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*  Ancestral reconstruction
The "genome rearrangement problem", first posed by Watterson and colleagues, asks: given two genomes (permutations) and a set ... Because HIV is extremely diverse, a vaccine designed to work on one patient's viral population might not work for a different ... "multiple genome rearrangement problem": given a set of genomes and a set of allowable operations, find (i) a binary tree with ... "Reconstructing contiguous regions of an ancestral genome". Genome Research. 16 (12): 1557-1565. doi:10.1101/gr.5383506. ISSN ...
*  Epigenetics of human herpesvirus latency
LAT manages this suppression of the viral genome through miRNAs that block viral transcription factors such as ICP0 and ICP4 ... One epigenetic mechanism employed in the control of latency for CMV is heterochromatization of the viral genome. Studies have ... Cameron, Craig E.; Gotte, Matthias; Raney, Kevin (2009-05-28). Viral Genome Replication. Springer Science & Business Media. ... These miRNAs also change the methylation of the histones in the viral genome. In the latent phase there is a lot of H3K9 ...
*  Extrachromosomal DNA
Viral DNA is an example of extrachromosomal DNA. Understanding viral genomes is very important for understanding the evolution ... Some viruses, such as HIV and oncogenetic viruses, incorporate their own DNA into the genome of the host cell. Viral genomes ... viral dsRNA by TLR3, viral ssRNA by TLR7/TLR8, viral or bacterial unmethylated DNA by TLR9. TLR9 has evolved to detect CpG DNA ... The recognition of viral DNA is an important part of immune responses. For this virus to persist, the circular genome must be ...
*  Platonic solid
... this saves space in the viral genome. In meteorology and climatology, global numerical models of atmospheric flow are of ... Viral structures are built of repeated identical protein subunits and the icosahedron is the easiest shape to assemble using ...
*  Caulimoviridae
Firstly, the viral genome enters the cytoplasm. The viral DNA forms supercoiled mini-chromosome structures upon entering the ... they do not require the integration of viral genome into the host's in order to replicate and for this reason their genome does ... Harper G, Hull R, Lockhart B, Olszewski N (2002). "Viral sequences integrated into plant genomes". Annu Rev Phytopathol. 40: ... It can either be used as a template for viral protein synthesis, or it can undergo reverse transcription by viral encoded ...
*  Regular icosahedron
... this saves space in the viral genome. Various bacterial organelles with an icosahedral shape were also found. The icosahedral ... Viral structures are built of repeated identical protein subunits known as capsomeres, and the icosahedron is the easiest shape ... and Other Semi-Regular Polyhedra Virtual Reality Polyhedra The Encyclopedia of Polyhedra Tulane.edu A discussion of viral ...
*  Lagovirus
The viral genome encodes viral structural protein. Virions consist of 1 structural protein(s) (major species located in the ... The genome has a guanine + cytosine content of 49.3-50.1 %. The 5' end of the genome has a usually genome-linked protein (VPg ... Viral structural protein: Capsid protein has a molar mass of 59000-71000 Da; is the coat protein. Capsid protein has a ... Viral replication is cytoplasmic. Entry into the host cell is achieved by attachment to host receptors, which mediates ...
*  Vesicular exanthema of swine virus
... end of the genome has a viral protein genome-linked (VPg). The 3'-terminus has a poly (A) tract. The viral genome encodes viral ... Under in vitro conditions virions are inactivated in acid environment of pH 3-5. The genome is not segmented and contains a ... The complete genome is 7900 nucleotides long. The 5'- ...
*  Vesivirus
The viral genome encodes viral structural protein. Virions consist of 1 viral structural protein (major species), or 2 Viral ... The genome has a guanine + cytosine content of 45-49%. The 5' end of the genome has a genome-linked protein (VPg). The 3' ... complete genome". "Calicivirus isolate Allston 2009/US, complete genome, complete genome". ICTVdB-The Universal Virus Database ... Viral structural protein: Capsid protein has a molar mass of 58000-60000 Da; is the coat protein. Capsid protein has a ...
