User:Karate bb/sandbox

Article evaluation

I will be evaluating the wikipedia article on Virophages

In reading this article I could tell that it was considered a 'stub' which is where a wikipedia article is too short or lacking information to be considered a helpful online encyclopedia page. In looking at the article and its talk page I found that it is a part of many different wiki projects listed here: WikiProject Viruses, WikiProject Microbiology, WikiProject Molecular and Cell Biology, and WikiProject Biology.

As far as relevance is concerned, the article contains definitions of viruses themselves. It talks about their genomes and comparable organisms. I find this to be irrelevant because there is another article dedicated to viruses themselves and explaining their genetic makeup and explaining how they may or may not be related to other organisms. I also don't see how virophages are present in popular culture which could be considered irrelevant too. However, the taxonomy of virophages shed some light on how they are classified using an appropriate source ICTV (International Committee on Taxonomy of Viruses)

I find this article to be very neutral. Since it contains little information about virophages and only cites a major contributor as the ICTV and one other PDF linked in the article. No wording in this article strikes me as biased.

I checked the only reference link to a pdf. The PDF link did not work however, when clicking on the DOI number that took me to the article cited. I read through the article and the cited passage goes along with the message of the cited article.The article has only one reference which I will add more to in adding more information to this stub page.

The concept of virophages are pretty new, 2016 was the year the reference article was published, I think that a lot of information has yet to be discovered about them and their taxonomy so it would make sense that there are some areas for improvement in the aspect of content.

The talk page on this article was very helpful. It looked like a collaborative space where authors could collaborate on the title of the article as well as some content. They talked about naming and word choice. I agree with the feedback except where they suggested the page be named Sputnik Virophage. While I understand that this is a known example of a virophage I think that an encyclopedia page would be more beneficial if it gave an overview of the whole Virophage group of viruses for a source of broad information.

The discussion of this article on wikipedia will differ from class discussion because in class we would have talked about implied reactions with other viruses, people, etc. In the wikipedia article it is more about straight fact about what virophages are and what they do. In class we would have also probably speculated on how they will infect future populations and how they could be used as a transport for medications/drugs but in wikipedia this needs to be backed up fact and not speculation

What I plan to add to the Virophage article

Since this article is considered a 'stub' I will be adding more information about the general nature of virophages. While I understand that they are newly discovered, there are still articles that compare them to satellite viruses.I will be working with the student author of the Satellite Viruses page to distinguish what sets Virophages apart from Satellite Viruses. I would like to add newly discovered virophages to the article as well since sputnik is older. Something that this article needs is also the more specific factors that make up the group virophages.

Editing Virophage

Virophages are small, double stranded DNA viral phages that, in order for their replication to occur, require the co-infrection of another virus. The virophage genome is about 20 kilo-base pairs long (kbp) with isometric capsids. The co-infecting viruses are typically giant viruses. These virophages rely on the viral replication factory of the co-infecting giant virus for their own replication. One of the characteristics of virophages are that they have a parasitic relationship with co-infecting virus. The dependence upon the giant virus for replication often results in the deactivation of the giant viruses. The virophage often times improves the recovery and survival of the host organism. The most current listing of discovered virophages include Sputnik, Sputnik_2, Sputnik_3, Zamilon and Mavirus which were all found in eukaryotic hosts with their co-infecting giant virus. (on live page) Virophage genomes are about 20,000 base pairs long (20 kbp) with isometric capsids. Virophages are around 17-30 kilobase pairs long (kbp) while their Giant Virus counterparts can be as large as 1-2 megabase pairs long (Mbp). Some of the largest genomes of virophages are similar to the genome size of the adenovirus.

	Genome Size (kbp)	Capsid Size (diameter)
Virophage: Zamilon Virophage	17 kbp	50-60nm
Virus: Poliovirus	7 kbp	30nm
Giant Virus: Cafeteria roenbergensis virus	700 kbp	75nm

Discovery

One of the first virophage was discovered in a Cooling Tower in Paris, France. It was discovered with its co-infecting giant virus, Acanthamoeba castellanii mamavirus (ACMV). That virophage was named Sputnik and its replication relied entirely on the co-infection of ACMV and its cytoplasmic replication machinery. Sputnik was also discovered to have an inhibitory affect on ACMV and improved the survival of the host. After that discovery many other virophages were discovered by analyzing samples and sequencing data.

A majority of these virophages are being discovered by analyzing metagenomic data sets. In metagenomic analysis, DNA data is sequenced and ran through multiple bioinformatic algorithms which, based on what is being analyzed, pull out certain important patters and characteristics. In these data sets are giant viruses and virophages. They are separated by looking for sequences that around 17 to 20 kilobase pairs long and have similarities to already sequenced virophages. These virophages can also have linear or circular double stranded DNA genomes. When the sample is isolated in culture it has icosahedral capsid particles that measure around 40 to 80 nano meters long. Virophage particles are so small that electron microscopy must be used to view these particles. Because of metagenomic assemblies, around 57 complete and partial virophage genomes have been identified.

Host Range and Replication

Virophages, in order for them to replicate, need to have a co-infecting virus in which they exploit the replication machinery. The virophages do not have the necessary equipment to replicate on their own. Virophages uses giant viral replication machinery to replicate their own genomes and continue their existance. The host range for virophages include giant viruses with double stranded DNA genomes. Virophages use the transcriptional machinery of these giant viruses for their own replication instead of the host's transcriptional machinery. For example, the discovery of the virophage associated with the Samba virus decreased the viruses concentration in the host while the virophage was replicating using the giant virus. The host amoeba also showed a partial recovery from the infection by the Samba virus.

Genome

Virophages have small double stranded DNA genomes either circular or linear in shape. The size of these genomes can vary depending on the giant virus it infects. Most virophages have genomes around 17-20 kb. Virophages do not contain genes for replication and instead rely on co-infecting giant viruses. Their genome is protected by an icosahedral capisd measuring around 40-80 nano meters long.

Distinguishable Characteristics

Unlike satellite viruses, virophages have a parasitic effect on their co-infecting virus. The virophages have been known to render a giant virus inactive and improve the condition of the host organism. Virophages often infect eukaryotic cells such as amoeba.