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Reconstructing latent periods in genome sequences with insertions and deletions

Raman Arora, Colin Dewey, William A. Sethares
2009 2009 IEEE International Workshop on Genomic Signal Processing and Statistics  
This reconstructs likely insertions and deletions in the sequence and results in better estimates of the statistical period and cyclostationary profiles than the ML approach.  ...  Tandem and latent repeats in genome sequences provide insight into its various structural and functional roles.  ...  An iterative algorithm is proposed for recovering latent periods by reconstructing likely insertions and deletions in the ancestral cyclostationary sequence.  ... 
doi:10.1109/gensips.2009.5174377 dblp:conf/gensips/AroraDS09 fatcat:ngtsmnqarzdj7cstz6lf4dpdcm

Alterations in the U3 region of the long terminal repeat of an infectious thymotropic type B retrovirus

J K Ball, H Diggelmann, G A Dekaban, G F Grossi, R Semmler, P A Waight, R F Fletcher
1988 Journal of Virology  
a very short latent period.  ...  Nucleotide sequence studies confirmed these results and showed that in this region 440 nucleotides of the MMTV (C3H) sequences were deleted and substituted with a segment of 122 nucleotides.  ...  a very short latent period.  ... 
doi:10.1128/jvi.62.8.2985-2993.1988 fatcat:hzrqsdpb2jchbatbi32rtlfs3i

Alterations in the U3 region of the long terminal repeat of an infectious thymotropic type B retrovirus

J K Ball, H Diggelmann, G A Dekaban, G F Grossi, R Semmler, P A Waight, R F Fletcher
1988 Journal of Virology  
a very short latent period.  ...  Nucleotide sequence studies confirmed these results and showed that in this region 440 nucleotides of the MMTV (C3H) sequences were deleted and substituted with a segment of 122 nucleotides.  ...  a very short latent period.  ... 
pmid:2839715 pmcid:PMC253737 fatcat:6mg65acimvhwrasbvv67y2ae4m

Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection

Mariko Hakamata, Hayato Takihara, Tomotada Iwamoto, Aki Tamaru, Atsushi Hashimoto, Takahiro Tanaka, Shaban A. Kaboso, Gebremichal Gebretsadik, Aleksandr Ilinov, Akira Yokoyama, Yuriko Ozeki, Akihito Nishiyama (+5 others)
2020 Scientific Reports  
We sequenced genomes of these isolates and analyzed the propensity and rate of genomic mutations. Generation time versus mutation rate curves were significantly higher for RP.  ...  The ratio of oxidative versus non-oxidation damages induced mutations was higher in SP than RP, suggesting that persistent Mtb are exposed to oxidative stress in the latent state.  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the wok for publication.  ... 
doi:10.1038/s41598-020-75028-2 pmid:33093577 fatcat:sdosyrrdujbgdnzvljybjjs5eq

Delimitation of essential genes of cassava latent virus DNA 2

Pantea Etessami, Rowena Callis, Susan Ellwood, John Stanley
1988 Nucleic Acids Research  
Insertion and deletion mutagenesis of both extended open reading frames (ORFs) of cassava latent virus DNA 2 destroys infectivity.  ...  By cloning specific fragments into DNA 1 coat protein deletion vectors we have delimited the DNA 2 coding regions and provide substantive evidence that both are essential for virus infection.  ...  Sequence analysis showed that the leader sequence was deleted up to, but not including, nucleotide 581 in pJSl95.  ... 
doi:10.1093/nar/16.11.4811 pmid:3387209 pmcid:PMC336698 fatcat:nvx6vmwlhvbqvo4bosqlxpelh4

Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure

Ya-Chi Ho, Liang Shan, Nina N. Hosmane, Jeffrey Wang, Sarah B. Laskey, Daniel I.S. Rosenbloom, Jun Lai, Joel N. Blankson, Janet D. Siliciano, Robert F. Siliciano
2013 Cell  
Alireza Rabi, Gregory Laird, and Drs. Stuart  ...  Noninduced proviruses included those with intact genomes (red bars), insertions or deletions (blue bars), and hypermutation (white bars).  ...  Left to right: intact genome, 16 bp J deletion, deletion with defined junction, and deletion with undefined junction. Clone name is given below each gel.  ... 
doi:10.1016/j.cell.2013.09.020 pmid:24243014 pmcid:PMC3896327 fatcat:xgxi3nwocba6lhvmqx4hi6oay4

