{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:12:18Z","timestamp":1772169138089,"version":"3.50.1"},"reference-count":40,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T00:00:00Z","timestamp":1643587200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wellcome","award":["101842\/Z13\/Z"],"award-info":[{"award-number":["101842\/Z13\/Z"]}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns4:p>\n                    <ns4:bold>Background:<\/ns4:bold>\n                    <ns4:italic>Trypanosoma brucei<\/ns4:italic>\n                    is a protozoan parasite and the etiological agent of human and animal African trypanosomiasis. The organism\n                    <ns4:italic\/>\n                    cycles between its mammalian host and tsetse vector. The host-dwelling bloodstream form of the parasite is covered with a monolayer of variant surface glycoprotein (VSG) that enables it to escape both the innate and adaptive immune systems. Within this coat reside lower-abundance surface glycoproteins that function as receptors and\/or nutrient transporters. The glycosylation of the\n                    <ns4:italic>Trypanosoma brucei<\/ns4:italic>\n                    surface proteome is essential to evade the immune response and is mediated by three oligosaccharyltransferase genes; two of which, TbSTT3A and TbSTT3B, are expressed in the bloodstream form of the parasite.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    We processed a recent dataset of our laboratory to visualise putative glycosylation sites of the Trypanosoma brucei proteome. We provided a visualisation for the predictions of glycosylation carried by TbSTT3A and TbSTT3B, and we augmented the visualisation with predictions for Glycosylphosphatidylinositol anchoring sites, domains and topology of the Trypanosoma brucei proteome.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusions:<\/ns4:bold>\n                    We created a web service to explore the glycosylation sites of the Trypanosoma brucei oligosaccharyltransferases substrates, using data described in a recent publication of our laboratory. We also made a machine learning algorithm available as a web service, described in our recent publication, to distinguish between TbSTT3A and TbSTT3B substrates.\n                  <\/ns4:p>","DOI":"10.12688\/wellcomeopenres.17640.1","type":"journal-article","created":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T08:35:08Z","timestamp":1643618108000},"page":"33","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Visualisation of experimentally determined and predicted protein N-glycosylation and predicted glycosylphosphatidylinositol anchor addition in Trypanosoma brucei."],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0051-017X","authenticated-orcid":false,"given":"Michele","family":"Tinti","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1321-8714","authenticated-orcid":false,"given":"Michael A. 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Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,28]],"date-time":"2022-02-28T07:15:22Z","timestamp":1646032522000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,31]]},"references-count":40,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.17640.1","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.19514.r48420","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19514.r48597","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19514.r48597","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19514.r48420","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19514.r48799","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,31]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.19514.r48420, James D. Bangs, Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY, USA, 02 Feb 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1#referee-response-48420","order":0,"name":"referee-response-48420","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Michele Tinti<\/b>; \n<i>Posted: 09 Feb 2022<\/i>; 1) Thanks for spotting this inconsistency. We will fix it in the next version of the paper.  2) I like this suggestion. I will add a polarity score to the feature panel; I'm thinking of using a sliding window of 5 amino acids.  3) I used a slighter older screenshot than intended. I will replace the figure in the next version of the paper.  4) Unfortunately, I don't think I can do any better for this functionality. I can zoom out with a two-finger click on my Mac laptop if it helps.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1#referee-comment-4904","order":1,"name":"referee-comment-4904","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.19514.r48597, Michael P. Barrett, Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK, 28 Feb 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-33\/v1#referee-response-48597","order":2,"name":"referee-response-48597","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [101842, <a href=https:\/\/doi.org\/10.35802\/101842>https:\/\/doi.org\/10.35802\/101842<\/a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}