The other probe gave banding patterns which were unique for each strain tested. The use of these probes for epidemiological studies is suggested. An E. coli plasmid, pIJ666, was successfully introduced into Mycobacterium smegmatis ATCC607 and stably maintained through several subcultures. One of the selective markers, a chloramphenicol resistance gene from Tn9, was efficiently expressed in M. smegmatis ATCC607. The development of a transformation system in M. smegmatis from this initial study is indicated.
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Cheng, Lok-lam, and 鄭樂霖. "Approximate string matching in DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B29350591.

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Meade, Andrew Paul. "The computational analysis of DNA sequences." Thesis, University of Reading, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.412195.

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Sindi, Suzanne Soraya. "Describing and modeling repetitive sequences in DNA." College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/3796.

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Thesis (Ph. D.) -- University of Maryland, College Park, 2006.
Thesis research directed by: Applied Mathematics and Scientific Computation Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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李若谷 and Yeuk-goat Billy Li. "Statistical models for dependence in DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1995. http://hub.hku.hk/bib/B31235025.

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Li, Juan, and 李娟. "Molecular characterization of chicken repetitive DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B42577287.

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Books on the topic "DNA sequences"

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Raz, Eyal, ed. Immunostimulatory DNA Sequences. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4.

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Repetitive DNA. Basel: Karger, 2012.

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Patel, Umesh Anilkumar. DNA sequences associated with the nuclear matrix. Portsmouth: Portsmouth Polytechnic, School of Biological Sciences, 1989.

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Koo, Dae-Hwan. Effective protection of DNA sequences and gene innovations. Tokyo: Institute of Intellectural Property, 2007.

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McBride, A. J. A. Studies on DNA supercoiling and potential Z-DNA forming sequences in streptomyces. Manchester: UMIST, 1995.

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Smith, Duncan Richard. Studies on DNA sequences directing ribosomal transcription in Xenopus laevis. Portsmouth: Portsmouth Polytechnic, Dept. of Biological Sciences, 1987.

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Kasprzak, Marta. Combinatorial models and methods for reading genomic sequences. Poznań: Wydawn. Politechniki Poznańskiej, 2004.

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Manocha, Marcus M. S. Isolation and characterization of genomic DNA sequences that enhance the stability of plasmid DNA in mammalian cells. St. Catharines, Ont: Brock University, Centre for Biotechnology, 2005.

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C, Clarke B., Robertson A, and Jeffreys A. J, eds. The evolution of DNA sequences: Proceedings of a Royal Society Discussion Meeting, held on 13 and 14 March 1985. London: Royal Society, 1986.

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Evans, Paul David. The interactions of the E.coli trp repressor with its operator DNA sequences. Birmingham: University of Birmingham, 1995.

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Book chapters on the topic "DNA sequences"

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Petersen, Gitte. "Reading DNA Sequences." In Molecular Tools for Screening Biodiversity, 332–33. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-009-0019-6_60.

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Van Uden, John, and Eyal Raz. "Introduction to immunostimulatory DNA sequences." In Immunostimulatory DNA Sequences, 1–9. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_1.

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Krieg, Arthur M. "Signal transduction induced by immunostimulatory CpG DNA." In Immunostimulatory DNA Sequences, 97–105. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_10.

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Weiner, George J. "Immunostimulatory DNA sequences and cancer therapy." In Immunostimulatory DNA Sequences, 107–16. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_11.

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Broide, David, Jae Youn Cho, Marina Miller, Jyothi Nayar, Greg Stachnick, Diego Castaneda, Mark Roman, and Eyal Raz. "Modulation of asthmatic response by immunostimulatory DNA sequences." In Immunostimulatory DNA Sequences, 117–24. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_12.

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McCluskie, Michael J., Risini D. Weeratna, and Heather L. Davis. "The role of CpG in DNA vaccines." In Immunostimulatory DNA Sequences, 125–32. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_13.

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Horner, Anthony A., Nadya Cinman, Arash Ronaghy, and Eyal Raz. "Mucosal adjuvanticity of immunostimulatory DNA sequences." In Immunostimulatory DNA Sequences, 133–46. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_14.

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Wagner, Hermann, Hans Häcker, and Grayson B. Lipford. "Immunostimulatory DNA sequences help to eradicate intracellular pathogens." In Immunostimulatory DNA Sequences, 147–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_15.

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Pisetsky, David S. "The antigenic properties of bacterial DNA in normal and aberrant immunity." In Immunostimulatory DNA Sequences, 153–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_16.

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Wagner, Hermann, Grayson B. Lipford, and Hans Häcker. "The role of immunostimulatory CpG-DNA in septic shock." In Immunostimulatory DNA Sequences, 167–71. Berlin, Heidelberg: Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56866-4_17.

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Conference papers on the topic "DNA sequences"

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Shahzad, M., Nazish Alia, and Sadaf Mahmood. "DNA Innovate: Visualizing DNA sequences." In 2009 International Conference on Information and Communication Technologies (ICICT). IEEE, 2009. http://dx.doi.org/10.1109/icict.2009.5267200.