Detection of herpes simplex virus-specific DNA sequences in latently infected mice and in humans

S Efstathiou, A C Minson, H J Field, J R Anderson, P Wildy
1986 Journal of Virology  
Herpes simplex virus-specific DNA sequences have been detected by Southern hybridization analysis in both central and peripheral nervous system tissues of latently infected mice.  ...  This "endless" herpes simplex virus DNA is both qualitatively and quantitatively stable in mouse neural tissue analyzed over a 4-month period.  ...  S.E. holds a Cooperative Award in Science and Engineering supported by the Wellcome Foundation Ltd. J.R.A. is in receipt of a grant from the East Anglia Regional Health Authority. LITERATURE CITED  ... 
doi:10.1128/jvi.57.2.446-455.1986 fatcat:qjbweliwobcmfaynzvmtzopqfy

Detection of herpes simplex virus-specific DNA sequences in latently infected mice and in humans

S Efstathiou, A C Minson, H J Field, J R Anderson, P Wildy
1986 Journal of Virology  
Herpes simplex virus-specific DNA sequences have been detected by Southern hybridization analysis in both central and peripheral nervous system tissues of latently infected mice.  ...  This "endless" herpes simplex virus DNA is both qualitatively and quantitatively stable in mouse neural tissue analyzed over a 4-month period.  ...  S.E. holds a Cooperative Award in Science and Engineering supported by the Wellcome Foundation Ltd. J.R.A. is in receipt of a grant from the East Anglia Regional Health Authority. LITERATURE CITED  ... 
pmid:3003377 pmcid:PMC252756 fatcat:c24lwv5qyndpvkbx3cm4tbpu2e

Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing

Alexander C. Outhred, Nadine Holmes, Rosemarie Sadsad, Elena Martinez, Peter Jelfs, Grant A. Hill-Cawthorne, Gwendolyn L. Gilbert, Ben J. Marais, Vitali Sintchenko, Yoshihiko Hoshino
2016 PLoS ONE  
Whole genome sequencing, with analysis of single-nucleotide polymorphisms, insertions, deletions, structural variants and subpopulations, enabled the highest possible level of discrimination between cluster  ...  In addition to single-nucleotide polymorphisms, the analyses also sought to identify insertions, deletions and structural variants.  ...  We are also grateful to Chris Lowbridge, Tracie Reinten and Vicky Sheppeard, from Health Protection NSW, and to Michael Roper for valuable advice and technical support.  ... 
doi:10.1371/journal.pone.0150550 pmid:26938641 pmcid:PMC4777479 fatcat:wbyccnnyaffuzjk5q6utpo4icq

Mapping of the gene coding for Epstein-Barr virus-determined nuclear antigen EBNA3 and its transient overexpression in a human cell line by using an adenovirus expression vector

I Joab, D T Rowe, M Bodescot, J C Nicolas, P J Farrell, M Perricaudet
1987 Journal of Virology  
The expressed protein had the same molecular weight, subcellular localization, and immunological characteristics as the EBV-determined nuclear antigen EBNA3, which is made in lymphocytes latently infected  ...  The T2 cDNA contains viral genomic sequences from the short BLRF3 open reading frame fused to the adjacent BERF1 long open reading frame.  ...  The equivalent of the T2 cDNA sequence was reconstructed (for technical ease) by using the 5' region from the cDNA and the intron-free 3' region from the viral genome (Fig. 2) .  ... 
pmid:3041055 pmcid:PMC255922 fatcat:tzxdibnpzfdwrd243e2h4dxraq

Mapping of the gene coding for Epstein-Barr virus-determined nuclear antigen EBNA3 and its transient overexpression in a human cell line by using an adenovirus expression vector

