{"id":11765,"date":"2024-10-01T15:17:26","date_gmt":"2024-10-01T14:17:26","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=11765"},"modified":"2024-10-01T15:25:42","modified_gmt":"2024-10-01T14:25:42","slug":"walk-through-a-cell","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2024\/10\/walk-through-a-cell\/","title":{"rendered":"Walk through a cell"},"content":{"rendered":"\n

In 2022, Maritan et al. <\/a>released the first ever macromolecular model of an entire cell. The cell in question is a bacterial cell from the genus Mycoplasma<\/em>. If you\u2019re a biologist, you likely know Mycoplasma <\/em>as a common cell culture contaminant.<\/p>\n\n\n\n

Now, through the work of app developer Timothy Davison, you can interactively explore this cell model from the comfort of your iPhone or Apple Vision Pro. Here are three reasons why I like CellWalk:<\/p>\n\n\n\n\n\n

1. It’s pretty<\/strong><\/p>\n\n\n\n

The visuals of CellWalk are striking. The app offers a rich depiction of the cell, allowing the user to zoom from the whole cell to individual atoms. I spent a while clicking through each protein I could see to see if I could guess what it was or what it did. Zooming out, CellWalk offers a beautiful tripartite cross section of the cell, showing first the lipid membrane, then a colourful jumble-bag of all its cellular proteins, and then finally the spaghetti-like polynucleic acids.<\/p>\n\n\n\n

\"\"<\/a>
Tripartite cross section of a Mycoplasma <\/em>cell. Screengrab taken from the CellWalk app on my phone.<\/figcaption><\/figure>\n\n\n\n\n\n\n\n

2. It challenges my preconceived notions of what a cell looks like<\/strong><\/p>\n\n\n\n

CellWalk challenged my unconscious perception what cell biology looks like. It highlights how densely packed DNA, RNA and proteins are within the cellular environment. In contrast to this were my undergraduate biology textbook diagrams of a sparsely populated cell, with some organelles dotted around an otherwise empty cytoplasm. I didn\u2019t know that that was how I thought of a cell until CellWalk presented me with a better model as an alternative. Importantly, Mycoplasma<\/em> is the smallest of all known bacterial cells, which themselves are an order of magnitude or two smaller than eukaryotic (animal, plant, fungal) cells. It begs the question, then, of how complex a eukaryotic cell model at the macromolecular resolution would be.<\/p>\n\n\n\n

\"\"<\/a>
Central cross section of a Mycoplasma <\/em>cell. Screengrab taken from the CellWalk app on my phone.<\/figcaption><\/figure>\n\n\n\n

3. It helps me to imagine of the smaller scales of biology<\/strong><\/p>\n\n\n\n

The scale of biology is wide, generally going from proteins to ecosystems. It is not too difficult for us to imagine multiple conspecifics making up a population, or a collection of tissues comprising an organ. However, at the cellular level and below, it becomes harder for us to envision the relative scale and abundance of biological entities. How big is a cell next to a protein? How much space does DNA take up in a cell? How densely populated is the cell surface with proteins? CellWalk strengthens our intuition of what life at the smallest scales looks like.<\/p>\n\n\n\n

\"\"<\/a>
A Mycoplasma <\/em>cell, filtered to only show DNA, RNA, and ribosomes. Screengrab taken from the CellWalk app on my phone.<\/figcaption><\/figure>\n\n\n\n

Thank you to the authors of CellWalk. You can download CellWalk here<\/a><\/u><\/strong>, and you can read the paper on how the model was made here<\/a><\/u><\/strong>. Finally, thank you to Garrett Morris for introducing me to the work!<\/p>\n","protected":false},"excerpt":{"rendered":"

In 2022, Maritan et al. released the first ever macromolecular model of an entire cell. The cell in question is a bacterial cell from the genus Mycoplasma. If you\u2019re a biologist, you likely know Mycoplasma as a common cell culture contaminant. Now, through the work of app developer Timothy Davison, you can interactively explore this […]<\/p>\n","protected":false},"author":124,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[621,385,228,202,265],"tags":[],"ppma_author":[765],"class_list":["post-11765","post","type-post","status-publish","format-standard","hentry","category-data-visualization","category-dna-and-rna","category-protein-structure","category-proteins","category-x-ray-crystallography"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":765,"user_id":124,"is_guest":0,"slug":"charlie","display_name":"Charlie Clark","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/f33ac8d0f95636e781da4ce2989c92c069e5e30f5f6f633972f991e3ccb9371f?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/11765","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/124"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=11765"}],"version-history":[{"count":5,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/11765\/revisions"}],"predecessor-version":[{"id":11794,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/11765\/revisions\/11794"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=11765"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=11765"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=11765"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=11765"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}