*  Deformed wing virus
The viral genome was published in 2006. The genome is 10140 nucleotides in length excluding the poly(A) tail and contains a ... If the VPg is present in the genome a copy will be bound to the 5' end of the RNA genome. The virion is a 30-nm icosahedral ... The genome structure is 5'UTR-L-VP2-(VP4)-VP1-VP3-RNA helicase-(VPg)-3C protease-RNA dependent RNA polymerase-3'UTR The ... The genome is 29.5% adenosine, 15.8% cytosine, 22.4% guanine and 32.3% uracil. Analysis of codon use found 39.5% uracil and ...
*  Extremophile
It has been shown that both plasmids and viral genomes can be transferred via MVs. Notably, a horizontal plasmid transfer has ... "Extracellular membrane vesicles harbouring viral genomes". Environ Microbiol. 16 (4): 1167-75. doi:10.1111/1462-2920.12235. ...
*  Helicos single molecule fluorescent sequencing
"Single-molecule DNA sequencing of a viral genome". Science. 320 (5872): 106-9. Bibcode:2008Sci...320..106H. doi:10.1126/science ... This sequencing method and equipment were used to sequence the genome of the M13 bacteriophage. The Helicos Genetic Analysis ... 12,000,000 to 20,000,000 reads that are 25 nucleotides or longer and align to the reference genome should be expected from each ...
*  Carrot Yellow-leaf Virus
The dsRNA genome is transcribed to produce new viral mRNAs/new ssRNA(+) genomes. Translation using host cell machinery produces ... which are short sequences homologous to the viral genome. When these short sequences bind to the genome, they prevent ... Without the tail, the body is less stable and RNA is exposed into the neighbour cell cytoplasm; the viral genome has ... Cell mechanisms are used to translate these and all the other viral proteins. The capsid proteins and ssRNA genome assemble and ...
*  Droplet-based microfluidics
"Single-Molecule DNA Sequencing of a Viral Genome". Science. 320 (5872): 106-109. doi:10.1126/science.1150427. Braslavsky, I.; ... "Genome sequencing in microfabricated high-density picolitre reactors". Nature. doi:10.1038/nature03959. Harris, T. D.; Buzby, P ...
*  Gammaherpesvirinae
At the left end of each viral genome are located ORFs encoding distinct transforming proteins.The Gammaherpes viral genes are ... the viral episomes are partitioned to daughter cells. This provides continuous existence of the viral genome within the host ... Viruses that establish lifelong latent infections must ensure that the viral genome is maintained within the latently infected ... The majority of gammaherpesviruses encode a specific protein that is critical for maintenance of the viral genome within ...
*  Overlapping gene
They are especially common in viral genomes. The existence of overlapping genes was first identified in viruses; the first DNA ... However, other studies dispute this conclusion and argue that the distribution of overlaps in viral genomes is more likely to ... Overlapping genes are particularly common in viral genomes. Some studies attribute this observation to selective pressure ... toward small genome sizes mediated by the physical constraints of packaging the genome in a viral capsid, particularly one of ...
*  Single-molecule magnetic sequencing
2008). "Single-molecule DNA sequencing of a viral genome". Science. 320 (5872): 106-109. doi:10.1126/science.1150427. PMID ... Such DNA hairpin setup can be made in two ways: 1) In the case of double-stranded DNA molecules (for whole genome sequencing, ...
*  Coronaviridae
The viral genome is 26-32 kb in length. Virions are spherical, 120-160 nm across (Coronavirinae), bacilliform, 170-200 by 75-88 ... The 5' and 3' ends of the genome have a cap and poly (A) tract, respectively. The viral envelope, obtained by budding through ... Studies have revealed cis-acting elements and trans-acting viral factors involved in coronavirus genome encapsidation and ... In common with the genomes of all other RNA viruses, coronavirus genomes contain cis-acting RNA elements that ensure the ...
