User talk:TobyBrann

Welcome
 Hello, TobyBrann, and Welcome to Wikipedia!  Welcome to Wikipedia! I hope you enjoy the encyclopedia and want to [[Wikipedia:Wikipe

Welcome to Wikiproject Biology!
Welcome! I'm one of the editors here. I recommend you take a look around the page, as well as the talk page. You may also find several other Wikiprojects listed on the main page which are a little more specific than just biology--you may be interested in those as well.

Wikipedia can be a big and overwhelming place sometimes. Please let me know if you could use any help on anything at all. That's what I am here for and why I contacted you. You can get a hold of me by replying to me here or leaving a message on my talk page. Even better, ping me by typing {{Ping|Prometheus720} and signing your name with four tildes (~) at the end of your message. That will ensure that I get it!

Finally, I'd like to direct you to the bottom of that talk page I linked. I am in the initial portion of a revamp of all of Wikiproject Biology, and you are in a prime position to help us. As a new user, you have a fresh opinion on what the project pages look like and how helpful they are to you. I'd love to hear your feedback, questions, and criticisms, even if you don't wish to contribute any more than that.

Good luck to you, and thank you so much for joining us at Wikiproject Biology! Please contact me if you need anything at all. See you around!Prometheus720 (talk) 09:11, 23 May 2019 (UTC)

Integrative & Conjugative Element Discussion
Hello. I strongly apologise to bother you, but if you do not mind, I would like to ask you a favor. Since you are an experienced Wikipedia user as well as an expert in the field of genetics, I decided to message you. Could you create a Wikipedia article re. integrative and conjugative elements (ICEs), please? The subject has been covered in various papers and science books, and it appears to be quite significant. If you find some time, I will be very grateful for your help. Thanks a lot! --Pinoczet (talk) 03:45, 1 March 2021 (UTC)
 * Thank you for the reply, I appreciate it. I wrote an informal draft version of the article. Since they are neither plasmids nor transposable elements, I believe ICEs should have a standalone Wikipedia article. The 'draft': Integrative and conjugative elements (ICEs) constitute a diverse group of mobile genetic elements present in gram-positive and gram-negative bacteria. In a donor cell, ICEs are primarily located on the chromosome, but have the ability to excise themselves from the genome and conjugal transfer to recipient cells. Although ICEs exhibit various mechanisms promoting their integration, transfer and regulation, they have many common basic features. ICEs comprise all (including, but not limited to, conjugative transposons) self-replicating, integrating and conjugative mobile genetic elements, regardless of their particular conjugation and integration mechanisms. Some immobile genomic pathogenicity islands are also believed to be defective ICEs that have lost their ability to conjugate. Due to their physical association with chromosomes, identifying integrative and conjugative elements has proven challenging, but computer-based analyzes of bacterial genomes indicate they are widespread among many microorganisms. ICEs combine certain features of the following mobile genetic elements: bacteriophages, that have the ability to insert into and excise from the bacterial chromosome, transposons, that besides the above characteristics, can additionally be subject to horizontal gene transfer, and conjugative plasmids, that transfer from donor to recipient bacteria via conjugation. In contrast to plasmids and phages, integrative and conjugative elements cannot remain in an extrachromosomal form in the cytoplasm of bacterial cells, and they replicate only with the chromosome they reside in. ICEs possess the structure organized into three gene modules, that are responsible for their integration with the chromosome, excision from the genome and conjugation, as well as regulatory genes. All integrative and conjugative elements encode integrases that are a key factor for controlling the excision, transfer and integration of an ICE. The representative example of ICE integrases is the integrase encoded by lambda phage. The transfer of an integrated ICE element from the donor to recipient bacterium must be preceded by its excision from the chromosome that is promoted by small DNA binding proteins, the so-called recombination directionality factors. The dynamics of the integration and excision processes are specific to each integrative and conjugative element. ICEs have been detected in Proteobacteria (e.g., Pseudomonas spp., Aeromonas spp., E. coli, Haemophilus spp.), Actinobacteria and Firmicutes. Among many other virulence determinants, ICEs spread antibiotics and metal ions resistance genes across diverse prokaryotic lineages.   ICE elements may also facilitate the mobilisation of other DNA modules, e.g. genomic islands. --Pinoczet (talk) 00:10, 2 March 2021 (UTC)