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Al Junid, S. A. M., M. A. Haron, Z. Abd Majid, F. N. Osman, H. Hashim, M. F. M. Idros, and M. R. Dohad. "Optimization of DNA Sequences Data to Accelerate DNA Sequence Alignment on FPGA." In Asia Modelling Symposium. 4th Asia International Conference on Mathematical Modelling and Computer Simulation (AMS 2010). IEEE, 2010. http://dx.doi.org/10.1109/ams.2010.54.

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Cheng, Kin-On, Ngai-Fong Law, and Wan-Chi Siu. "Compressing population DNA sequences using multiple reference sequences." In 2017 Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA ASC). IEEE, 2017. http://dx.doi.org/10.1109/apsipa.2017.8282136.

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Linton, Eric, Paul Albee, Patrick Kinnicutt, and En-Bing Lin. "Multiresolution Analysis of DNA Sequences." In 2010 Second International Conference on Computer Research and Development. IEEE, 2010. http://dx.doi.org/10.1109/iccrd.2010.32.

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Hon Keung Kwan, Rajandeep Atwal, and Benjamin Y. M. Kwan. "Wavelet analysis of DNA sequences." In 2008 International Conference on Communications, Circuits and Systems (ICCCAS). IEEE, 2008. http://dx.doi.org/10.1109/icccas.2008.4657895.

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Elharti, Abdelmoula, and Donna M. Kocak. "Comparing DNA sequences using wavelets." In International Symposium on Optical Science and Technology, edited by Mark S. Schmalz. SPIE, 2000. http://dx.doi.org/10.1117/12.409243.

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Bacry, Emmanuel, Alain Arneodo, Jean F. Muzy, and Pierre-Vincent Graves. "Wavelet analysis of DNA sequences." In SPIE's 1995 International Symposium on Optical Science, Engineering, and Instrumentation, edited by Andrew F. Laine and Michael A. Unser. SPIE, 1995. http://dx.doi.org/10.1117/12.217604.

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Menaka, K. "Message Encryption Using DNA Sequences." In 2014 World Congress on Computing and Communication Technologies (WCCCT). IEEE, 2014. http://dx.doi.org/10.1109/wccct.2014.35.

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Kwan, Hon Keung, and Swarna Bai Arniker. "Numerical representation of DNA sequences." In 2009 IEEE International Conference on Electro/Information Technology (eit '09). IEEE, 2009. http://dx.doi.org/10.1109/eit.2009.5189632.

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Arniker, Swarna Bai, and Hon Keung Kwan. "Graphical representation of DNA sequences." In 2009 IEEE International Conference on Electro/Information Technology (eit '09). IEEE, 2009. http://dx.doi.org/10.1109/eit.2009.5189633.

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Reports on the topic "DNA sequences"

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Churchill, G. A. Accurate restoration of DNA sequences. Progress report. Office of Scientific and Technical Information (OSTI), May 1994. http://dx.doi.org/10.2172/10149735.

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Milosavljevic, A. Discovering related DNA sequences via mutual information. Office of Scientific and Technical Information (OSTI), October 1994. http://dx.doi.org/10.2172/10187913.

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Pogozelski, Wendy, Salvatore Priore, Matthew Bernard, and Anthony Macula. Investigation of a Sybr-Green-Based Method to Validate DNA Sequences for DNA Computing. Fort Belvoir, VA: Defense Technical Information Center, May 2005. http://dx.doi.org/10.21236/ada435503.

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Gupta, G., S. V. Santhana Mariappan, X. Chen, P. Catasti, L. A. III Silks, R. K. Moyzis, E. M. Bradbury, and A. E. Garcia. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair. Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505319.

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Searles, D. B. Foundations for a syntatic pattern recognition system for genomic DNA sequences. Office of Scientific and Technical Information (OSTI), March 1993. http://dx.doi.org/10.2172/6707698.

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Jaehoon Jeong, Jaehoon Jeong. How are the repetitive circular DNA sequences present on chloroplasts created? Experiment, July 2022. http://dx.doi.org/10.18258/28385.

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Kieleczawa, J., F. W. Studier, and C. W. Fuller. Improved reliability and sensitivity for priming DNA sequences with contiguous strings of hexamers. Office of Scientific and Technical Information (OSTI), December 1994. http://dx.doi.org/10.2172/10130256.

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Fields, C. A. Identification of genes in anonymous DNA sequences. Annual performance report, February 1, 1991--January 31, 1992. Office of Scientific and Technical Information (OSTI), June 1996. http://dx.doi.org/10.2172/243485.

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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 &quot;controlled exposure program&quot; used by farmers to produce KHV &quot;naturally resistant fish&quot; 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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Fields, C. A. Identification of genes in anonymous DNA sequences. Final report: Report period, 15 April 1993--15 April 1994. Office of Scientific and Technical Information (OSTI), September 1994. http://dx.doi.org/10.2172/10182960.

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