Template talk:Tryptophan metabolism by human microbiota

Svg version

@Slashme: Thanks for creating an svg version of the diagram. I noticed there's some weird text rendering in some places, specifically the underlined letters in the following words in the diagram: Tryptophan (top), antioxidant (bottom left), fibril (bottom left), calcification (right). Can you reupload the diagram with a different text font or just tweak the text spacing in those places? Seppi333 (Insert 2¢) 21:32, 1 November 2017 (UTC)

@Seppi333: That's a known bug in the SVG rendering: I've already done a bit of tweaking, but you're right - it's not quite right yet. I'll give it another go soon. --Slashme (talk) 21:49, 1 November 2017 (UTC)

@Slashme: Yeah... I'm familiar with the borked text rendering of text in svg images. Based upon past experience, copying the entire contents of an svg file into a new file in inkscape and re-saving it over the old file sometimes does the trick. The alternative in this particular case would be to take advantage of the fact that this diagram is displayed in an annotated image template by overlaying most of the horizontally-oriented text in the image onto the diagram as wikitext. An example of what this looks like is shown in the collapse tab below (note: I greatly increased the default font size for illustrative purposes); {{Psychostimulant addiction}} is a good example of a wikitext-annotated svg image that's currently used in various articles. Seppi333 (Insert 2¢) 22:06, 1 November 2017 (UTC)

The cause of the issue seems to be that librsvg is not handling small font sizes gracefully: probably a rounding error somewhere. I'll try enlarging the text and then scaling it down: that got me almost all the way the first time around. I just need to fix a few things at af:Triptofaan first. --Slashme (talk) 22:17, 1 November 2017 (UTC)

If you intend to use this image in af:Triptofaan, it'd probably be better to just remove the text in the image and annotate it since you don't need to create a new svg file for every different Wikipedia where it will be used. It'll only take me about 15-20 minutes to annotate all of the text in this image back onto it if it's removed. Reusing the image on a different language variant of Wikipedia only requires copying template:annotated image 4 to that Wikipedia and replacing the English text in this template's annotations with text in the appropriate language (e.g., compare Template:Catecholamine and trace amine biosynthesis and sr:Шаблон:Catecholamine and trace amine biosynthesis). If you'd prefer that approach, all I'd need you to do is delete the following image text: Tryptophan (top), IPA (all occurrences in the image), I3A (all occurences in the image), Indole (all occurences in the image), PXR (center-left), AhR (center-bottom), L-cell (center), TJ (center), GLP-1 (center), Intestinal epithelium (left), Gut immune cells (center-bottom), Indoxyl sulfate (center-right), AST-120 (i.e., the red text), the "Associated with vascular disease" text and all of the text beneath it in the bottom right region of the diagram, the "Neuroprotectant" text and all of the text beneath it, the "Maintains mucosal reactivity" text and the text beneath it, the "Mucosal homeostasis" text and all of the text beneath it. If you don't plan on reusing the diagram on another Wikipedia, then there probably isn't any point in replacing the image text with annotations though. Seppi333 (Insert 2¢) 22:38, 1 November 2017 (UTC)

@Seppi333: Thank you very much for that offer! I've created a new file with no text. Let me know if you need me to put back the text on the arrows coming down from Tryptophan. --Slashme (talk) 23:10, 1 November 2017 (UTC)

@Slashme: Would you be able to move the circle in the center on the right side (i.e., using the original image as a reference, the circle with the letters "TJ" inside) into the line that it's next to? "TJ" indicates a tight junction, which is actually what each vertical line in that part of the diagram represents. Alternatively, I suppose the circle could just be removed and the letters "TJ" could just be placed right alongside the line.
Anyway, I'm going to finish adding the coordinates for the annotations later since I need to log off for now. It shouldn't take long, so it'll definitely be done by tomorrow. Seppi333 (Insert 2¢) 00:25, 2 November 2017 (UTC)

@Seppi333: Sure thing! I'll do it as soon as I get home this afternoon. By the way, the annotated diagram looks brilliant! --Slashme (talk) 08:25, 2 November 2017 (UTC)

@Seppi333: Done - you might need to shift-reload if it still looks as if the circle is in the same place. --Slashme (talk) 19:00, 2 November 2017 (UTC)

Hah, ok. Looks like I need to shift all of the annotations a few pixels to the right. I can get to that in a little bit. Seppi333 (Insert 2¢) 19:02, 2 November 2017 (UTC)

Your waffles are extremely tasty! See how nice af:Triptofaan looks now. --Slashme (talk) 21:55, 2 November 2017 (UTC)

Looks great! I'm done with the English version. I said that would take me 20-30 minutes, hahahaha. That took me more like 1-2 hours since I'm excessively finicky when it comes to positioning text within small spaces. Seppi333 (Insert 2¢) 03:42, 3 November 2017 (UTC)

An example of this template with an annotation

Tryptophan metabolism by human gastrointestinal microbiota ()

Waffles
are
tasty

This diagram shows the biosynthesis of bioactive compounds (indole and certain derivatives) from tryptophan by bacteria in the gut. Indole is produced from tryptophan by bacteria that express tryptophanase. Clostridium sporogenes metabolizes indole into 3-indolepropionic acid (IPA), a highly potent neuroprotective antioxidant that scavenges hydroxyl radicals. In the intestine, IPA binds to pregnane X receptors (PXR) in intestinal cells, thereby facilitating mucosal homeostasis and barrier function. Following absorption from the intestine and distribution to the brain, IPA confers a neuroprotective effect against cerebral ischemia and Alzheimer’s disease. Lactobacillus species metabolize tryptophan into indole-3-aldehyde (I3A) which acts on the aryl hydrocarbon receptor (AhR) in intestinal immune cells, in turn increasing interleukin-22 (IL-22) production. Indole itself acts as a glucagon-like peptide-1 (GLP-1) secretagogue in intestinal L cells and as a ligand for AhR. Indole can also be metabolized by the liver into indoxyl sulfate, a compound that is toxic in high concentrations and associated with vascular disease and renal dysfunction. AST-120 (activated charcoal), an intestinal sorbent that is taken by mouth, adsorbs indole, in turn decreasing the concentration of indoxyl sulfate in blood plasma.

reflist

Template name

Would this be better named as ..metabolism by gut flora which is more specific?--Iztwoz (talk) 07:31, 8 January 2018 (UTC)

@Iztwoz: When I was creating this template, it didn't occur to me; however, when I was creating the annotated image header, I realized I probably should've named the template "Tryptophan metabolism by human gastrointestinal microbiota". The use of the term flora to describe microbes has gradually become more and more archaic in recent decades. I wouldn't mind renaming the template, but a lengthy template name isn't always useful even if it is a better descriptor. Despite that, {{Tryptophan metabolism by human microbiota}} could always be used to call this template instead of the longer template name since it would become a template redirect if this page is moved to {{Tryptophan metabolism by human gastrointestinal microbiota}}. So, if you want to rename/move the template to the longer title, I'd be okay with that. Seppi333 (Insert 2¢) 00:07, 9 January 2018 (UTC)