Viroids
Hi, I hope you are doing well. While reading the article Viroid, I found an interesting paper that describes the term retroviroid-like elements. These entities seem to be quite specific viroid-like RNAs, please check the following link: Plant Virology. Perhaps it should be mentioned there? If you find some time, I will be grateful for your help. Thanks a lot! Kind regards, --Pinoczet (talk) 08:00, 26 June 2021 (UTC)
 * Thank you for the reply, I appreciate it. Yes, I agree with you. Based on the source I linked to, perhaps it would be reasonable to somehow work CarSV RNA into the classification of viroids, too? Either way, I will rely on your intuition in this matter. Thanks a lot! Regards, --Pinoczet (talk) 16:00, 26 June 2021 (UTC)
 * Hello again. Thank you very much for the message. Your recent edit was flawless, great job! I thought it might be reasonable to cognately expand the article Plasmid, too (see: Retroplasmids: Linear and Circular Plasmids that Replicate via Reverse Transcription). Actually, Wiktionary already has an entry on the term retroplasmid. Furthermore, although most plasmids are double-stranded DNA molecules, some consist of single-straned DNA or, contrary to the given definition, RNA (see: RNA Plasmids). What are your thoughts? Kind regards and warm greetings, --Pinoczet (talk) 17:35, 15 July 2021 (UTC)
 * PS. The 'draft': Retroplasmids are linear and circular double-stranded DNA plasmids that replicate via reverse transcription in fungal mitochondria. Although most plasmids are double-stranded DNA molecules, some consist of single-stranded DNA or RNA. RNA plasmids are extrachromosomally replicating, non-infectious (mostly double-stranded) linear RNA replicons, both encapsidated and unencapsidated, which have been found in fungi and various plants, from algae to land plants. --Pinoczet (talk) 20:30, 17 July 2021 (UTC)
 * Hi, thank you for the message. Firstly, I strongly apologise for creating a little confusion, I was not precise enough in my previous statements. Secondly, retroplasmids and RNA plasmids are two separate issues. The former are, colloquially speaking, more typical plasmids, i.e. they are double-stranded DNA molecules. Their distinguishing feature is that they replicate via reverse transcription, and so far retroplasmids have been detected in fungal mitochondria. The latter, i.e. RNA plasmids, are (most commonly) double-stranded RNA replicons found in fungi (e.g. yeast) and various plants (e.g. Bryopsis, maize, rice). They replicate extrachromosomally, and are (mostly) non-infectious, i.e. not horizontally transmissible. In the paper I linked above (RNA Plasmids), the authors claimed that unencapsidated dsRNAs could hardly be viewed as anything other than plasmids, but additionally there exist a variety of encapsidated dsRNAs that form the so-called virus-like particles (VLPs), i.e. they have the characteristics of both viruses and plasmids. The quotation: … the viruslike nature of the encapsidated RNAs has caused them to be viewed as viruses by many authors. The use of the terms “mycovirus” and “cryptic virus” to describe the viruslike particles (VLP) of fungi and higher plants, respectively, reflects this view. In most cases these particles are not infectious, do not appear to have an extracellular phase of existence, and therefore may not be regarded as true viruses by others. Nevertheless, to make a clear distinction between these particles and conventional infectious viruses may seem somewhat arbitrary. I included the wikilink to the VLPs in my 'draft' to emphasize that they are not true virions. As the researchers pointed out, [w]e have attempted to merge the consideration of these diverse types of autonomously replicating cellular RNAs, but we recognize that the widespread perception of RNA replication as a viral property makes it impossible to dissociate consideration of RNA plasmids from RNA viruses and other infectious RNAs. They argue, however, that these dsRNAs (both encapsidated and unencapsidated) should be collectively considered as RNA plasmids, due to their common attributes, as opposed to 'infectious RNAs' (RNA viruses, viroids, satellite RNAs). The full text of the scientific article can be found online (it is very interesting!). If you find some time, I will be grateful for your help. Thanks a lot! Regards, --Pinoczet (talk) 13:45, 19 July 2021 (UTC)
 * I believe that the terms "retroplasmid" and "RNA plasmid" should be discussed in the article Plasmid. However, I am not sure which section (or perhaps a new one?) would be the most appropriate here. --Pinoczet (talk) 13:45, 24 July 2021 (UTC)

Hi again. I hope you are doing well, my friend. I would like to ask a question regarding the article Transposable element. I believe it should include some information on the so-called Class III TEs (see: Pierre Capy et al., Dynamics and Evolution of Transposable Elements, 1998). To my knowledge, the examples include Foldbacks, TU elements, and MITEs. It seems these transposable elements may be and actually are considered Class III TEs, at least by some researchers. However, I am not sure how this information should be properly added to the article. I was about to describe it at the end of the Classification section, but I still feel I do not have enough knowledge on this subject. Since I know you are an expert in the field of parasitic genomics, I decided to contact you. What are your thoughts? If you find some time, I will be grateful for your help. Thanks a lot! Kind regards, --Pinoczet (talk) 20:35, 29 August 2021 (UTC)
 * Hello! Thank you for the reply, I appreciate it. Yes, I agree with your conclusions, that's how I understand it too. Another example may be Foldback (FB) elements, see e.g.: The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective (Foldback (FB) elements, which are characterized by their property of reannealing after denaturation with zero-order kinetics, are quite distinct from prototypical class I or II elements …). John Baez (2017) described Class III TEs as a grab-bag consisting of transposons that don't clearly fit into the other two categories, and added: Examples include the "Foldback" elements in fruit flies, the "Tu" elements in sea urchins, and "MITEs", or "miniature inverted repeat transposable elements", which are found mainly in plants and fungi. --Pinoczet (talk) 16:00, 10 September 2021 (UTC)
 * Perhaps you have an idea on how to properly implement the information regarding Class III TEs? I was planning to describe them in the Classification section of the article Transposable element, but since you are an expert in the field of transposons, I decided to rely on your knowledge here. Thanks a lot! :) --Pinoczet (talk) 14:30, 15 September 2021 (UTC)
 * Thank you for the reply. Could you briefly describe Class III TEs in the Classification section, please? I must admit I have difficulty with the correct wording of this paragraph so that it is acceptable according to Wikipedia standards. That's a very good idea to create a separate article in the future, too. Kind regards, --Pinoczet (talk) 14:30, 18 September 2021 (UTC)