I Joab, D T Rowe, M Bodescot, J C Nicolas, P J Farrell, M Perricaudet
1987 Journal of Virology  
The expressed protein had the same molecular weight, subcellular localization, and immunological characteristics as the EBV-determined nuclear antigen EBNA3, which is made in lymphocytes latently infected  ...  The T2 cDNA contains viral genomic sequences from the short BLRF3 open reading frame fused to the adjacent BERF1 long open reading frame.  ...  The equivalent of the T2 cDNA sequence was reconstructed (for technical ease) by using the 5' region from the cDNA and the intron-free 3' region from the viral genome (Fig. 2) .  ... 
doi:10.1128/jvi.61.10.3340-3344.1987 fatcat:vdow3fqmdrbofchqljku6obfry

Mapping genetic elements of Epstein-Barr virus that facilitate extrachromosomal persistence of Epstein-Barr virus-derived plasmids in human cells

S Lupton, A J Levine
1985 Molecular and Cellular Biology  
A small in-frame deletion and linker insertion mutation in the region encoding the carboxy-terminal portion of EBNA-1, which replaced 19 amino acid codons with 2, had no effect on the maintenance of p410  ...  Two mutations in the BamHI-K-derived portion of p410+, a large in-frame deletion and a linker insertion frameshift mutation, both of which alter the carboxy-terminal portion of EBNA-1, destroyed the ability  ...  We thank Noel Mann for help in preparing the manuscript. This work was supported by grants M47E and M47F from the American Cancer Society.  ... 
doi:10.1128/mcb.5.10.2533 pmid:3016506 pmcid:PMC366987 fatcat:v4okejo3vjdu5oa3mgnbiyvf5e

Molecular and biological properties of BK virus-IR, a BK virus variant isolated from a human tumor

M Pagnani, M Negrini, P Reschiglian, A Corallini, P G Balboni, S Scherneck, G Macino, G Milanesi, G Barbanti-Brodano
1986 Journal of Virology  
BKV-IR bears a 253-base-pair (bp) deletion and an 80-bp insertion in the early region of the genome. The deletion abolishes the expression of small-t antigen.  ...  As compared with wild-type BKV, BKV-IR transformed hamster cells with a reduced efficiency and induced ependymomas in hamsters at a lower frequency and with a longer latency period.  ...  To better characterize the genome of BKV-IR, we carried out a nucleotide sequence analysis of the regions of BKV-IR DNA containing the insertion and the deletion and compared them with the corresponding  ... 
doi:10.1128/jvi.59.2.500-505.1986 fatcat:fdpxbymyyvcmfdbq4z7w4lu3ca

Molecular and biological properties of BK virus-IR, a BK virus variant isolated from a human tumor

M Pagnani, M Negrini, P Reschiglian, A Corallini, P G Balboni, S Scherneck, G Macino, G Milanesi, G Barbanti-Brodano
1986 Journal of Virology  
BKV-IR bears a 253-base-pair (bp) deletion and an 80-bp insertion in the early region of the genome. The deletion abolishes the expression of small-t antigen.  ...  As compared with wild-type BKV, BKV-IR transformed hamster cells with a reduced efficiency and induced ependymomas in hamsters at a lower frequency and with a longer latency period.  ...  To better characterize the genome of BKV-IR, we carried out a nucleotide sequence analysis of the regions of BKV-IR DNA containing the insertion and the deletion and compared them with the corresponding  ... 
pmid:3016311 pmcid:PMC253103 fatcat:rsl6zqy77refzfzhibmukl2gh4

Protection from herpes simplex virus type 1 lethal and latent infections by secreted recombinant glycoprotein B constitutively expressed in human cells with a BK virus episomal vector

R Manservigi, M P Grossi, R Gualandri, P G Balboni, A Marchini, A Rotola, P Rimessi, D Di Luca, E Cassai, G Barbanti-Brodano
1990 Journal of Virology  
The herpes simplex virus type 1 (HSV-1) glycoprotein B (gB-1) gene, deleted of 639 nucleotides that encode the transmembrane anchor sequence and reconstructed with the extramembrane and intracytoplasmic  ...  Mice immunized with secreted gB-1 produced HSV-1and HSV-2-neutralizing antibodies and were protected against HSV-1 lethal, latent, and recurrent infections.  ...  The deleted gB-1 gene was then reconstructed by self-ligation to put in frame sequences coding for the extramembrane and C-terminal intracytoplasmic domains (Fig. 1 ).  ... 
doi:10.1128/jvi.64.1.431-436.1990 fatcat:nd7peb2y7rf3vmsyz3avvp6kqu
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