*  Turnip crinkle virus (TCV) hairpin H4
H4 enhances transcription and translation of the viral genome. Sun, X; Simon, AE (Aug 15, 2006). "A cis-replication element ... genome. The 3' end of the TCV genome contains the hairpin H4, a T-shaped structure (TSS), which contains hairpins 4a, 4b and ...
*  Extranuclear inheritance
Extranuclear transmission of viral genomes and symbiotic bacteria is also possible. An example of viral genome transmission is ... genomic recombination of these genomes is rarely found in offspring contrary to nuclear genomes, in which recombination is ... During this time viral material may be passed from mother to child in the bloodstream or breastmilk. This is of particular ... The extranuclear genomes of mitochondria and chloroplasts however replicate independently of cell division. They replicate in ...
*  Asparagus virus 1
The viral genome encodes structural proteins and non-structural proteins. Lipids are not reported. The virus is serologically ... The Mr of the genome constitutes 6% of the virion by weight. The genome is monopartite, only one particle size is recovered of ... Biological Properties Natural Host Domain Viral hosts belong to the Domain Eucarya. Domain Eucarya Kingdom Plantae. Kingdom ...
*  Plant virus
Some viral families, such as the Bromoviridae instead opt to have multipartite genomes, genomes split between multiple viral ... In the presence of the viral genome, the discs are stacked, then a tube is created with room for the nucleic acid genome in the ... The structure of a virus is given by its coat of proteins, which surround the viral genome. Assembly of viral particles takes ... The resulting capped leader RNA is used to prime transcription on the viral genome. However some plant viruses do not use cap, ...
*  TRIM28
KAP1 acts as a transcriptional corepressor of the viral genome. The protein binds to the histones of the viral chromatin and ... This heterochromatin formation prevents the transcription of the viral genome. mTOR has been implicated in the phosphorylation ... NURSA C153 FactorBook KAP1 TRIM28 human gene location in the UCSC Genome Browser. TRIM28 human gene details in the UCSC Genome ... Studies have shown that KAP1 can repress transcription by binding directly to the genome (which can be sufficient in and of ...
*  Paramyxoviridae
If the viral genome follows a multiple promoter model, the level inhibition of transcription should correlate with the length ... Many paramyxovirus genomes follow the "rule of six". The total length of the genome is almost always a multiple of six. This is ... Animal viruses Paramyxoviridae Genomes Viral Bioinformatics Resource Center Viralzone: Paramyxoviridae ICTV Virus Pathogen ... However, the genome was best described by a single promoter model. When paramyxovirus genome was exposed to UV light, the level ...
*  Grapevine Pinot gris virus
... and found stretches of viral RNA genome that corresponded to sequences found in the RNA genomes of both Grapevine Berry Inner ... Smaller percentages of other viral genomes were also found. Because its complete genomic sequence could not be found in the ... then proceeds with an untranslated region of 82 base pairs and terminates in the polyA tail that is typical of viral genomes. ... GPGV is a positive single-stranded RNA virus, meaning that the genome of the virus is made up of RNA nucleotides. While ...
*  Synthetic virology
Live synthetic viruses have their entire genomes constructed from synthetic viral genes, which are then assembled using various ... That is, their genome contains all the necessary information to produce new viable viruses. This technology is now being used ... As of March 2014, the full-length genome sequences of 3843 different viruses, including smallpox, are publicly available in an ... methodologies to yield complete viral genomes. The first man-made infectious viruses generated without any natural template ...
*  Hepatitis D
... viral genome". Nature. 323 (6088): 508-14. doi:10.1038/323508a0. PMID 3762705. Fauquet, CM; Mayo MA; Maniloff J; Desselberger U ... The hepatitis D circular genome is unique to animal viruses because of its high GC nucleotide content. The HDV genome exists as ... With a genome of approximately 1700 nucleotides, HDV is the smallest "virus" known to infect animals. It has been proposed that ... The entire genome was cloned and sequenced in 1986. It was subsequently placed in its own genus: Deltavirus. Three genotypes (I ...